Starting phenix.real_space_refine on Wed Jan 22 22:07:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cop_45788/01_2025/9cop_45788_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cop_45788/01_2025/9cop_45788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cop_45788/01_2025/9cop_45788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cop_45788/01_2025/9cop_45788.map" model { file = "/net/cci-nas-00/data/ceres_data/9cop_45788/01_2025/9cop_45788_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cop_45788/01_2025/9cop_45788_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 112 5.16 5 C 23036 2.51 5 N 6378 2.21 5 O 6963 1.98 5 H 33498 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 69993 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 9129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9129 Classifications: {'peptide': 596} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 564} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 7396 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain breaks: 1 Chain: "E" Number of atoms: 8981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 8981 Classifications: {'peptide': 587} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 555} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "F" Number of atoms: 7313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7313 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "I" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3435 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1483 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "K" Number of atoms: 3056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3056 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "L" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1026 Classifications: {'peptide': 86} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "M" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 2896 Classifications: {'peptide': 213} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 208} Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 142 Chain: "N" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1466 Classifications: {'peptide': 115} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ASN:plan1': 2, 'PHE:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "P" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3168 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 9, 'TRANS': 426} Chain breaks: 2 Unresolved non-hydrogen bonds: 1385 Unresolved non-hydrogen angles: 1766 Unresolved non-hydrogen dihedrals: 1119 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 30, 'TYR:plan': 10, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 15, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 711 Chain: "x" Number of atoms: 17086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 17086 Classifications: {'peptide': 1192} Modifications used: {'NH3': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 47, 'TRANS': 1139} Chain breaks: 1 Unresolved non-hydrogen bonds: 811 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 645 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 23, 'TRP:plan': 1, 'ASP:plan': 33, 'PHE:plan': 7, 'GLU:plan': 25, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 435 Chain: "y" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1779 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 736 Unresolved non-hydrogen angles: 932 Unresolved non-hydrogen dihedrals: 591 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 14, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 380 Chain: "z" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1723 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 24.67, per 1000 atoms: 0.35 Number of scatterers: 69993 At special positions: 0 Unit cell: (128.75, 229.69, 254.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 112 16.00 P 4 15.00 Mg 2 11.99 O 6963 8.00 N 6378 7.00 C 23036 6.00 H 33498 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.69 Conformation dependent library (CDL) restraints added in 4.7 seconds 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9526 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 38 sheets defined 50.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 741 through 752 removed outlier: 3.726A pdb=" N MET A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 4.135A pdb=" N ALA A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 827 removed outlier: 3.680A pdb=" N TRP A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 838 through 848 Processing helix chain 'A' and resid 873 through 877 removed outlier: 3.610A pdb=" N ASP A 877 " --> pdb=" O ALA A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 897 through 903 removed outlier: 3.596A pdb=" N ARG A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 Processing helix chain 'A' and resid 932 through 958 removed outlier: 3.858A pdb=" N LEU A 956 " --> pdb=" O GLN A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 980 Processing helix chain 'A' and resid 994 through 1018 Processing helix chain 'A' and resid 1021 through 1029 Processing helix chain 'A' and resid 1029 through 1039 Processing helix chain 'A' and resid 1040 through 1042 No H-bonds generated for 'chain 'A' and resid 1040 through 1042' Processing helix chain 'A' and resid 1043 through 1046 Processing helix chain 'A' and resid 1047 through 1069 Processing helix chain 'A' and resid 1070 through 1071 No H-bonds generated for 'chain 'A' and resid 1070 through 1071' Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.931A pdb=" N LYS B 13 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.602A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 254 through 271 Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.607A pdb=" N TYR B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 307 through 317 removed outlier: 3.698A pdb=" N ILE B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 395 through 421 removed outlier: 3.678A pdb=" N VAL B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 426 through 442 Processing helix chain 'B' and resid 453 through 466 removed outlier: 3.554A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 468 No H-bonds generated for 'chain 'B' and resid 467 through 468' Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 477 through 486 removed outlier: 4.519A pdb=" N ASP B 486 " --> pdb=" O ASP B 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 121 Processing helix chain 'E' and resid 238 through 244 Processing helix chain 'E' and resid 262 through 274 Processing helix chain 'E' and resid 743 through 752 removed outlier: 3.696A pdb=" N VAL E 748 " --> pdb=" O GLU E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 780 through 783 Processing helix chain 'E' and resid 784 through 800 removed outlier: 3.659A pdb=" N ILE E 788 " --> pdb=" O ARG E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 827 Processing helix chain 'E' and resid 838 through 848 Processing helix chain 'E' and resid 873 through 877 removed outlier: 3.839A pdb=" N ASP E 877 " --> pdb=" O ALA E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 880 through 890 Processing helix chain 'E' and resid 897 through 903 Processing helix chain 'E' and resid 918 through 930 removed outlier: 4.679A pdb=" N LYS E 924 " --> pdb=" O ASN E 920 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE E 925 " --> pdb=" O VAL E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 932 through 958 removed outlier: 3.829A pdb=" N GLN E 952 " --> pdb=" O GLU E 948 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL E 953 " --> pdb=" O GLU E 949 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU E 956 " --> pdb=" O GLN E 952 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 962 Processing helix chain 'E' and resid 963 through 980 Processing helix chain 'E' and resid 994 through 1018 Processing helix chain 'E' and resid 1021 through 1029 removed outlier: 4.006A pdb=" N ASP E1027 " --> pdb=" O SER E1023 " (cutoff:3.500A) Processing helix chain 'E' and resid 1029 through 1039 Processing helix chain 'E' and resid 1040 through 1042 No H-bonds generated for 'chain 'E' and resid 1040 through 1042' Processing helix chain 'E' and resid 1050 through 1052 No H-bonds generated for 'chain 'E' and resid 1050 through 1052' Processing helix chain 'E' and resid 1053 through 1058 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 179 through 191 Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.519A pdb=" N ALA F 222 " --> pdb=" O ASN F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.627A pdb=" N TYR F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 285 " --> pdb=" O MET F 281 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 307 through 317 removed outlier: 3.521A pdb=" N THR F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 341 Processing helix chain 'F' and resid 344 through 352 Processing helix chain 'F' and resid 361 through 367 Processing helix chain 'F' and resid 382 through 387 Processing helix chain 'F' and resid 395 through 421 removed outlier: 3.663A pdb=" N ASP F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 425 Processing helix chain 'F' and resid 426 through 443 Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'I' and resid 27 through 113 removed outlier: 4.498A pdb=" N ILE I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL I 51 " --> pdb=" O LYS I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 133 Proline residue: I 119 - end of helix Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'I' and resid 152 through 164 Processing helix chain 'I' and resid 203 through 214 removed outlier: 3.725A pdb=" N GLU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 224 Processing helix chain 'J' and resid 17 through 23 Processing helix chain 'J' and resid 24 through 59 removed outlier: 3.665A pdb=" N SER J 45 " --> pdb=" O LYS J 41 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 67 removed outlier: 3.757A pdb=" N GLY J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 104 removed outlier: 4.038A pdb=" N GLN J 77 " --> pdb=" O GLU J 73 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 4.059A pdb=" N GLU K 44 " --> pdb=" O ASP K 40 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL K 51 " --> pdb=" O LYS K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 58 No H-bonds generated for 'chain 'K' and resid 56 through 58' Processing helix chain 'K' and resid 59 through 113 removed outlier: 3.561A pdb=" N VAL K 88 " --> pdb=" O MET K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 133 Proline residue: K 119 - end of helix Processing helix chain 'K' and resid 145 through 164 removed outlier: 5.186A pdb=" N ASP K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY K 161 " --> pdb=" O MET K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 214 removed outlier: 3.686A pdb=" N GLU K 212 " --> pdb=" O LYS K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 224 Processing helix chain 'L' and resid 30 through 37 removed outlier: 3.931A pdb=" N GLN L 34 " --> pdb=" O ASP L 30 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA L 35 " --> pdb=" O LYS L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 52 removed outlier: 3.825A pdb=" N LYS L 47 " --> pdb=" O ILE L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 103 removed outlier: 4.440A pdb=" N GLY L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU L 67 " --> pdb=" O GLY L 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE L 97 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 62 removed outlier: 4.300A pdb=" N GLN M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 87 removed outlier: 3.631A pdb=" N VAL M 87 " --> pdb=" O GLN M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 131 Processing helix chain 'M' and resid 132 through 176 removed outlier: 3.969A pdb=" N TYR M 139 " --> pdb=" O ALA M 135 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER M 140 " --> pdb=" O LYS M 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU M 152 " --> pdb=" O GLU M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 215 removed outlier: 3.665A pdb=" N ALA M 215 " --> pdb=" O GLN M 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 18 Processing helix chain 'N' and resid 21 through 26 Processing helix chain 'N' and resid 46 through 59 Processing helix chain 'N' and resid 71 through 77 removed outlier: 3.840A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 83 Processing helix chain 'N' and resid 106 through 115 Processing helix chain 'P' and resid 10 through 22 Processing helix chain 'P' and resid 26 through 33 removed outlier: 3.741A pdb=" N LEU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 52 Processing helix chain 'P' and resid 77 through 87 removed outlier: 3.556A pdb=" N THR P 86 " --> pdb=" O HIS P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.118A pdb=" N LYS P 94 " --> pdb=" O GLU P 90 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL P 96 " --> pdb=" O CYS P 92 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN P 97 " --> pdb=" O LYS P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 120 removed outlier: 3.781A pdb=" N LYS P 115 " --> pdb=" O ASP P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 131 removed outlier: 4.123A pdb=" N GLU P 125 " --> pdb=" O PRO P 121 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN P 126 " --> pdb=" O LYS P 122 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER P 131 " --> pdb=" O LEU P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 143 removed outlier: 3.978A pdb=" N ILE P 141 " --> pdb=" O GLN P 137 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 155 removed outlier: 4.017A pdb=" N GLY P 154 " --> pdb=" O VAL P 151 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU P 155 " --> pdb=" O GLN P 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 151 through 155' Processing helix chain 'P' and resid 157 through 165 Processing helix chain 'P' and resid 167 through 175 removed outlier: 4.116A pdb=" N ILE P 171 " --> pdb=" O ASN P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 193 Processing helix chain 'P' and resid 196 through 222 removed outlier: 3.896A pdb=" N LYS P 209 " --> pdb=" O LEU P 205 " (cutoff:3.500A) Proline residue: P 212 - end of helix removed outlier: 3.539A pdb=" N LEU P 218 " --> pdb=" O LEU P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 255 Processing helix chain 'P' and resid 256 through 265 removed outlier: 3.725A pdb=" N GLN P 265 " --> pdb=" O ASN P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 267 through 281 removed outlier: 3.973A pdb=" N LEU P 272 " --> pdb=" O LEU P 268 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU P 275 " --> pdb=" O PHE P 271 " (cutoff:3.500A) Processing helix chain 'P' and resid 283 through 298 Processing helix chain 'P' and resid 304 through 317 removed outlier: 3.609A pdb=" N ASN P 317 " --> pdb=" O LEU P 313 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 328 Processing helix chain 'P' and resid 332 through 351 Processing helix chain 'P' and resid 354 through 366 removed outlier: 4.091A pdb=" N GLU P 358 " --> pdb=" O THR P 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 371 through 375 Processing helix chain 'P' and resid 376 through 384 removed outlier: 4.473A pdb=" N TRP P 380 " --> pdb=" O ASP P 376 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER P 381 " --> pdb=" O ASN P 377 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP P 382 " --> pdb=" O GLY P 378 " (cutoff:3.500A) Processing helix chain 'P' and resid 395 through 410 Processing helix chain 'P' and resid 413 through 432 removed outlier: 3.511A pdb=" N LEU P 424 " --> pdb=" O ILE P 420 " (cutoff:3.500A) Processing helix chain 'P' and resid 435 through 444 removed outlier: 3.710A pdb=" N ASP P 439 " --> pdb=" O PRO P 435 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL P 440 " --> pdb=" O GLU P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 454 Processing helix chain 'P' and resid 459 through 470 removed outlier: 4.239A pdb=" N LYS P 467 " --> pdb=" O TYR P 463 " (cutoff:3.500A) Processing helix chain 'x' and resid 21 through 25 Processing helix chain 'x' and resid 109 through 111 No H-bonds generated for 'chain 'x' and resid 109 through 111' Processing helix chain 'x' and resid 154 through 157 removed outlier: 3.992A pdb=" N GLN x 157 " --> pdb=" O GLN x 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 154 through 157' Processing helix chain 'x' and resid 203 through 207 Processing helix chain 'x' and resid 233 through 237 Processing helix chain 'x' and resid 259 through 267 Processing helix chain 'x' and resid 268 through 273 Processing helix chain 'x' and resid 363 through 367 Processing helix chain 'x' and resid 443 through 445 No H-bonds generated for 'chain 'x' and resid 443 through 445' Processing helix chain 'x' and resid 692 through 694 No H-bonds generated for 'chain 'x' and resid 692 through 694' Processing helix chain 'x' and resid 706 through 708 No H-bonds generated for 'chain 'x' and resid 706 through 708' Processing helix chain 'x' and resid 729 through 737 Processing helix chain 'x' and resid 745 through 751 Processing helix chain 'x' and resid 761 through 771 removed outlier: 3.787A pdb=" N GLN x 767 " --> pdb=" O GLN x 763 " (cutoff:3.500A) Processing helix chain 'x' and resid 773 through 794 Processing helix chain 'x' and resid 797 through 801 Processing helix chain 'x' and resid 808 through 814 Processing helix chain 'x' and resid 816 through 820 Processing helix chain 'x' and resid 833 through 847 removed outlier: 3.746A pdb=" N THR x 845 " --> pdb=" O THR x 841 " (cutoff:3.500A) Processing helix chain 'x' and resid 853 through 874 Processing helix chain 'x' and resid 878 through 893 removed outlier: 3.552A pdb=" N VAL x 882 " --> pdb=" O ASP x 878 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG x 883 " --> pdb=" O TYR x 879 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER x 893 " --> pdb=" O LYS x 889 " (cutoff:3.500A) Processing helix chain 'x' and resid 902 through 911 removed outlier: 3.501A pdb=" N HIS x 911 " --> pdb=" O SER x 907 " (cutoff:3.500A) Processing helix chain 'x' and resid 914 through 923 Processing helix chain 'x' and resid 924 through 926 No H-bonds generated for 'chain 'x' and resid 924 through 926' Processing helix chain 'x' and resid 928 through 933 Processing helix chain 'x' and resid 936 through 941 removed outlier: 3.941A pdb=" N TRP x 940 " --> pdb=" O ARG x 936 " (cutoff:3.500A) Processing helix chain 'x' and resid 942 through 959 removed outlier: 4.324A pdb=" N LYS x 948 " --> pdb=" O GLN x 944 " (cutoff:3.500A) Processing helix chain 'x' and resid 969 through 976 Processing helix chain 'x' and resid 978 through 989 Processing helix chain 'x' and resid 994 through 1003 removed outlier: 3.567A pdb=" N SER x1003 " --> pdb=" O VAL x 999 " (cutoff:3.500A) Processing helix chain 'x' and resid 1008 through 1025 Processing helix chain 'x' and resid 1027 through 1038 removed outlier: 3.677A pdb=" N THR x1038 " --> pdb=" O PHE x1034 " (cutoff:3.500A) Processing helix chain 'x' and resid 1040 through 1051 removed outlier: 3.729A pdb=" N ASN x1046 " --> pdb=" O LYS x1042 " (cutoff:3.500A) Processing helix chain 'x' and resid 1054 through 1066 Processing helix chain 'x' and resid 1071 through 1081 Processing helix chain 'x' and resid 1081 through 1089 Processing helix chain 'x' and resid 1090 through 1101 Processing helix chain 'x' and resid 1103 through 1110 removed outlier: 3.802A pdb=" N LYS x1109 " --> pdb=" O GLU x1105 " (cutoff:3.500A) Processing helix chain 'x' and resid 1114 through 1118 Processing helix chain 'x' and resid 1120 through 1124 Processing helix chain 'x' and resid 1132 through 1136 removed outlier: 3.573A pdb=" N PHE x1135 " --> pdb=" O ASN x1132 " (cutoff:3.500A) Processing helix chain 'x' and resid 1139 through 1153 removed outlier: 3.942A pdb=" N LEU x1143 " --> pdb=" O ASP x1139 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR x1146 " --> pdb=" O LEU x1142 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN x1151 " --> pdb=" O ASN x1147 " (cutoff:3.500A) Processing helix chain 'x' and resid 1154 through 1157 Processing helix chain 'x' and resid 1161 through 1176 removed outlier: 3.587A pdb=" N ILE x1167 " --> pdb=" O VAL x1163 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR x1170 " --> pdb=" O LYS x1166 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU x1173 " --> pdb=" O CYS x1169 " (cutoff:3.500A) Processing helix chain 'x' and resid 1184 through 1195 Processing helix chain 'y' and resid 24 through 54 removed outlier: 4.037A pdb=" N ILE y 31 " --> pdb=" O CYS y 27 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLU y 32 " --> pdb=" O SER y 28 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU y 33 " --> pdb=" O TRP y 29 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS y 36 " --> pdb=" O GLU y 32 " (cutoff:3.500A) Proline residue: y 37 - end of helix Proline residue: y 40 - end of helix removed outlier: 3.766A pdb=" N ASN y 45 " --> pdb=" O ASN y 41 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET y 52 " --> pdb=" O LYS y 48 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU y 53 " --> pdb=" O CYS y 49 " (cutoff:3.500A) Processing helix chain 'y' and resid 102 through 107 removed outlier: 3.965A pdb=" N ARG y 105 " --> pdb=" O GLN y 102 " (cutoff:3.500A) Processing helix chain 'y' and resid 121 through 141 removed outlier: 3.700A pdb=" N SER y 125 " --> pdb=" O LEU y 121 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE y 127 " --> pdb=" O GLN y 123 " (cutoff:3.500A) Processing helix chain 'y' and resid 142 through 144 No H-bonds generated for 'chain 'y' and resid 142 through 144' Processing helix chain 'y' and resid 146 through 170 removed outlier: 3.905A pdb=" N PHE y 150 " --> pdb=" O ASP y 146 " (cutoff:3.500A) Processing helix chain 'y' and resid 176 through 180 Processing helix chain 'y' and resid 191 through 196 Processing helix chain 'y' and resid 299 through 303 Processing helix chain 'y' and resid 319 through 348 removed outlier: 3.577A pdb=" N ASN y 336 " --> pdb=" O ALA y 332 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER y 344 " --> pdb=" O ASN y 340 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS y 345 " --> pdb=" O LEU y 341 " (cutoff:3.500A) Processing helix chain 'z' and resid 22 through 26 Processing helix chain 'z' and resid 28 through 33 Processing helix chain 'z' and resid 36 through 40 Processing helix chain 'z' and resid 83 through 98 Processing helix chain 'z' and resid 103 through 108 removed outlier: 4.122A pdb=" N ASP z 108 " --> pdb=" O GLU z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 117 through 125 Processing helix chain 'z' and resid 127 through 141 removed outlier: 4.206A pdb=" N TYR z 132 " --> pdb=" O GLN z 128 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU z 133 " --> pdb=" O GLU z 129 " (cutoff:3.500A) Processing helix chain 'z' and resid 143 through 161 Processing helix chain 'z' and resid 162 through 170 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 32 removed outlier: 6.551A pdb=" N ILE A 37 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A 31 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 35 through 39 current: chain 'A' and resid 57 through 65 removed outlier: 5.650A pdb=" N VAL A 61 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN A 72 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 63 " --> pdb=" O THR A 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 73 current: chain 'B' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 41 current: chain 'B' and resid 62 through 71 removed outlier: 6.563A pdb=" N ILE B 76 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE B 70 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 74 through 79 current: chain 'E' and resid 35 through 39 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 35 through 39 current: chain 'E' and resid 57 through 65 removed outlier: 5.706A pdb=" N VAL E 61 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN E 72 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 63 " --> pdb=" O THR E 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 73 current: chain 'F' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 38 through 41 current: chain 'F' and resid 62 through 71 removed outlier: 6.551A pdb=" N ILE F 76 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE F 70 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 74 through 79 current: chain 'I' and resid 171 through 174 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 171 through 174 current: chain 'I' and resid 198 through 202 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 198 through 202 current: chain 'K' and resid 171 through 174 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 171 through 174 current: chain 'K' and resid 197 through 199 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 97 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 106 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 105 through 106 current: chain 'A' and resid 770 through 776 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 770 through 776 current: chain 'A' and resid 862 through 871 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 862 through 871 current: chain 'A' and resid 915 through 916 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 removed outlier: 3.636A pdb=" N GLY A 160 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.599A pdb=" N GLU A 200 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE A 186 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE A 198 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 234 removed outlier: 4.568A pdb=" N CYS A 247 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA8, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.392A pdb=" N ARG B 111 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU B 242 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE B 113 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU B 244 " --> pdb=" O PHE B 113 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 278 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE B 172 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.278A pdb=" N ARG B 321 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 94 through 97 Processing sheet with id=AB3, first strand: chain 'E' and resid 171 through 174 removed outlier: 3.779A pdb=" N GLY E 160 " --> pdb=" O ILE E 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 152 through 154 removed outlier: 5.812A pdb=" N ILE E 183 " --> pdb=" O GLU E 202 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU E 202 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 224 through 227 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 224 through 227 current: chain 'E' and resid 770 through 775 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 770 through 775 current: chain 'E' and resid 862 through 870 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 862 through 870 current: chain 'E' and resid 915 through 916 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 756 through 757 Processing sheet with id=AB7, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.576A pdb=" N ASP F 130 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 111 through 114 removed outlier: 6.563A pdb=" N ARG F 111 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU F 242 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE F 113 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU F 244 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER F 209 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE F 277 " --> pdb=" O SER F 209 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL F 211 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR F 279 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA F 213 " --> pdb=" O THR F 279 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG F 321 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 151 through 152 Processing sheet with id=AC1, first strand: chain 'F' and resid 334 through 336 Processing sheet with id=AC2, first strand: chain 'M' and resid 94 through 97 Processing sheet with id=AC3, first strand: chain 'N' and resid 37 through 38 removed outlier: 9.353A pdb=" N PHE N 38 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL N 10 " --> pdb=" O PHE N 38 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU N 7 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU N 68 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA N 9 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ASN N 70 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE N 11 " --> pdb=" O ASN N 70 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU N 92 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU N 67 " --> pdb=" O LEU N 92 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE N 94 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE N 69 " --> pdb=" O ILE N 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'x' and resid 3 through 6 removed outlier: 4.198A pdb=" N VAL x 712 " --> pdb=" O TYR x 719 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'x' and resid 17 through 20 Processing sheet with id=AC6, first strand: chain 'x' and resid 55 through 60 removed outlier: 3.865A pdb=" N ALA x 57 " --> pdb=" O SER x 70 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LYS x 79 " --> pdb=" O GLN x 92 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN x 92 " --> pdb=" O LYS x 79 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'x' and resid 113 through 117 removed outlier: 3.572A pdb=" N SER x 122 " --> pdb=" O ILE x 116 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'x' and resid 150 through 152 Processing sheet with id=AC9, first strand: chain 'x' and resid 195 through 200 removed outlier: 3.716A pdb=" N ALA x 197 " --> pdb=" O LEU x 220 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL x 225 " --> pdb=" O CYS x 221 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'x' and resid 254 through 258 removed outlier: 6.213A pdb=" N MET x 292 " --> pdb=" O HIS x 315 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS x 315 " --> pdb=" O MET x 292 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL x 294 " --> pdb=" O ILE x 313 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'x' and resid 336 through 337 removed outlier: 4.230A pdb=" N GLN x 336 " --> pdb=" O SER x 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'x' and resid 348 through 350 Processing sheet with id=AD4, first strand: chain 'x' and resid 391 through 394 removed outlier: 6.841A pdb=" N ASN x 410 " --> pdb=" O THR x 429 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR x 429 " --> pdb=" O ASN x 410 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL x 412 " --> pdb=" O GLN x 427 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'x' and resid 436 through 442 removed outlier: 4.016A pdb=" N ALA x 456 " --> pdb=" O LEU x 452 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU x 461 " --> pdb=" O LEU x 477 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU x 477 " --> pdb=" O GLU x 461 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'x' and resid 495 through 496 removed outlier: 3.728A pdb=" N VAL x 523 " --> pdb=" O HIS x 507 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'x' and resid 548 through 549 removed outlier: 3.827A pdb=" N SER x 548 " --> pdb=" O SER x 565 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA x 578 " --> pdb=" O PRO x 562 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE x 564 " --> pdb=" O TYR x 576 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR x 575 " --> pdb=" O ALA x 592 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS x 586 " --> pdb=" O ASN x 581 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'x' and resid 602 through 607 removed outlier: 3.766A pdb=" N CYS x 604 " --> pdb=" O VAL x 616 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL x 622 " --> pdb=" O ASN x 617 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP x 627 " --> pdb=" O LEU x 633 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU x 633 " --> pdb=" O ASP x 627 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'x' and resid 645 through 648 removed outlier: 5.972A pdb=" N ALA x 666 " --> pdb=" O LYS x 688 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS x 688 " --> pdb=" O ALA x 666 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU x 668 " --> pdb=" O ILE x 686 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'y' and resid 85 through 87 removed outlier: 7.696A pdb=" N THR y 85 " --> pdb=" O VAL y 92 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL y 92 " --> pdb=" O THR y 85 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN y 87 " --> pdb=" O TYR y 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'y' and resid 201 through 202 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 201 through 202 current: chain 'y' and resid 216 through 223 removed outlier: 7.182A pdb=" N LEU y 218 " --> pdb=" O LYS y 310 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS y 310 " --> pdb=" O LEU y 218 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN y 220 " --> pdb=" O CYS y 308 " (cutoff:3.500A) 1882 hydrogen bonds defined for protein. 5307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.83 Time building geometry restraints manager: 17.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33463 1.03 - 1.23: 538 1.23 - 1.42: 14604 1.42 - 1.62: 21815 1.62 - 1.82: 189 Bond restraints: 70609 Sorted by residual: bond pdb=" C PRO A 85 " pdb=" O PRO A 85 " ideal model delta sigma weight residual 1.233 1.149 0.084 1.10e-02 8.26e+03 5.87e+01 bond pdb=" C PRO E 217 " pdb=" O PRO E 217 " ideal model delta sigma weight residual 1.233 1.150 0.084 1.34e-02 5.57e+03 3.89e+01 bond pdb=" C MET E 807 " pdb=" O MET E 807 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.24e-02 6.50e+03 3.71e+01 bond pdb=" C PRO E 34 " pdb=" O PRO E 34 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.23e-02 6.61e+03 3.32e+01 bond pdb=" C TYR A 915 " pdb=" O TYR A 915 " ideal model delta sigma weight residual 1.234 1.164 0.070 1.22e-02 6.72e+03 3.28e+01 ... (remaining 70604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 126078 3.01 - 6.02: 1142 6.02 - 9.03: 58 9.03 - 12.04: 24 12.04 - 15.05: 3 Bond angle restraints: 127305 Sorted by residual: angle pdb=" N ASN x 880 " pdb=" CA ASN x 880 " pdb=" C ASN x 880 " ideal model delta sigma weight residual 113.50 102.03 11.47 1.23e+00 6.61e-01 8.69e+01 angle pdb=" N GLU F 129 " pdb=" CA GLU F 129 " pdb=" C GLU F 129 " ideal model delta sigma weight residual 113.72 102.96 10.76 1.30e+00 5.92e-01 6.85e+01 angle pdb=" N ARG E 784 " pdb=" CA ARG E 784 " pdb=" C ARG E 784 " ideal model delta sigma weight residual 112.89 103.99 8.90 1.24e+00 6.50e-01 5.15e+01 angle pdb=" CA GLY B 82 " pdb=" C GLY B 82 " pdb=" O GLY B 82 " ideal model delta sigma weight residual 122.52 117.05 5.47 7.90e-01 1.60e+00 4.80e+01 angle pdb=" N GLU F 106 " pdb=" CA GLU F 106 " pdb=" C GLU F 106 " ideal model delta sigma weight residual 113.18 105.45 7.73 1.21e+00 6.83e-01 4.08e+01 ... (remaining 127300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.10: 31385 20.10 - 40.20: 1776 40.20 - 60.30: 543 60.30 - 80.39: 87 80.39 - 100.49: 25 Dihedral angle restraints: 33816 sinusoidal: 17389 harmonic: 16427 Sorted by residual: dihedral pdb=" CA ASP x1177 " pdb=" C ASP x1177 " pdb=" N ILE x1178 " pdb=" CA ILE x1178 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA LEU F 41 " pdb=" C LEU F 41 " pdb=" N GLU F 42 " pdb=" CA GLU F 42 " ideal model delta harmonic sigma weight residual 180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA MET F 391 " pdb=" C MET F 391 " pdb=" N THR F 392 " pdb=" CA THR F 392 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 33813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4722 0.057 - 0.115: 920 0.115 - 0.172: 244 0.172 - 0.229: 33 0.229 - 0.287: 7 Chirality restraints: 5926 Sorted by residual: chirality pdb=" CA HIS E 152 " pdb=" N HIS E 152 " pdb=" C HIS E 152 " pdb=" CB HIS E 152 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE B 151 " pdb=" N ILE B 151 " pdb=" C ILE B 151 " pdb=" CB ILE B 151 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA LEU F 275 " pdb=" N LEU F 275 " pdb=" C LEU F 275 " pdb=" CB LEU F 275 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 5923 not shown) Planarity restraints: 11425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 452 " 0.059 9.50e-02 1.11e+02 4.14e-01 3.85e+03 pdb=" NE ARG B 452 " 0.168 2.00e-02 2.50e+03 pdb=" CZ ARG B 452 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG B 452 " -0.060 2.00e-02 2.50e+03 pdb=" NH2 ARG B 452 " 0.021 2.00e-02 2.50e+03 pdb="HH11 ARG B 452 " -0.852 2.00e-02 2.50e+03 pdb="HH12 ARG B 452 " 0.664 2.00e-02 2.50e+03 pdb="HH21 ARG B 452 " -0.405 2.00e-02 2.50e+03 pdb="HH22 ARG B 452 " 0.420 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 446 " 0.123 2.00e-02 2.50e+03 4.34e-01 2.82e+03 pdb=" CD GLN B 446 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN B 446 " -0.119 2.00e-02 2.50e+03 pdb=" NE2 GLN B 446 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 446 " 0.744 2.00e-02 2.50e+03 pdb="HE22 GLN B 446 " -0.738 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 272 " -0.050 9.50e-02 1.11e+02 3.49e-01 2.74e+03 pdb=" NE ARG F 272 " 0.166 2.00e-02 2.50e+03 pdb=" CZ ARG F 272 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG F 272 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG F 272 " -0.029 2.00e-02 2.50e+03 pdb="HH11 ARG F 272 " -0.754 2.00e-02 2.50e+03 pdb="HH12 ARG F 272 " 0.697 2.00e-02 2.50e+03 pdb="HH21 ARG F 272 " -0.106 2.00e-02 2.50e+03 pdb="HH22 ARG F 272 " -0.002 2.00e-02 2.50e+03 ... (remaining 11422 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 1120 2.07 - 2.71: 113969 2.71 - 3.34: 207078 3.34 - 3.97: 262372 3.97 - 4.60: 415851 Nonbonded interactions: 1000390 Sorted by model distance: nonbonded pdb=" O ASN z 142 " pdb="HD21 ASN z 142 " model vdw 1.442 2.450 nonbonded pdb="HH22 ARG F 301 " pdb=" O THR F 343 " model vdw 1.622 2.450 nonbonded pdb=" O GLY E 237 " pdb="HE22 GLN E 983 " model vdw 1.623 2.450 nonbonded pdb=" O SER B 234 " pdb=" HG1 THR B 238 " model vdw 1.624 2.450 nonbonded pdb=" HZ2 LYS x1109 " pdb=" OE2 GLU x1164 " model vdw 1.625 2.450 ... (remaining 1000385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 24 through \ 758 or (resid 759 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 760 through 1061 or (resid 1062 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 1063 or resid 11 \ 01 through 1102)) selection = (chain 'E' and (resid 23 through 263 or (resid 264 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 265 through 1063 or resid 110 \ 1 through 1102)) } ncs_group { reference = (chain 'B' and ((resid 14 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 15 through 487)) selection = (chain 'F' and (resid 14 through 197 or resid 206 through 487)) } ncs_group { reference = (chain 'I' and ((resid 36 and (name N or name CA or name C or name O or name CB \ or name HA )) or (resid 37 through 38 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 39 through 40 or (resid 41 through \ 43 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 44 or (resid 45 through 49 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 52 through 53 \ or (resid 54 through 55 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 56 through 232)) selection = chain 'K' } ncs_group { reference = (chain 'J' and ((resid 29 and (name N or name CA or name C or name O or name CB \ or name HA )) or (resid 30 through 34 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 35 or (resid 36 through 38 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 3 \ 9 through 40 or (resid 41 through 43 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 44 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 48 \ or (resid 49 through 50 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 51 or (resid 52 through 61 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 62 through 64 \ or (resid 65 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 66 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 69 or (resid 70 through 71 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 72 through 114)) selection = (chain 'L' and (resid 29 through 44 or (resid 45 through 47 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 48 through 10 \ 5 or (resid 106 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 107 through 113 or (resid 114 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.050 Extract box with map and model: 2.260 Check model and map are aligned: 0.420 Set scattering table: 0.510 Process input model: 120.090 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 37111 Z= 0.429 Angle : 0.938 15.047 50507 Z= 0.630 Chirality : 0.052 0.287 5926 Planarity : 0.007 0.123 6607 Dihedral : 13.666 100.492 12975 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 0.95 % Allowed : 2.02 % Favored : 97.03 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4997 helix: 0.57 (0.12), residues: 2198 sheet: -1.37 (0.19), residues: 682 loop : -0.74 (0.14), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP x 124 HIS 0.014 0.001 HIS E 152 PHE 0.032 0.002 PHE x 950 TYR 0.032 0.002 TYR F 468 ARG 0.010 0.001 ARG x 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 1212 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1180 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1023 SER cc_start: 0.8214 (t) cc_final: 0.7957 (p) REVERT: F 56 THR cc_start: 0.5586 (m) cc_final: 0.5301 (m) REVERT: F 358 ILE cc_start: 0.5945 (mm) cc_final: 0.5723 (mt) REVERT: F 433 LEU cc_start: 0.6536 (mt) cc_final: 0.6129 (mt) REVERT: I 149 ILE cc_start: 0.6815 (mt) cc_final: 0.6590 (mt) REVERT: I 189 VAL cc_start: 0.6560 (t) cc_final: 0.6040 (t) REVERT: K 124 LEU cc_start: 0.8396 (mt) cc_final: 0.8192 (mm) REVERT: M 101 VAL cc_start: 0.7171 (p) cc_final: 0.6904 (p) outliers start: 32 outliers final: 9 residues processed: 1202 average time/residue: 2.1355 time to fit residues: 3217.4372 Evaluate side-chains 742 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 733 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain E residue 780 PRO Chi-restraints excluded: chain F residue 269 GLN Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 229 ARG Chi-restraints excluded: chain I residue 233 ASP Chi-restraints excluded: chain x residue 122 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 0.9990 chunk 377 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 390 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 290 optimal weight: 20.0000 chunk 452 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 982 GLN B 374 ASN ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 167 ASN M 183 ASN M 207 GLN x 629 ASN ** x1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x1194 ASN z 171 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.100682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.073035 restraints weight = 271298.246| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.57 r_work: 0.3209 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 37111 Z= 0.429 Angle : 0.882 10.207 50507 Z= 0.469 Chirality : 0.051 0.305 5926 Planarity : 0.007 0.119 6607 Dihedral : 6.053 102.792 5406 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.86 % Allowed : 17.05 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.12), residues: 4997 helix: 0.52 (0.11), residues: 2225 sheet: -1.75 (0.18), residues: 689 loop : -1.03 (0.14), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 140 HIS 0.012 0.002 HIS B 396 PHE 0.052 0.002 PHE A 893 TYR 0.022 0.002 TYR F 28 ARG 0.045 0.002 ARG z 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 950 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 820 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7797 (t70) cc_final: 0.7511 (t0) REVERT: A 138 ILE cc_start: 0.7238 (mt) cc_final: 0.6994 (mm) REVERT: A 807 MET cc_start: 0.7516 (ptm) cc_final: 0.7064 (ttt) REVERT: A 828 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6988 (mt-10) REVERT: A 882 VAL cc_start: 0.6963 (t) cc_final: 0.6752 (t) REVERT: A 914 SER cc_start: 0.7470 (m) cc_final: 0.7235 (m) REVERT: A 951 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6244 (mm-30) REVERT: A 1057 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8355 (mmtt) REVERT: B 163 SER cc_start: 0.8065 (t) cc_final: 0.7762 (t) REVERT: B 220 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7405 (tp30) REVERT: B 387 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7433 (pp) REVERT: B 438 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8209 (mtmm) REVERT: E 259 PHE cc_start: 0.7787 (p90) cc_final: 0.7544 (p90) REVERT: E 266 ILE cc_start: 0.8149 (mt) cc_final: 0.7943 (mp) REVERT: E 744 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6815 (mm-30) REVERT: E 747 GLU cc_start: 0.8094 (tt0) cc_final: 0.7869 (tp30) REVERT: E 751 GLU cc_start: 0.7712 (pt0) cc_final: 0.7489 (pt0) REVERT: E 777 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.7915 (m) REVERT: E 899 LYS cc_start: 0.8537 (pptt) cc_final: 0.8021 (tptm) REVERT: E 910 ASN cc_start: 0.7206 (t0) cc_final: 0.6798 (t0) REVERT: F 68 LEU cc_start: 0.8171 (mt) cc_final: 0.7881 (mm) REVERT: F 96 THR cc_start: 0.8703 (p) cc_final: 0.8464 (p) REVERT: F 215 MET cc_start: 0.7087 (mpp) cc_final: 0.6873 (mpp) REVERT: F 231 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7630 (pt0) REVERT: F 282 SER cc_start: 0.8712 (t) cc_final: 0.8495 (m) REVERT: F 437 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7845 (tm-30) REVERT: I 40 ASP cc_start: 0.9034 (t0) cc_final: 0.7803 (m-30) REVERT: I 129 LEU cc_start: 0.6327 (mt) cc_final: 0.6098 (mt) REVERT: I 180 ASN cc_start: 0.8428 (t0) cc_final: 0.8101 (t0) REVERT: I 182 ASP cc_start: 0.7820 (m-30) cc_final: 0.7604 (m-30) REVERT: I 209 LEU cc_start: 0.5775 (mt) cc_final: 0.5456 (mt) REVERT: I 212 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: J 84 LYS cc_start: 0.8577 (tppp) cc_final: 0.8359 (tppt) REVERT: K 169 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7962 (tm) REVERT: L 93 ASP cc_start: 0.7134 (m-30) cc_final: 0.6836 (m-30) REVERT: M 61 MET cc_start: 0.7015 (mmm) cc_final: 0.6809 (mmp) REVERT: M 160 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8226 (t0) REVERT: N 63 ASP cc_start: 0.7831 (m-30) cc_final: 0.7146 (p0) REVERT: N 112 VAL cc_start: 0.7235 (t) cc_final: 0.6907 (t) REVERT: x 49 ILE cc_start: 0.8745 (mt) cc_final: 0.8475 (pp) REVERT: x 198 MET cc_start: 0.7417 (pmt) cc_final: 0.7098 (pp-130) REVERT: x 288 MET cc_start: 0.6971 (mmt) cc_final: 0.6749 (mmt) REVERT: x 494 MET cc_start: 0.8459 (mtp) cc_final: 0.7946 (mtp) REVERT: x 865 GLU cc_start: 0.8741 (tp30) cc_final: 0.8296 (tm-30) REVERT: x 1055 MET cc_start: 0.9290 (tpp) cc_final: 0.8722 (tpp) REVERT: x 1191 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8331 (tt) REVERT: z 92 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8143 (tm-30) outliers start: 130 outliers final: 38 residues processed: 901 average time/residue: 2.0690 time to fit residues: 2356.9020 Evaluate side-chains 681 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 636 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 912 SER Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 777 SER Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 807 MET Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 269 GLN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 195 ASP Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain x residue 31 CYS Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 122 SER Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 407 PHE Chi-restraints excluded: chain x residue 684 LEU Chi-restraints excluded: chain x residue 702 SER Chi-restraints excluded: chain x residue 853 THR Chi-restraints excluded: chain x residue 976 LEU Chi-restraints excluded: chain x residue 1002 ILE Chi-restraints excluded: chain x residue 1076 LEU Chi-restraints excluded: chain x residue 1191 LEU Chi-restraints excluded: chain z residue 27 LEU Chi-restraints excluded: chain z residue 97 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 474 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 360 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 371 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 ASN B 21 ASN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN B 227 GLN ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 243 ASN L 112 ASN M 207 GLN x 260 ASN x 629 ASN z 81 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.099385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.071425 restraints weight = 270013.963| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.46 r_work: 0.3181 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 37111 Z= 0.309 Angle : 0.681 12.547 50507 Z= 0.357 Chirality : 0.045 0.259 5926 Planarity : 0.005 0.083 6607 Dihedral : 5.327 88.209 5389 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.26 % Allowed : 21.62 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 4997 helix: 1.07 (0.11), residues: 2237 sheet: -1.89 (0.18), residues: 681 loop : -0.96 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 894 HIS 0.012 0.001 HIS E 152 PHE 0.030 0.002 PHE x 254 TYR 0.017 0.002 TYR F 146 ARG 0.014 0.001 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 695 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 585 time to evaluate : 4.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8327 (t70) cc_final: 0.8053 (t0) REVERT: A 129 ILE cc_start: 0.8916 (tp) cc_final: 0.8603 (tt) REVERT: A 769 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8550 (ttp-170) REVERT: A 828 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7712 (mt-10) REVERT: A 912 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8895 (p) REVERT: A 979 ASP cc_start: 0.7591 (m-30) cc_final: 0.7361 (m-30) REVERT: A 1057 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8401 (mmtt) REVERT: A 1062 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7533 (ttm) REVERT: B 163 SER cc_start: 0.8396 (t) cc_final: 0.7587 (t) REVERT: B 220 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7669 (tp30) REVERT: B 375 VAL cc_start: 0.8918 (m) cc_final: 0.8659 (p) REVERT: B 391 MET cc_start: 0.7554 (mtm) cc_final: 0.6740 (mtt) REVERT: B 438 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8373 (mtmm) REVERT: B 466 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8433 (mtt-85) REVERT: B 473 LEU cc_start: 0.8160 (mt) cc_final: 0.7655 (mp) REVERT: E 102 MET cc_start: 0.8219 (mmm) cc_final: 0.7628 (mmm) REVERT: E 119 GLU cc_start: 0.7961 (tp30) cc_final: 0.7745 (tp30) REVERT: E 266 ILE cc_start: 0.8539 (mt) cc_final: 0.8313 (mp) REVERT: E 773 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7483 (t) REVERT: E 781 VAL cc_start: 0.8315 (p) cc_final: 0.7960 (p) REVERT: E 817 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8167 (mt-10) REVERT: E 849 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8086 (ttt180) REVERT: E 899 LYS cc_start: 0.8574 (pptt) cc_final: 0.8098 (tptm) REVERT: E 1021 ASN cc_start: 0.8471 (t0) cc_final: 0.7859 (t0) REVERT: E 1023 SER cc_start: 0.8651 (t) cc_final: 0.8314 (p) REVERT: F 39 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8220 (t) REVERT: F 61 THR cc_start: 0.8829 (t) cc_final: 0.8622 (p) REVERT: F 231 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7741 (pt0) REVERT: F 383 MET cc_start: 0.8160 (ttp) cc_final: 0.7950 (ttt) REVERT: F 437 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8013 (tp30) REVERT: F 449 TYR cc_start: 0.8341 (m-80) cc_final: 0.7865 (m-80) REVERT: I 182 ASP cc_start: 0.8144 (m-30) cc_final: 0.7798 (m-30) REVERT: I 208 LYS cc_start: 0.8353 (tttt) cc_final: 0.8113 (tttt) REVERT: J 110 HIS cc_start: 0.8176 (t70) cc_final: 0.7966 (t70) REVERT: M 160 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8325 (t0) REVERT: N 104 GLU cc_start: 0.8771 (mm-30) cc_final: 0.7698 (mp0) REVERT: x 198 MET cc_start: 0.7487 (pmt) cc_final: 0.7063 (pp-130) REVERT: x 382 PHE cc_start: 0.7283 (m-10) cc_final: 0.7042 (m-10) REVERT: x 494 MET cc_start: 0.8440 (mtp) cc_final: 0.7817 (mtp) REVERT: x 1055 MET cc_start: 0.9377 (tpp) cc_final: 0.9077 (tpp) REVERT: z 92 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8147 (tm-30) REVERT: z 125 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8970 (pttp) outliers start: 110 outliers final: 31 residues processed: 661 average time/residue: 2.0477 time to fit residues: 1721.5522 Evaluate side-chains 524 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 485 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 769 ARG Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 912 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 773 VAL Chi-restraints excluded: chain E residue 849 ARG Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 1002 MET Chi-restraints excluded: chain E residue 1040 LYS Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 122 SER Chi-restraints excluded: chain x residue 407 PHE Chi-restraints excluded: chain x residue 684 LEU Chi-restraints excluded: chain x residue 702 SER Chi-restraints excluded: chain x residue 745 ASP Chi-restraints excluded: chain x residue 1191 LEU Chi-restraints excluded: chain z residue 97 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 47 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 492 optimal weight: 30.0000 chunk 294 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 330 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN F 64 GLN F 243 ASN ** F 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN M 7 GLN x 420 HIS x 629 ASN x 880 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.097071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.068137 restraints weight = 271662.301| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.47 r_work: 0.3111 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.9028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 37111 Z= 0.390 Angle : 0.745 13.484 50507 Z= 0.392 Chirality : 0.047 0.212 5926 Planarity : 0.006 0.093 6607 Dihedral : 5.398 95.152 5386 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.54 % Favored : 94.44 % Rotamer: Outliers : 2.82 % Allowed : 22.39 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 4997 helix: 1.04 (0.11), residues: 2244 sheet: -1.96 (0.18), residues: 690 loop : -1.17 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 894 HIS 0.008 0.001 HIS A 214 PHE 0.040 0.002 PHE x 254 TYR 0.020 0.002 TYR x 879 ARG 0.023 0.001 ARG N 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 533 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 438 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8673 (t70) cc_final: 0.8453 (t0) REVERT: A 114 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8708 (ttmt) REVERT: A 129 ILE cc_start: 0.9144 (tp) cc_final: 0.8854 (tt) REVERT: A 200 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: A 769 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8896 (ttp-170) REVERT: A 889 ILE cc_start: 0.8849 (mm) cc_final: 0.8644 (mt) REVERT: A 979 ASP cc_start: 0.8455 (m-30) cc_final: 0.8214 (m-30) REVERT: B 220 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8126 (OUTLIER) REVERT: B 391 MET cc_start: 0.8722 (mtm) cc_final: 0.8444 (mtt) REVERT: B 428 GLU cc_start: 0.7929 (pp20) cc_final: 0.7660 (tm-30) REVERT: B 438 LYS cc_start: 0.9144 (mtpp) cc_final: 0.8774 (mtmm) REVERT: E 57 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9126 (mp) REVERT: E 807 MET cc_start: 0.8935 (ttp) cc_final: 0.8705 (ttt) REVERT: E 978 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7719 (mp0) REVERT: E 1023 SER cc_start: 0.8778 (t) cc_final: 0.8469 (p) REVERT: F 311 ASP cc_start: 0.8778 (m-30) cc_final: 0.8524 (t0) REVERT: F 437 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8219 (tp30) REVERT: I 182 ASP cc_start: 0.8379 (m-30) cc_final: 0.8069 (m-30) REVERT: I 191 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8977 (p) REVERT: J 99 ILE cc_start: 0.8135 (tt) cc_final: 0.7866 (pp) REVERT: K 169 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8060 (tm) REVERT: M 62 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7289 (mp10) REVERT: M 160 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8514 (t0) REVERT: M 192 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8880 (mt) REVERT: N 92 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7685 (mt) REVERT: N 104 GLU cc_start: 0.8829 (mm-30) cc_final: 0.7921 (mp0) REVERT: x 189 LEU cc_start: 0.7857 (mt) cc_final: 0.7499 (mt) REVERT: x 198 MET cc_start: 0.7726 (pmt) cc_final: 0.7156 (pp-130) REVERT: x 379 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6574 (OUTLIER) REVERT: x 426 LEU cc_start: 0.8853 (tp) cc_final: 0.8572 (tm) REVERT: x 494 MET cc_start: 0.8528 (mtp) cc_final: 0.7909 (mtp) REVERT: x 741 ILE cc_start: 0.9189 (pt) cc_final: 0.8858 (pp) REVERT: x 1035 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8205 (t80) REVERT: z 92 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8383 (tm-30) REVERT: z 116 VAL cc_start: 0.7959 (p) cc_final: 0.7329 (p) outliers start: 95 outliers final: 35 residues processed: 515 average time/residue: 2.2601 time to fit residues: 1454.1602 Evaluate side-chains 409 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 365 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 769 ARG Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 899 LYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain x residue 27 ILE Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 407 PHE Chi-restraints excluded: chain x residue 418 LEU Chi-restraints excluded: chain x residue 684 LEU Chi-restraints excluded: chain x residue 702 SER Chi-restraints excluded: chain x residue 745 ASP Chi-restraints excluded: chain x residue 795 SER Chi-restraints excluded: chain x residue 803 SER Chi-restraints excluded: chain x residue 1035 PHE Chi-restraints excluded: chain z residue 97 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 303 optimal weight: 9.9990 chunk 465 optimal weight: 50.0000 chunk 139 optimal weight: 2.9990 chunk 479 optimal weight: 50.0000 chunk 105 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 329 optimal weight: 40.0000 chunk 485 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 410 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 905 HIS M 7 GLN M 26 ASN x 629 ASN z 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.094839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065375 restraints weight = 269563.533| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.47 r_work: 0.3038 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 1.0199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 37111 Z= 0.385 Angle : 0.675 12.332 50507 Z= 0.356 Chirality : 0.045 0.229 5926 Planarity : 0.005 0.138 6607 Dihedral : 5.218 90.305 5385 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 2.70 % Allowed : 23.37 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4997 helix: 1.19 (0.11), residues: 2244 sheet: -1.98 (0.18), residues: 711 loop : -1.06 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP x 229 HIS 0.008 0.002 HIS A 214 PHE 0.021 0.002 PHE F 113 TYR 0.021 0.002 TYR N 40 ARG 0.011 0.001 ARG z 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 375 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8582 (t70) cc_final: 0.8380 (t70) REVERT: A 129 ILE cc_start: 0.9307 (tp) cc_final: 0.9041 (tt) REVERT: A 178 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8422 (ptm160) REVERT: A 200 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: A 948 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 1050 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: A 1057 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8767 (mmtm) REVERT: B 296 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8271 (tm-30) REVERT: E 148 GLN cc_start: 0.8457 (tt0) cc_final: 0.8181 (pp30) REVERT: E 740 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: E 807 MET cc_start: 0.9145 (ttp) cc_final: 0.8865 (ttt) REVERT: E 848 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8433 (pp20) REVERT: E 899 LYS cc_start: 0.8954 (pptt) cc_final: 0.8567 (tptm) REVERT: E 978 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7963 (mp0) REVERT: E 1023 SER cc_start: 0.9009 (t) cc_final: 0.8735 (p) REVERT: F 280 ASP cc_start: 0.7383 (t0) cc_final: 0.6929 (t0) REVERT: F 355 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8625 (mt-10) REVERT: F 437 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8406 (tp30) REVERT: I 182 ASP cc_start: 0.8574 (m-30) cc_final: 0.8296 (m-30) REVERT: K 152 MET cc_start: 0.8898 (ptp) cc_final: 0.8685 (ptp) REVERT: M 29 TYR cc_start: 0.8528 (t80) cc_final: 0.8311 (t80) REVERT: M 61 MET cc_start: 0.6637 (mmp) cc_final: 0.5807 (tmm) REVERT: M 160 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8567 (t0) REVERT: M 193 ASP cc_start: 0.8759 (t70) cc_final: 0.8417 (t0) REVERT: N 92 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7754 (mt) REVERT: N 102 ASP cc_start: 0.8381 (t0) cc_final: 0.7990 (t0) REVERT: N 104 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8002 (mp0) REVERT: x 261 TRP cc_start: 0.8984 (t60) cc_final: 0.8744 (p-90) REVERT: x 379 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6681 (mp0) REVERT: x 426 LEU cc_start: 0.8934 (tp) cc_final: 0.8639 (tm) REVERT: x 741 ILE cc_start: 0.9340 (pt) cc_final: 0.9091 (mp) REVERT: z 83 ARG cc_start: 0.8778 (mtp-110) cc_final: 0.8572 (ttp80) REVERT: z 92 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8400 (tm-30) REVERT: z 121 ARG cc_start: 0.9077 (ttm110) cc_final: 0.8615 (mtp-110) outliers start: 91 outliers final: 33 residues processed: 448 average time/residue: 2.4118 time to fit residues: 1330.5830 Evaluate side-chains 355 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 314 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 740 GLU Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 848 GLU Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 1040 LYS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 177 ILE Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 407 PHE Chi-restraints excluded: chain x residue 418 LEU Chi-restraints excluded: chain x residue 684 LEU Chi-restraints excluded: chain x residue 745 ASP Chi-restraints excluded: chain x residue 795 SER Chi-restraints excluded: chain x residue 1035 PHE Chi-restraints excluded: chain x residue 1171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 43 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 432 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 629 ASN z 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.094784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064911 restraints weight = 268259.542| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.51 r_work: 0.3026 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 1.0486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37111 Z= 0.245 Angle : 0.595 8.108 50507 Z= 0.308 Chirality : 0.042 0.206 5926 Planarity : 0.004 0.069 6607 Dihedral : 4.984 94.870 5385 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.28 % Allowed : 24.32 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.12), residues: 4997 helix: 1.46 (0.11), residues: 2244 sheet: -1.98 (0.18), residues: 700 loop : -0.99 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 815 HIS 0.005 0.001 HIS A 905 PHE 0.015 0.001 PHE E1055 TYR 0.015 0.001 TYR z 140 ARG 0.009 0.001 ARG z 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 331 time to evaluate : 4.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8569 (t70) cc_final: 0.8337 (t70) REVERT: A 178 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8454 (ptm160) REVERT: A 200 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: A 202 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: A 866 SER cc_start: 0.9392 (OUTLIER) cc_final: 0.9173 (m) REVERT: A 1057 LYS cc_start: 0.9036 (mtmt) cc_final: 0.8702 (mmtm) REVERT: B 296 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8244 (tm-30) REVERT: E 109 ILE cc_start: 0.8133 (tt) cc_final: 0.7853 (tt) REVERT: E 148 GLN cc_start: 0.8481 (tt0) cc_final: 0.8171 (pp30) REVERT: E 807 MET cc_start: 0.9181 (ttp) cc_final: 0.8889 (ttt) REVERT: E 848 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8427 (pp20) REVERT: E 978 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7942 (mp0) REVERT: E 1023 SER cc_start: 0.8982 (t) cc_final: 0.8698 (p) REVERT: F 71 ARG cc_start: 0.8783 (ttt-90) cc_final: 0.8381 (ttm110) REVERT: F 355 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8530 (mt-10) REVERT: F 437 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8423 (tp30) REVERT: I 182 ASP cc_start: 0.8653 (m-30) cc_final: 0.8391 (m-30) REVERT: I 213 GLU cc_start: 0.9066 (tp30) cc_final: 0.8730 (tp30) REVERT: K 152 MET cc_start: 0.8910 (ptp) cc_final: 0.8608 (ptp) REVERT: K 165 GLN cc_start: 0.8837 (mt0) cc_final: 0.8540 (mt0) REVERT: L 100 GLU cc_start: 0.8884 (tp30) cc_final: 0.8410 (tm-30) REVERT: M 160 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8652 (t0) REVERT: M 193 ASP cc_start: 0.8898 (t70) cc_final: 0.8586 (t0) REVERT: N 102 ASP cc_start: 0.8455 (t0) cc_final: 0.8173 (t0) REVERT: N 104 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8151 (mp0) REVERT: x 198 MET cc_start: 0.7685 (pmt) cc_final: 0.6863 (pp-130) REVERT: x 261 TRP cc_start: 0.8997 (t60) cc_final: 0.8716 (p-90) REVERT: x 379 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6710 (mp0) REVERT: x 426 LEU cc_start: 0.8937 (tp) cc_final: 0.8663 (tm) REVERT: x 746 ILE cc_start: 0.8398 (pp) cc_final: 0.8146 (pt) REVERT: z 83 ARG cc_start: 0.8846 (mtp-110) cc_final: 0.8576 (mtm110) REVERT: z 89 LYS cc_start: 0.8874 (tptp) cc_final: 0.8558 (mmtt) REVERT: z 92 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8412 (tm-30) outliers start: 77 outliers final: 42 residues processed: 396 average time/residue: 2.3334 time to fit residues: 1155.6547 Evaluate side-chains 357 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 254 CYS Chi-restraints excluded: chain E residue 848 GLU Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 1040 LYS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 177 ILE Chi-restraints excluded: chain N residue 72 HIS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain x residue 77 ILE Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 345 LEU Chi-restraints excluded: chain x residue 407 PHE Chi-restraints excluded: chain x residue 418 LEU Chi-restraints excluded: chain x residue 556 THR Chi-restraints excluded: chain x residue 684 LEU Chi-restraints excluded: chain x residue 745 ASP Chi-restraints excluded: chain x residue 795 SER Chi-restraints excluded: chain x residue 803 SER Chi-restraints excluded: chain x residue 921 SER Chi-restraints excluded: chain x residue 1035 PHE Chi-restraints excluded: chain x residue 1152 ARG Chi-restraints excluded: chain x residue 1171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 391 optimal weight: 0.4980 chunk 373 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 486 optimal weight: 30.0000 chunk 434 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 489 optimal weight: 3.9990 chunk 386 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 157 optimal weight: 0.0870 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 629 ASN ** x1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.094588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064688 restraints weight = 267928.430| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.51 r_work: 0.3019 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 1.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37111 Z= 0.226 Angle : 0.581 10.719 50507 Z= 0.298 Chirality : 0.042 0.216 5926 Planarity : 0.004 0.096 6607 Dihedral : 4.843 96.291 5385 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.96 % Allowed : 24.32 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.12), residues: 4997 helix: 1.66 (0.11), residues: 2239 sheet: -1.93 (0.18), residues: 715 loop : -0.86 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP x 172 HIS 0.006 0.001 HIS A 905 PHE 0.013 0.001 PHE x 347 TYR 0.025 0.001 TYR z 132 ARG 0.013 0.001 ARG z 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 392 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 326 time to evaluate : 4.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8546 (t70) cc_final: 0.8317 (t70) REVERT: A 148 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7874 (pp30) REVERT: A 178 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8391 (ptm160) REVERT: A 202 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: A 866 SER cc_start: 0.9367 (OUTLIER) cc_final: 0.9142 (m) REVERT: A 942 GLU cc_start: 0.8766 (tt0) cc_final: 0.8434 (tt0) REVERT: A 1057 LYS cc_start: 0.9089 (mtmt) cc_final: 0.8811 (mmtt) REVERT: B 296 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8136 (tm-30) REVERT: E 109 ILE cc_start: 0.8113 (tt) cc_final: 0.7910 (tt) REVERT: E 148 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8203 (pp30) REVERT: E 807 MET cc_start: 0.9178 (ttp) cc_final: 0.8904 (ttt) REVERT: E 848 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8413 (pp20) REVERT: E 978 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7960 (mp0) REVERT: E 1023 SER cc_start: 0.9044 (t) cc_final: 0.8762 (p) REVERT: F 71 ARG cc_start: 0.8798 (ttt-90) cc_final: 0.8409 (ttm110) REVERT: F 437 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8496 (tp30) REVERT: I 182 ASP cc_start: 0.8710 (m-30) cc_final: 0.8447 (m-30) REVERT: I 213 GLU cc_start: 0.9045 (tp30) cc_final: 0.8722 (tp30) REVERT: K 152 MET cc_start: 0.8904 (ptp) cc_final: 0.8581 (ptp) REVERT: K 165 GLN cc_start: 0.8881 (mt0) cc_final: 0.8567 (mt0) REVERT: L 100 GLU cc_start: 0.8853 (tp30) cc_final: 0.8409 (tm-30) REVERT: M 160 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8678 (t0) REVERT: M 193 ASP cc_start: 0.8994 (t70) cc_final: 0.8658 (t0) REVERT: N 102 ASP cc_start: 0.8544 (t0) cc_final: 0.8294 (t0) REVERT: N 104 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8162 (mp0) REVERT: x 198 MET cc_start: 0.7719 (pmt) cc_final: 0.6999 (pp-130) REVERT: x 261 TRP cc_start: 0.8984 (t60) cc_final: 0.8720 (p-90) REVERT: x 426 LEU cc_start: 0.8861 (tp) cc_final: 0.8603 (tm) REVERT: x 746 ILE cc_start: 0.8425 (pp) cc_final: 0.8169 (pt) REVERT: x 869 GLU cc_start: 0.8926 (tt0) cc_final: 0.8700 (tm-30) REVERT: z 83 ARG cc_start: 0.8796 (mtp-110) cc_final: 0.8501 (mtm110) REVERT: z 86 VAL cc_start: 0.9325 (p) cc_final: 0.9009 (p) REVERT: z 89 LYS cc_start: 0.8894 (tptp) cc_final: 0.8562 (mmtt) REVERT: z 92 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8419 (tm-30) REVERT: z 133 GLU cc_start: 0.8985 (tp30) cc_final: 0.8762 (tp30) REVERT: z 165 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8740 (tp30) outliers start: 66 outliers final: 34 residues processed: 379 average time/residue: 2.3888 time to fit residues: 1134.2063 Evaluate side-chains 345 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 303 time to evaluate : 4.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 254 CYS Chi-restraints excluded: chain E residue 848 GLU Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 1040 LYS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 177 ILE Chi-restraints excluded: chain N residue 72 HIS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 77 ILE Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 345 LEU Chi-restraints excluded: chain x residue 407 PHE Chi-restraints excluded: chain x residue 418 LEU Chi-restraints excluded: chain x residue 556 THR Chi-restraints excluded: chain x residue 684 LEU Chi-restraints excluded: chain x residue 745 ASP Chi-restraints excluded: chain x residue 921 SER Chi-restraints excluded: chain x residue 1035 PHE Chi-restraints excluded: chain x residue 1171 LEU Chi-restraints excluded: chain z residue 165 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 24 optimal weight: 1.9990 chunk 371 optimal weight: 8.9990 chunk 280 optimal weight: 50.0000 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 338 optimal weight: 50.0000 chunk 157 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 431 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN E 833 GLN F 190 GLN F 331 GLN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 629 ASN z 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.092256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.062138 restraints weight = 268174.307| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.55 r_work: 0.2937 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 1.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 37111 Z= 0.427 Angle : 0.647 12.104 50507 Z= 0.339 Chirality : 0.044 0.283 5926 Planarity : 0.005 0.100 6607 Dihedral : 5.066 102.502 5385 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.16 % Allowed : 23.87 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 4997 helix: 1.53 (0.11), residues: 2241 sheet: -1.94 (0.18), residues: 719 loop : -0.91 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 815 HIS 0.007 0.001 HIS A 214 PHE 0.027 0.002 PHE x 347 TYR 0.031 0.002 TYR z 132 ARG 0.010 0.001 ARG z 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 380 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 4.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8681 (t70) cc_final: 0.8459 (t70) REVERT: A 178 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8491 (ptm160) REVERT: A 202 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8370 (tm-30) REVERT: A 942 GLU cc_start: 0.8835 (tt0) cc_final: 0.8540 (tt0) REVERT: B 296 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8195 (tm-30) REVERT: E 72 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8688 (pm20) REVERT: E 148 GLN cc_start: 0.8553 (tt0) cc_final: 0.8245 (pp30) REVERT: E 848 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8453 (pp20) REVERT: E 1023 SER cc_start: 0.9149 (t) cc_final: 0.8871 (p) REVERT: F 71 ARG cc_start: 0.8861 (ttt-90) cc_final: 0.8488 (ttm110) REVERT: F 280 ASP cc_start: 0.7912 (t0) cc_final: 0.7645 (t0) REVERT: F 311 ASP cc_start: 0.8851 (t0) cc_final: 0.8633 (t70) REVERT: F 355 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: F 450 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: I 213 GLU cc_start: 0.9058 (tp30) cc_final: 0.8838 (tp30) REVERT: J 77 GLN cc_start: 0.8903 (tp40) cc_final: 0.8660 (tp40) REVERT: K 102 GLU cc_start: 0.9129 (tt0) cc_final: 0.8652 (tp30) REVERT: K 152 MET cc_start: 0.9139 (ptp) cc_final: 0.8839 (ptp) REVERT: K 165 GLN cc_start: 0.8993 (mt0) cc_final: 0.8653 (mt0) REVERT: L 91 LYS cc_start: 0.8965 (ptmt) cc_final: 0.8643 (ttpp) REVERT: L 100 GLU cc_start: 0.8962 (tp30) cc_final: 0.8575 (tm-30) REVERT: M 57 MET cc_start: 0.6817 (ttt) cc_final: 0.6590 (ttt) REVERT: M 160 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8822 (t0) REVERT: M 193 ASP cc_start: 0.9137 (t70) cc_final: 0.8784 (t0) REVERT: N 92 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7638 (mp) REVERT: N 104 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8205 (mp0) REVERT: x 261 TRP cc_start: 0.9034 (t60) cc_final: 0.8802 (p-90) REVERT: x 426 LEU cc_start: 0.8876 (tp) cc_final: 0.8643 (tm) REVERT: x 746 ILE cc_start: 0.8441 (pp) cc_final: 0.8206 (pt) REVERT: x 869 GLU cc_start: 0.8993 (tt0) cc_final: 0.8770 (tm-30) REVERT: x 1171 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8599 (mm) REVERT: z 83 ARG cc_start: 0.8768 (mtp-110) cc_final: 0.8524 (mtm110) REVERT: z 86 VAL cc_start: 0.9364 (p) cc_final: 0.9039 (p) REVERT: z 89 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8726 (mmtt) REVERT: z 92 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8624 (tm-30) REVERT: z 133 GLU cc_start: 0.8998 (tp30) cc_final: 0.8757 (tp30) REVERT: z 148 ASP cc_start: 0.9061 (m-30) cc_final: 0.8645 (t0) outliers start: 73 outliers final: 39 residues processed: 368 average time/residue: 2.4102 time to fit residues: 1096.3491 Evaluate side-chains 335 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 254 CYS Chi-restraints excluded: chain E residue 848 GLU Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 1040 LYS Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 450 GLU Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 177 ILE Chi-restraints excluded: chain N residue 72 HIS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain x residue 77 ILE Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 407 PHE Chi-restraints excluded: chain x residue 556 THR Chi-restraints excluded: chain x residue 745 ASP Chi-restraints excluded: chain x residue 795 SER Chi-restraints excluded: chain x residue 803 SER Chi-restraints excluded: chain x residue 1035 PHE Chi-restraints excluded: chain x residue 1171 LEU Chi-restraints excluded: chain z residue 89 LYS Chi-restraints excluded: chain z residue 165 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 452 optimal weight: 0.7980 chunk 316 optimal weight: 50.0000 chunk 161 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 292 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 chunk 440 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 955 GLN ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 744 ASN z 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.093642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063644 restraints weight = 267321.716| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.49 r_work: 0.2999 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 1.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37111 Z= 0.194 Angle : 0.580 10.087 50507 Z= 0.297 Chirality : 0.042 0.157 5926 Planarity : 0.004 0.070 6607 Dihedral : 4.824 97.480 5385 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.54 % Allowed : 24.76 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.12), residues: 4997 helix: 1.79 (0.11), residues: 2232 sheet: -1.91 (0.18), residues: 703 loop : -0.73 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP x 929 HIS 0.012 0.001 HIS x 350 PHE 0.016 0.001 PHE x 347 TYR 0.023 0.001 TYR z 132 ARG 0.014 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 360 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 4.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8522 (t70) cc_final: 0.8313 (t70) REVERT: A 148 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7810 (pp30) REVERT: A 178 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8401 (ptm160) REVERT: A 202 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8257 (tm-30) REVERT: A 866 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.9136 (m) REVERT: A 942 GLU cc_start: 0.8794 (tt0) cc_final: 0.8535 (tt0) REVERT: A 1037 SER cc_start: 0.9295 (OUTLIER) cc_final: 0.8927 (p) REVERT: B 296 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8089 (tm-30) REVERT: B 301 ARG cc_start: 0.9188 (mmm-85) cc_final: 0.8493 (mtm180) REVERT: E 72 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8628 (pm20) REVERT: E 148 GLN cc_start: 0.8499 (tt0) cc_final: 0.8214 (pp30) REVERT: E 807 MET cc_start: 0.9187 (ttp) cc_final: 0.8971 (ttt) REVERT: E 848 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8380 (pp20) REVERT: E 978 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8187 (mp0) REVERT: E 1023 SER cc_start: 0.9139 (t) cc_final: 0.8876 (p) REVERT: F 71 ARG cc_start: 0.8833 (ttt-90) cc_final: 0.8472 (ttm110) REVERT: F 280 ASP cc_start: 0.7722 (t0) cc_final: 0.7408 (t0) REVERT: F 311 ASP cc_start: 0.8755 (t0) cc_final: 0.8511 (t70) REVERT: F 355 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: F 437 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8530 (tp30) REVERT: F 450 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: I 213 GLU cc_start: 0.8976 (tp30) cc_final: 0.8761 (tp30) REVERT: J 27 TYR cc_start: 0.8754 (t80) cc_final: 0.8361 (t80) REVERT: K 102 GLU cc_start: 0.9094 (tt0) cc_final: 0.8640 (tp30) REVERT: K 152 MET cc_start: 0.9115 (ptp) cc_final: 0.8814 (ptp) REVERT: K 165 GLN cc_start: 0.8951 (mt0) cc_final: 0.8599 (mt0) REVERT: L 91 LYS cc_start: 0.8970 (ptmt) cc_final: 0.8606 (ttpp) REVERT: L 100 GLU cc_start: 0.8921 (tp30) cc_final: 0.8572 (tm-30) REVERT: M 61 MET cc_start: 0.6799 (mmp) cc_final: 0.5689 (tmm) REVERT: M 160 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8797 (t0) REVERT: M 193 ASP cc_start: 0.9090 (t70) cc_final: 0.8767 (t0) REVERT: N 92 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7660 (mp) REVERT: N 102 ASP cc_start: 0.8490 (t0) cc_final: 0.8187 (t0) REVERT: N 104 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8252 (mp0) REVERT: x 49 ILE cc_start: 0.9132 (mp) cc_final: 0.8850 (mp) REVERT: x 261 TRP cc_start: 0.9020 (t60) cc_final: 0.8798 (p-90) REVERT: x 426 LEU cc_start: 0.8882 (tp) cc_final: 0.8643 (tm) REVERT: x 746 ILE cc_start: 0.8434 (pp) cc_final: 0.8203 (pt) REVERT: x 1171 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8569 (mm) REVERT: z 83 ARG cc_start: 0.8772 (mtp-110) cc_final: 0.8561 (mtm110) REVERT: z 86 VAL cc_start: 0.9376 (p) cc_final: 0.8952 (p) REVERT: z 89 LYS cc_start: 0.8976 (tptp) cc_final: 0.8619 (mmtt) REVERT: z 92 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8499 (tm-30) REVERT: z 133 GLU cc_start: 0.8983 (tp30) cc_final: 0.8639 (tp30) REVERT: z 148 ASP cc_start: 0.9054 (m-30) cc_final: 0.8668 (t0) outliers start: 52 outliers final: 30 residues processed: 353 average time/residue: 2.4655 time to fit residues: 1076.0328 Evaluate side-chains 335 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 848 GLU Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 1040 LYS Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 450 GLU Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 177 ILE Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain N residue 72 HIS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain x residue 77 ILE Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 345 LEU Chi-restraints excluded: chain x residue 556 THR Chi-restraints excluded: chain x residue 745 ASP Chi-restraints excluded: chain x residue 795 SER Chi-restraints excluded: chain x residue 803 SER Chi-restraints excluded: chain x residue 1035 PHE Chi-restraints excluded: chain x residue 1171 LEU Chi-restraints excluded: chain z residue 143 ILE Chi-restraints excluded: chain z residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 193 optimal weight: 1.9990 chunk 453 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 438 optimal weight: 4.9990 chunk 450 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 321 optimal weight: 30.0000 chunk 145 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.093091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062865 restraints weight = 267520.506| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.50 r_work: 0.2978 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 1.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37111 Z= 0.256 Angle : 0.582 10.977 50507 Z= 0.300 Chirality : 0.042 0.159 5926 Planarity : 0.004 0.073 6607 Dihedral : 4.791 100.954 5385 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.25 % Allowed : 25.09 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.12), residues: 4997 helix: 1.80 (0.11), residues: 2242 sheet: -1.89 (0.18), residues: 701 loop : -0.72 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 815 HIS 0.007 0.001 HIS x 350 PHE 0.016 0.001 PHE x 347 TYR 0.027 0.001 TYR z 132 ARG 0.013 0.001 ARG z 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9994 Ramachandran restraints generated. 4997 Oldfield, 0 Emsley, 4997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue THR 1070 is missing expected H atoms. Skipping. Residue MET 759 is missing expected H atoms. Skipping. Residue MET 1062 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue VAL 51 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue TYR 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue TYR 112 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue THR 214 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue VAL 10 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue VAL 139 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue TYR 184 is missing expected H atoms. Skipping. Residue VAL 185 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue ILE 196 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue VAL 202 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue TYR 244 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue LEU 249 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue THR 254 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue TYR 267 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue VAL 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue THR 281 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue SER 287 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 312 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue VAL 322 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue TYR 330 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 365 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue VAL 375 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue TYR 392 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue LYS 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 411 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 419 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue VAL 430 is missing expected H atoms. Skipping. Residue VAL 431 is missing expected H atoms. Skipping. Residue LEU 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue LYS 443 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue MET 451 is missing expected H atoms. Skipping. Residue LEU 453 is missing expected H atoms. Skipping. Residue LEU 454 is missing expected H atoms. Skipping. Residue SER 457 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue TYR 463 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue THR 469 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue ILE 183 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue SER 208 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 225 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue LEU 248 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue ILE 274 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 280 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue SER 301 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue THR 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue SER 375 is missing expected H atoms. Skipping. Residue LYS 387 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue THR 429 is missing expected H atoms. Skipping. Residue ILE 430 is missing expected H atoms. Skipping. Residue THR 432 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue LYS 487 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue ILE 518 is missing expected H atoms. Skipping. Residue LYS 519 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LYS 533 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 537 is missing expected H atoms. Skipping. Residue ILE 539 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue VAL 558 is missing expected H atoms. Skipping. Residue SER 559 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue LYS 569 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue THR 573 is missing expected H atoms. Skipping. Residue THR 575 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue VAL 580 is missing expected H atoms. Skipping. Residue TYR 582 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ILE 595 is missing expected H atoms. Skipping. Residue MET 600 is missing expected H atoms. Skipping. Residue VAL 616 is missing expected H atoms. Skipping. Residue SER 618 is missing expected H atoms. Skipping. Residue THR 619 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue MET 623 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue SER 656 is missing expected H atoms. Skipping. Residue THR 677 is missing expected H atoms. Skipping. Residue THR 728 is missing expected H atoms. Skipping. Residue SER 738 is missing expected H atoms. Skipping. Residue VAL 822 is missing expected H atoms. Skipping. Residue THR 848 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 897 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue ILE 990 is missing expected H atoms. Skipping. Residue SER 1040 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LYS 1127 is missing expected H atoms. Skipping. Residue SER 1134 is missing expected H atoms. Skipping. Residue LEU 1136 is missing expected H atoms. Skipping. Residue LYS 1155 is missing expected H atoms. Skipping. Residue ILE 1158 is missing expected H atoms. Skipping. Residue SER 1160 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue VAL 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue MET 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue MET 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue TYR 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue ILE 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue THR 299 is missing expected H atoms. Skipping. Residue VAL 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue VAL 313 is missing expected H atoms. Skipping. Residue SER 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue ILE 323 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue MET 334 is missing expected H atoms. Skipping. Residue LEU 341 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LEU 347 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 10 is missing expected H atoms. Skipping. Residue THR 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue SER 113 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 298 time to evaluate : 4.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8537 (t70) cc_final: 0.8321 (t70) REVERT: A 178 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8443 (ptm160) REVERT: A 202 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: A 866 SER cc_start: 0.9360 (OUTLIER) cc_final: 0.9122 (m) REVERT: A 942 GLU cc_start: 0.8836 (tt0) cc_final: 0.8585 (tt0) REVERT: A 1037 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.8953 (p) REVERT: B 296 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 301 ARG cc_start: 0.9196 (mmm-85) cc_final: 0.8402 (mtm180) REVERT: E 72 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8635 (pm20) REVERT: E 148 GLN cc_start: 0.8516 (tt0) cc_final: 0.8209 (pp30) REVERT: E 807 MET cc_start: 0.9187 (ttp) cc_final: 0.8981 (ttt) REVERT: E 848 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8432 (pp20) REVERT: E 978 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8213 (mp0) REVERT: E 1023 SER cc_start: 0.9193 (t) cc_final: 0.8913 (p) REVERT: F 71 ARG cc_start: 0.8815 (ttt-90) cc_final: 0.8448 (ttm110) REVERT: F 280 ASP cc_start: 0.7769 (t0) cc_final: 0.7469 (t0) REVERT: F 311 ASP cc_start: 0.8783 (t0) cc_final: 0.8559 (t70) REVERT: F 450 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: I 213 GLU cc_start: 0.8994 (tp30) cc_final: 0.8787 (tp30) REVERT: J 27 TYR cc_start: 0.8807 (t80) cc_final: 0.8425 (t80) REVERT: K 102 GLU cc_start: 0.9102 (tt0) cc_final: 0.8648 (tp30) REVERT: K 152 MET cc_start: 0.9134 (ptp) cc_final: 0.8822 (ptp) REVERT: K 165 GLN cc_start: 0.8967 (mt0) cc_final: 0.8591 (mt0) REVERT: L 91 LYS cc_start: 0.8949 (ptmt) cc_final: 0.8597 (ttpp) REVERT: L 100 GLU cc_start: 0.8961 (tp30) cc_final: 0.8601 (tm-30) REVERT: M 160 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8836 (t0) REVERT: M 193 ASP cc_start: 0.9127 (t70) cc_final: 0.8789 (t0) REVERT: N 92 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8077 (mp) REVERT: N 102 ASP cc_start: 0.8643 (t0) cc_final: 0.8297 (t0) REVERT: N 104 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8281 (mp0) REVERT: x 49 ILE cc_start: 0.9157 (mp) cc_final: 0.8918 (mp) REVERT: x 261 TRP cc_start: 0.9024 (t60) cc_final: 0.8779 (p-90) REVERT: x 426 LEU cc_start: 0.8912 (tp) cc_final: 0.8692 (tm) REVERT: x 746 ILE cc_start: 0.8422 (pp) cc_final: 0.8196 (pt) REVERT: x 1171 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8677 (mm) REVERT: z 86 VAL cc_start: 0.9398 (p) cc_final: 0.9004 (p) REVERT: z 89 LYS cc_start: 0.8968 (tptp) cc_final: 0.8604 (mmtt) REVERT: z 92 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8551 (tm-30) REVERT: z 133 GLU cc_start: 0.8963 (tp30) cc_final: 0.8592 (tp30) REVERT: z 148 ASP cc_start: 0.9059 (m-30) cc_final: 0.8669 (t0) outliers start: 42 outliers final: 27 residues processed: 335 average time/residue: 2.5463 time to fit residues: 1048.6316 Evaluate side-chains 321 residues out of total 4441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 848 GLU Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 450 GLU Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 177 ILE Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain N residue 72 HIS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain x residue 77 ILE Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 345 LEU Chi-restraints excluded: chain x residue 407 PHE Chi-restraints excluded: chain x residue 556 THR Chi-restraints excluded: chain x residue 745 ASP Chi-restraints excluded: chain x residue 795 SER Chi-restraints excluded: chain x residue 803 SER Chi-restraints excluded: chain x residue 1035 PHE Chi-restraints excluded: chain x residue 1171 LEU Chi-restraints excluded: chain z residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 391 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 407 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 378 optimal weight: 9.9990 chunk 350 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 153 GLN z 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.093084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063085 restraints weight = 266704.994| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.48 r_work: 0.2981 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 1.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37111 Z= 0.224 Angle : 0.576 11.605 50507 Z= 0.295 Chirality : 0.041 0.157 5926 Planarity : 0.004 0.078 6607 Dihedral : 4.722 100.152 5385 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.22 % Allowed : 25.15 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.12), residues: 4997 helix: 1.88 (0.11), residues: 2232 sheet: -1.86 (0.18), residues: 706 loop : -0.66 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP x 460 HIS 0.007 0.001 HIS x 350 PHE 0.017 0.001 PHE x 347 TYR 0.026 0.001 TYR z 132 ARG 0.010 0.001 ARG B 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54041.27 seconds wall clock time: 917 minutes 59.02 seconds (55079.02 seconds total)