Starting phenix.real_space_refine on Sun Dec 29 18:14:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7w_18235/12_2024/8q7w_18235_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7w_18235/12_2024/8q7w_18235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7w_18235/12_2024/8q7w_18235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7w_18235/12_2024/8q7w_18235.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7w_18235/12_2024/8q7w_18235_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7w_18235/12_2024/8q7w_18235_trim.cif" } resolution = 3.9 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= 0.003 sd= 0.042 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 106 5.49 5 Mg 1 5.21 5 S 109 5.16 5 C 19325 2.51 5 N 5594 2.21 5 O 6135 1.98 5 H 26552 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 57822 Number of models: 1 Model: "" Number of chains: 16 Chain: "5" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 3301 Classifications: {'RNA': 104} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 15, 'rna3p_pur': 39, 'rna3p_pyr': 42} Link IDs: {'rna2p': 22, 'rna3p': 81} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 27194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1645, 27194 Classifications: {'peptide': 1645} Link IDs: {'PCIS': 3, 'PTRANS': 90, 'TRANS': 1551} Chain breaks: 8 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 432 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "C" Number of atoms: 13374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 13374 Classifications: {'peptide': 846} Link IDs: {'PTRANS': 49, 'TRANS': 796} Chain: "D" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2193 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 936 Unresolved non-hydrogen angles: 1208 Unresolved non-hydrogen dihedrals: 796 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 16, 'GLN%COO:plan1': 1, 'TYR:plan': 11, 'ASN:plan1': 15, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 11, 'GLU:plan': 11, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 522 Chain: "E" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4482 Classifications: {'peptide': 529} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 499} Chain breaks: 7 Unresolved chain link angles: 28 Unresolved non-hydrogen bonds: 1464 Unresolved non-hydrogen angles: 1855 Unresolved non-hydrogen dihedrals: 1214 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 29, 'TYR:plan': 12, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 13, 'GLU:plan': 40, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 763 Chain: "F" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 173 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "G" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 2 Chain: "a" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "b" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 511 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 125 Chain: "c" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 688 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 165 Chain: "d" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1312 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "e" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 541 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "f" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 513 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "g" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 525 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU E 464 " occ=0.88 ... (5 atoms not shown) pdb=" HA GLU E 464 " occ=0.60 Time building chain proxies: 19.79, per 1000 atoms: 0.34 Number of scatterers: 57822 At special positions: 0 Unit cell: (151.28, 171.12, 215.76, 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 109 16.00 P 106 15.00 Mg 1 11.99 O 6135 8.00 N 5594 7.00 C 19325 6.00 H 26552 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: 11.10 Conformation dependent library (CDL) restraints added in 3.9 seconds 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7674 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 32 sheets defined 40.0% alpha, 18.1% beta 32 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 19.70 Creating SS restraints... Processing helix chain 'A' and resid 27 through 45 removed outlier: 4.234A pdb=" N LYS A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.223A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.131A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.639A pdb=" N ASN A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 182 " --> pdb=" O TYR A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 182' Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.730A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.528A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 471 through 478 removed outlier: 3.734A pdb=" N SER A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 509 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 541 through 565 removed outlier: 3.963A pdb=" N HIS A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 removed outlier: 3.997A pdb=" N ASP A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 577 " --> pdb=" O GLN A 573 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 598 through 617 removed outlier: 3.619A pdb=" N ARG A 603 " --> pdb=" O MET A 599 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 657 removed outlier: 3.975A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 698 through 706 removed outlier: 4.157A pdb=" N ASN A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 722 removed outlier: 4.343A pdb=" N HIS A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 763 removed outlier: 3.873A pdb=" N ARG A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 798 removed outlier: 3.582A pdb=" N CYS A 772 " --> pdb=" O ASP A 768 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.533A pdb=" N ALA A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 850 removed outlier: 4.240A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 887 Processing helix chain 'A' and resid 912 through 933 removed outlier: 3.747A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 961 Processing helix chain 'A' and resid 989 through 998 Processing helix chain 'A' and resid 1002 through 1012 Processing helix chain 'A' and resid 1036 through 1053 removed outlier: 3.598A pdb=" N GLN A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1102 through 1117 removed outlier: 3.585A pdb=" N ALA A1106 " --> pdb=" O THR A1102 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1159 Processing helix chain 'A' and resid 1169 through 1173 removed outlier: 3.575A pdb=" N ASN A1172 " --> pdb=" O GLN A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1248 removed outlier: 3.626A pdb=" N MET A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1272 removed outlier: 3.794A pdb=" N ILE A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1281 removed outlier: 4.135A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1281' Processing helix chain 'A' and resid 1282 through 1304 removed outlier: 3.548A pdb=" N VAL A1289 " --> pdb=" O LEU A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1316 removed outlier: 3.700A pdb=" N VAL A1315 " --> pdb=" O PRO A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1368 through 1372 removed outlier: 3.711A pdb=" N ILE A1372 " --> pdb=" O TYR A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1399 removed outlier: 3.723A pdb=" N GLU A1378 " --> pdb=" O PRO A1374 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A1398 " --> pdb=" O GLN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1424 removed outlier: 3.530A pdb=" N THR A1421 " --> pdb=" O ARG A1418 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A1424 " --> pdb=" O THR A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1435 through 1442 removed outlier: 4.018A pdb=" N ARG A1439 " --> pdb=" O GLY A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1446 Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1467 through 1478 removed outlier: 3.739A pdb=" N ARG A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1485 Processing helix chain 'A' and resid 1530 through 1538 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 removed outlier: 4.265A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A1575 " --> pdb=" O ILE A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1599 removed outlier: 3.575A pdb=" N GLN A1599 " --> pdb=" O GLN A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1688 Processing helix chain 'A' and resid 1722 through 1737 Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.556A pdb=" N LEU C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 154 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 212 through 220 removed outlier: 3.602A pdb=" N GLY C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 removed outlier: 3.574A pdb=" N LYS C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 266 removed outlier: 3.624A pdb=" N GLU C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 removed outlier: 3.781A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 319 through 331 removed outlier: 3.609A pdb=" N PHE C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 437 removed outlier: 4.105A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 removed outlier: 4.064A pdb=" N LYS C 448 " --> pdb=" O GLY C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 466 Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 607 removed outlier: 3.693A pdb=" N MET C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 Processing helix chain 'C' and resid 633 through 649 removed outlier: 3.551A pdb=" N LEU C 637 " --> pdb=" O GLY C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 702 Processing helix chain 'C' and resid 711 through 721 Processing helix chain 'C' and resid 725 through 731 removed outlier: 3.597A pdb=" N SER C 731 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 774 removed outlier: 4.509A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN C 768 " --> pdb=" O ASP C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 803 Processing helix chain 'C' and resid 804 through 823 removed outlier: 3.615A pdb=" N ILE C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Proline residue: C 810 - end of helix removed outlier: 3.563A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 850 removed outlier: 4.255A pdb=" N ALA C 845 " --> pdb=" O ASP C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 853 No H-bonds generated for 'chain 'C' and resid 851 through 853' Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 942 Processing helix chain 'E' and resid 243 through 255 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 287 through 292 removed outlier: 4.056A pdb=" N GLU E 292 " --> pdb=" O PRO E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 315 Processing helix chain 'E' and resid 319 through 328 Processing helix chain 'E' and resid 331 through 352 Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.633A pdb=" N LYS E 360 " --> pdb=" O TRP E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 377 removed outlier: 3.795A pdb=" N TYR E 377 " --> pdb=" O PHE E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 410 Processing helix chain 'E' and resid 415 through 427 Proline residue: E 423 - end of helix Processing helix chain 'E' and resid 440 through 455 removed outlier: 3.549A pdb=" N ALA E 444 " --> pdb=" O GLY E 440 " (cutoff:3.500A) Proline residue: E 448 - end of helix Processing helix chain 'E' and resid 457 through 462 removed outlier: 3.914A pdb=" N ILE E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 493 Processing helix chain 'E' and resid 507 through 517 removed outlier: 3.594A pdb=" N GLN E 511 " --> pdb=" O SER E 507 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET E 517 " --> pdb=" O PHE E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 534 Processing helix chain 'E' and resid 550 through 558 Processing helix chain 'E' and resid 559 through 569 Processing helix chain 'E' and resid 570 through 575 removed outlier: 6.094A pdb=" N SER E 573 " --> pdb=" O MET E 570 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN E 574 " --> pdb=" O PRO E 571 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 575 " --> pdb=" O VAL E 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 570 through 575' Processing helix chain 'E' and resid 579 through 583 removed outlier: 3.772A pdb=" N ALA E 582 " --> pdb=" O THR E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 593 Processing helix chain 'E' and resid 594 through 598 removed outlier: 4.294A pdb=" N HIS E 597 " --> pdb=" O SER E 594 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS E 598 " --> pdb=" O GLY E 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 594 through 598' Processing helix chain 'E' and resid 610 through 621 Processing helix chain 'E' and resid 647 through 649 No H-bonds generated for 'chain 'E' and resid 647 through 649' Processing helix chain 'E' and resid 650 through 661 Processing helix chain 'E' and resid 673 through 687 Processing helix chain 'E' and resid 704 through 713 removed outlier: 3.519A pdb=" N ASN E 709 " --> pdb=" O PHE E 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 753 Processing helix chain 'E' and resid 754 through 756 No H-bonds generated for 'chain 'E' and resid 754 through 756' Processing helix chain 'E' and resid 769 through 774 removed outlier: 3.540A pdb=" N SER E 773 " --> pdb=" O LYS E 770 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA E 774 " --> pdb=" O GLU E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 775 through 785 Processing helix chain 'E' and resid 793 through 797 Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.898A pdb=" N GLN E 802 " --> pdb=" O PRO E 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 114 Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.535A pdb=" N GLU F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'G' and resid 153 through 165 Processing helix chain 'G' and resid 170 through 179 Processing helix chain 'G' and resid 195 through 211 Processing helix chain 'G' and resid 221 through 231 removed outlier: 3.518A pdb=" N LEU G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 8 Processing helix chain 'a' and resid 75 through 79 removed outlier: 3.675A pdb=" N THR a 78 " --> pdb=" O PRO a 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 11 Processing helix chain 'c' and resid 18 through 23 removed outlier: 3.617A pdb=" N GLU c 22 " --> pdb=" O LYS c 18 " (cutoff:3.500A) Processing helix chain 'c' and resid 29 through 38 removed outlier: 3.842A pdb=" N THR c 33 " --> pdb=" O LEU c 29 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER c 35 " --> pdb=" O VAL c 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 13 removed outlier: 3.867A pdb=" N LYS d 8 " --> pdb=" O GLY d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 84 removed outlier: 3.839A pdb=" N LEU d 77 " --> pdb=" O PRO d 74 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS d 78 " --> pdb=" O ASP d 75 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN d 79 " --> pdb=" O MET d 76 " (cutoff:3.500A) Proline residue: d 81 - end of helix Processing helix chain 'e' and resid 16 through 28 Processing helix chain 'f' and resid 6 through 14 Processing helix chain 'g' and resid 9 through 13 removed outlier: 3.567A pdb=" N MET g 13 " --> pdb=" O LYS g 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 121 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA5, first strand: chain 'A' and resid 906 through 910 removed outlier: 4.036A pdb=" N VAL A 906 " --> pdb=" O MET A 899 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 894 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 5.518A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1185 through 1189 Processing sheet with id=AA8, first strand: chain 'A' and resid 1341 through 1346 Processing sheet with id=AA9, first strand: chain 'A' and resid 1502 through 1503 Processing sheet with id=AB1, first strand: chain 'A' and resid 1561 through 1563 removed outlier: 7.359A pdb=" N GLN A1552 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR G 88 " --> pdb=" O GLN A1552 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN A1554 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1606 through 1611 removed outlier: 8.079A pdb=" N ILE A1606 " --> pdb=" O SER A1634 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER A1634 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 191 removed outlier: 6.858A pdb=" N ARG C 130 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N MET C 203 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 132 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ASP C 230 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AB5, first strand: chain 'C' and resid 522 through 526 removed outlier: 7.042A pdb=" N CYS C 476 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 497 " --> pdb=" O CYS C 476 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N THR C 478 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ARG C 495 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AB7, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.965A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.965A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.902A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 663 through 666 removed outlier: 7.167A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.453A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 734 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP C 747 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE C 732 " --> pdb=" O ASP C 747 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 61 through 63 Processing sheet with id=AC4, first strand: chain 'D' and resid 69 through 74 removed outlier: 4.595A pdb=" N GLY D 85 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 103 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASN D 94 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN D 101 " --> pdb=" O ASN D 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 112 through 117 removed outlier: 6.619A pdb=" N ASP D 137 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG D 143 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 154 through 159 removed outlier: 3.569A pdb=" N SER D 171 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 196 through 201 removed outlier: 4.264A pdb=" N GLY D 212 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASP D 216 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 219 " --> pdb=" O TYR D 229 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR D 229 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP D 221 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU D 227 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 238 through 243 removed outlier: 3.592A pdb=" N ALA D 254 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 275 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.595A pdb=" N ALA D 302 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR D 310 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP D 313 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE D 319 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 330 through 335 Processing sheet with id=AD2, first strand: chain 'E' and resid 379 through 381 removed outlier: 6.412A pdb=" N ILE E 431 " --> pdb=" O MET E 604 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR E 606 " --> pdb=" O ILE E 431 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLY E 433 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 640 through 645 removed outlier: 6.595A pdb=" N GLU E 640 " --> pdb=" O ALA E 764 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR E 766 " --> pdb=" O GLU E 640 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS E 642 " --> pdb=" O THR E 766 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU E 768 " --> pdb=" O LYS E 642 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE E 644 " --> pdb=" O LEU E 768 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N CYS E 692 " --> pdb=" O VAL E 719 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 99 through 101 Processing sheet with id=AD5, first strand: chain 'f' and resid 54 through 55 removed outlier: 4.091A pdb=" N ASN f 46 " --> pdb=" O GLY f 60 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY f 60 " --> pdb=" O ASN f 46 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU f 61 " --> pdb=" O ARG c 111 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG c 111 " --> pdb=" O GLU f 61 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL c 109 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LYS c 51 " --> pdb=" O GLU c 72 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU c 72 " --> pdb=" O LYS c 51 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU c 53 " --> pdb=" O VAL c 70 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL c 70 " --> pdb=" O LEU c 53 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL c 66 " --> pdb=" O LYS c 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER c 97 " --> pdb=" O ASN c 69 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS c 71 " --> pdb=" O TYR c 95 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR c 95 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET c 73 " --> pdb=" O ASP c 93 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP c 93 " --> pdb=" O MET c 73 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR c 75 " --> pdb=" O ASN c 91 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN c 91 " --> pdb=" O THR c 75 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR a 28 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA a 42 " --> pdb=" O THR a 28 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR a 30 " --> pdb=" O LEU a 40 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU a 40 " --> pdb=" O THR a 30 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL a 32 " --> pdb=" O THR a 38 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR a 38 " --> pdb=" O VAL a 32 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU a 56 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS a 44 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN a 54 " --> pdb=" O LYS a 44 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR a 46 " --> pdb=" O PRO a 52 " (cutoff:3.500A) removed outlier: 14.058A pdb=" N LEU a 55 " --> pdb=" O GLY b 84 " (cutoff:3.500A) removed outlier: 11.934A pdb=" N GLY b 84 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N THR a 57 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG b 16 " --> pdb=" O GLU b 83 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR b 30 " --> pdb=" O ASP b 44 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP b 44 " --> pdb=" O THR b 30 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS b 32 " --> pdb=" O LEU b 42 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU b 42 " --> pdb=" O LYS b 32 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLY b 68 " --> pdb=" O ASP b 44 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP b 46 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL b 66 " --> pdb=" O ASP b 46 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE b 48 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LYS b 64 " --> pdb=" O PHE b 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU b 69 " --> pdb=" O LEU d 73 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS d 31 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASN d 45 " --> pdb=" O LYS d 31 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE d 33 " --> pdb=" O MET d 43 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET d 43 " --> pdb=" O ILE d 33 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA d 35 " --> pdb=" O CYS d 41 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS d 41 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU d 59 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR d 47 " --> pdb=" O GLN d 57 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLN d 57 " --> pdb=" O THR d 47 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR d 49 " --> pdb=" O VAL d 55 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL d 55 " --> pdb=" O THR d 49 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLN d 60 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS g 20 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU g 70 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER g 18 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA g 72 " --> pdb=" O LYS g 16 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS g 16 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN g 28 " --> pdb=" O CYS g 45 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N CYS g 45 " --> pdb=" O GLN g 28 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL g 41 " --> pdb=" O VAL g 61 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL g 61 " --> pdb=" O VAL g 41 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP g 43 " --> pdb=" O MET g 59 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N MET g 59 " --> pdb=" O ASP g 43 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N CYS g 45 " --> pdb=" O ILE g 57 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU e 86 " --> pdb=" O TRP e 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG e 42 " --> pdb=" O GLU e 63 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU e 63 " --> pdb=" O ARG e 42 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU e 44 " --> pdb=" O ALA e 61 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA e 61 " --> pdb=" O GLU e 44 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N CYS e 46 " --> pdb=" O ASP e 59 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP e 60 " --> pdb=" O GLY e 75 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY e 75 " --> pdb=" O ASP e 60 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU e 62 " --> pdb=" O GLN e 73 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLN e 73 " --> pdb=" O GLU e 62 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS f 22 " --> pdb=" O LEU f 70 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE f 72 " --> pdb=" O MET f 20 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET f 20 " --> pdb=" O ILE f 72 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N MET f 27 " --> pdb=" O LEU f 23 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU f 28 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU f 49 " --> pdb=" O GLU f 28 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS f 30 " --> pdb=" O THR f 47 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR f 47 " --> pdb=" O LYS f 30 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR f 32 " --> pdb=" O ALA f 45 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN f 43 " --> pdb=" O VAL f 34 " (cutoff:3.500A) 1373 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 28.84 Time building geometry restraints manager: 13.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 26515 1.13 - 1.30: 5119 1.30 - 1.47: 13169 1.47 - 1.64: 13636 1.64 - 1.81: 181 Bond restraints: 58620 Sorted by residual: bond pdb=" ND2 ASN A 857 " pdb="HD22 ASN A 857 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD1 PHE A 279 " pdb=" HD1 PHE A 279 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE ARG A1151 " pdb=" HE ARG A1151 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS A1683 " pdb=" H LYS A1683 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE2 TYR A 178 " pdb=" HE2 TYR A 178 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 58615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 97392 4.01 - 8.01: 7648 8.01 - 12.02: 52 12.02 - 16.03: 4 16.03 - 20.03: 4 Bond angle restraints: 105100 Sorted by residual: angle pdb=" C6 A 5 66 " pdb=" N6 A 5 66 " pdb=" H61 A 5 66 " ideal model delta sigma weight residual 120.00 99.97 20.03 3.00e+00 1.11e-01 4.46e+01 angle pdb=" CA ASP C 755 " pdb=" CB ASP C 755 " pdb=" CG ASP C 755 " ideal model delta sigma weight residual 112.60 118.85 -6.25 1.00e+00 1.00e+00 3.90e+01 angle pdb=" C6 A 5 30 " pdb=" N6 A 5 30 " pdb=" H61 A 5 30 " ideal model delta sigma weight residual 120.00 138.54 -18.54 3.00e+00 1.11e-01 3.82e+01 angle pdb=" N ILE A 182 " pdb=" CA ILE A 182 " pdb=" C ILE A 182 " ideal model delta sigma weight residual 113.53 107.86 5.67 9.80e-01 1.04e+00 3.34e+01 angle pdb=" C6 A 5 48 " pdb=" N6 A 5 48 " pdb=" H61 A 5 48 " ideal model delta sigma weight residual 120.00 136.21 -16.21 3.00e+00 1.11e-01 2.92e+01 ... (remaining 105095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 27210 35.68 - 71.36: 1068 71.36 - 107.04: 70 107.04 - 142.71: 5 142.71 - 178.39: 6 Dihedral angle restraints: 28359 sinusoidal: 14909 harmonic: 13450 Sorted by residual: dihedral pdb=" CA PHE A 166 " pdb=" C PHE A 166 " pdb=" N PRO A 167 " pdb=" CA PRO A 167 " ideal model delta harmonic sigma weight residual -180.00 -108.28 -71.72 0 5.00e+00 4.00e-02 2.06e+02 dihedral pdb=" C4' U 5 105 " pdb=" C3' U 5 105 " pdb=" C2' U 5 105 " pdb=" C1' U 5 105 " ideal model delta sinusoidal sigma weight residual -35.00 33.05 -68.05 1 8.00e+00 1.56e-02 9.39e+01 dihedral pdb=" C5' U 5 105 " pdb=" C4' U 5 105 " pdb=" C3' U 5 105 " pdb=" O3' U 5 105 " ideal model delta sinusoidal sigma weight residual 147.00 80.27 66.73 1 8.00e+00 1.56e-02 9.07e+01 ... (remaining 28356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4641 0.089 - 0.178: 479 0.178 - 0.267: 30 0.267 - 0.356: 7 0.356 - 0.444: 1 Chirality restraints: 5158 Sorted by residual: chirality pdb=" CA THR C 708 " pdb=" N THR C 708 " pdb=" C THR C 708 " pdb=" CB THR C 708 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" C3' U 5 105 " pdb=" C4' U 5 105 " pdb=" O3' U 5 105 " pdb=" C2' U 5 105 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C3' U 5 58 " pdb=" C4' U 5 58 " pdb=" O3' U 5 58 " pdb=" C2' U 5 58 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 5155 not shown) Planarity restraints: 9315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 A 5 26 " 0.057 2.00e-02 2.50e+03 1.24e-01 1.54e+02 pdb=" N6 A 5 26 " -0.214 2.00e-02 2.50e+03 pdb=" H61 A 5 26 " 0.079 2.00e-02 2.50e+03 pdb=" H62 A 5 26 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP C1101 " -0.147 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" C2 GTP C1101 " -0.010 2.00e-02 2.50e+03 pdb=" C4 GTP C1101 " 0.049 2.00e-02 2.50e+03 pdb=" C5 GTP C1101 " 0.035 2.00e-02 2.50e+03 pdb=" C6 GTP C1101 " -0.022 2.00e-02 2.50e+03 pdb=" C8 GTP C1101 " 0.039 2.00e-02 2.50e+03 pdb=" N1 GTP C1101 " -0.018 2.00e-02 2.50e+03 pdb=" N2 GTP C1101 " 0.030 2.00e-02 2.50e+03 pdb=" N3 GTP C1101 " 0.050 2.00e-02 2.50e+03 pdb=" N7 GTP C1101 " 0.058 2.00e-02 2.50e+03 pdb=" N9 GTP C1101 " 0.030 2.00e-02 2.50e+03 pdb=" O6 GTP C1101 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 724 " 0.092 2.00e-02 2.50e+03 3.79e-02 5.75e+01 pdb=" CG TRP C 724 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP C 724 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 724 " -0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP C 724 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP C 724 " -0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP C 724 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 724 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 724 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 724 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 TRP C 724 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP C 724 " 0.033 2.00e-02 2.50e+03 pdb=" HE3 TRP C 724 " -0.040 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 724 " -0.004 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 724 " 0.022 2.00e-02 2.50e+03 pdb=" HH2 TRP C 724 " 0.052 2.00e-02 2.50e+03 ... (remaining 9312 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.85: 548 1.85 - 2.54: 41259 2.54 - 3.22: 162228 3.22 - 3.91: 208659 3.91 - 4.60: 316202 Nonbonded interactions: 728896 Sorted by model distance: nonbonded pdb="HD21 ASN A1184 " pdb="HH11 ARG A1195 " model vdw 1.159 2.100 nonbonded pdb=" H3 U 5 12 " pdb=" H1 G 5 65 " model vdw 1.179 2.100 nonbonded pdb=" O LEU A 776 " pdb=" HG1 THR A 780 " model vdw 1.374 2.450 nonbonded pdb=" HE2 TYR A 318 " pdb=" HD2 HIS C 642 " model vdw 1.381 2.100 nonbonded pdb=" OE1 GLU A 343 " pdb="HH12 ARG E 301 " model vdw 1.383 2.450 ... (remaining 728891 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.390 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: 0.830 Extract box with map and model: 1.600 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 116.090 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.190 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 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 : 0.004 0.067 32068 Z= 0.287 Angle : 0.895 16.078 44164 Z= 0.537 Chirality : 0.054 0.444 5158 Planarity : 0.007 0.099 5420 Dihedral : 13.277 178.392 11620 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 0.08 % Allowed : 1.21 % Favored : 98.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.05 % 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: -2.86 (0.11), residues: 3998 helix: -2.43 (0.10), residues: 1432 sheet: -0.75 (0.19), residues: 704 loop : -1.80 (0.12), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP C 724 HIS 0.008 0.001 HIS A 333 PHE 0.035 0.002 PHE C 735 TYR 0.031 0.002 TYR C 847 ARG 0.014 0.001 ARG C 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 622 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 620 time to evaluate : 3.361 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: A 940 ILE cc_start: 0.8045 (mt) cc_final: 0.7794 (tt) REVERT: A 1237 MET cc_start: 0.7295 (mtm) cc_final: 0.7039 (ttp) REVERT: A 1278 VAL cc_start: 0.8229 (t) cc_final: 0.7914 (p) REVERT: A 1585 ILE cc_start: 0.7060 (mt) cc_final: 0.6503 (tp) REVERT: C 235 VAL cc_start: 0.7393 (t) cc_final: 0.7068 (t) REVERT: C 934 MET cc_start: 0.7875 (tmt) cc_final: 0.7311 (tmt) REVERT: E 314 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6600 (mmt-90) REVERT: G 165 LEU cc_start: 0.4515 (mt) cc_final: 0.3933 (mp) REVERT: d 76 MET cc_start: 0.6428 (pp-130) cc_final: 0.5459 (pp-130) outliers start: 2 outliers final: 0 residues processed: 622 average time/residue: 0.8844 time to fit residues: 826.2911 Evaluate side-chains 337 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 345 optimal weight: 5.9990 chunk 310 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 320 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN A 333 HIS A 483 GLN A 505 ASN A 704 ASN A 793 ASN ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN A1227 GLN A1293 ASN A1451 ASN A1552 GLN A1563 HIS C 201 ASN C 210 ASN C 743 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 32068 Z= 0.403 Angle : 0.698 9.452 44164 Z= 0.379 Chirality : 0.045 0.230 5158 Planarity : 0.006 0.098 5420 Dihedral : 15.088 174.051 5938 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 1.45 % Allowed : 6.69 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.29 (0.13), residues: 3998 helix: -0.25 (0.13), residues: 1465 sheet: -0.78 (0.18), residues: 731 loop : -1.31 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 293 HIS 0.011 0.002 HIS C 280 PHE 0.039 0.002 PHE A 166 TYR 0.018 0.002 TYR A 431 ARG 0.009 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 3.367 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: A 560 SER cc_start: 0.8771 (m) cc_final: 0.8358 (p) REVERT: A 638 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8783 (tp) REVERT: A 1067 MET cc_start: 0.7130 (ppp) cc_final: 0.6743 (ppp) REVERT: A 1364 LEU cc_start: 0.7386 (mt) cc_final: 0.6410 (pp) REVERT: A 1562 MET cc_start: 0.4457 (mtt) cc_final: 0.4043 (mtm) REVERT: A 1585 ILE cc_start: 0.7159 (mt) cc_final: 0.6666 (tp) REVERT: B 52 MET cc_start: 0.6238 (ttt) cc_final: 0.5596 (ttp) REVERT: C 822 MET cc_start: 0.7391 (mmm) cc_final: 0.6778 (mmm) REVERT: E 298 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6468 (tt) REVERT: E 314 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7042 (mmt-90) REVERT: G 106 ASN cc_start: 0.5587 (m-40) cc_final: 0.5353 (m-40) REVERT: d 58 LEU cc_start: 0.6158 (mt) cc_final: 0.5871 (mt) outliers start: 36 outliers final: 23 residues processed: 346 average time/residue: 0.8008 time to fit residues: 429.5441 Evaluate side-chains 279 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 717 TRP Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1423 PHE Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 287 ASN Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain G residue 200 ASP Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 37 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 chunk 309 optimal weight: 7.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 372 optimal weight: 20.0000 chunk 401 optimal weight: 40.0000 chunk 331 optimal weight: 10.0000 chunk 368 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1184 ASN ** A1332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 GLN ** A1469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32068 Z= 0.288 Angle : 0.602 9.681 44164 Z= 0.324 Chirality : 0.043 0.203 5158 Planarity : 0.005 0.091 5420 Dihedral : 14.935 175.822 5938 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.49 % Allowed : 8.18 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.77 (0.13), residues: 3998 helix: 0.39 (0.13), residues: 1495 sheet: -0.74 (0.18), residues: 738 loop : -1.12 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1375 HIS 0.011 0.002 HIS C 437 PHE 0.022 0.002 PHE C 339 TYR 0.030 0.002 TYR A1660 ARG 0.015 0.001 ARG A 781 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 3.416 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: A 95 MET cc_start: 0.6616 (tmm) cc_final: 0.6053 (tmm) REVERT: A 97 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.7145 (t70) REVERT: A 1009 MET cc_start: 0.8591 (tmm) cc_final: 0.8349 (tmm) REVERT: A 1067 MET cc_start: 0.7365 (ppp) cc_final: 0.7111 (ppp) REVERT: A 1104 ASP cc_start: 0.8551 (m-30) cc_final: 0.7547 (t70) REVERT: A 1140 MET cc_start: 0.9263 (ttt) cc_final: 0.8960 (ttt) REVERT: A 1236 SER cc_start: 0.8514 (m) cc_final: 0.8058 (p) REVERT: A 1585 ILE cc_start: 0.7316 (mt) cc_final: 0.6885 (tp) REVERT: C 433 MET cc_start: 0.7639 (ttp) cc_final: 0.7387 (ttm) REVERT: C 560 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7861 (t) REVERT: C 934 MET cc_start: 0.8361 (tmt) cc_final: 0.7716 (tmt) REVERT: E 314 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7026 (mmt-90) REVERT: d 82 MET cc_start: 0.7743 (ptp) cc_final: 0.7095 (mpp) outliers start: 37 outliers final: 25 residues processed: 292 average time/residue: 0.7295 time to fit residues: 351.0478 Evaluate side-chains 262 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1261 ASN Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1423 PHE Chi-restraints excluded: chain A residue 1707 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 476 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain E residue 248 HIS Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 287 ASN Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain G residue 200 ASP Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain d residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 367 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 373 optimal weight: 9.9990 chunk 395 optimal weight: 0.5980 chunk 195 optimal weight: 0.1980 chunk 353 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32068 Z= 0.161 Angle : 0.506 6.701 44164 Z= 0.270 Chirality : 0.041 0.167 5158 Planarity : 0.004 0.088 5420 Dihedral : 14.793 177.337 5938 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.25 % Allowed : 8.78 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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 (0.13), residues: 3998 helix: 0.96 (0.14), residues: 1490 sheet: -0.62 (0.19), residues: 722 loop : -0.96 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 531 HIS 0.011 0.001 HIS A1096 PHE 0.024 0.001 PHE A 482 TYR 0.014 0.001 TYR A 431 ARG 0.006 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 3.516 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: A 97 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.6955 (t70) REVERT: A 1009 MET cc_start: 0.8603 (tmm) cc_final: 0.8327 (tmm) REVERT: A 1022 MET cc_start: 0.7705 (mtp) cc_final: 0.7214 (tpt) REVERT: A 1067 MET cc_start: 0.7337 (ppp) cc_final: 0.7107 (ppp) REVERT: A 1104 ASP cc_start: 0.8523 (m-30) cc_final: 0.7482 (t70) REVERT: A 1140 MET cc_start: 0.9209 (ttt) cc_final: 0.8940 (ttt) REVERT: A 1236 SER cc_start: 0.8489 (m) cc_final: 0.8012 (p) REVERT: A 1585 ILE cc_start: 0.7315 (mt) cc_final: 0.6839 (tp) REVERT: A 1652 MET cc_start: 0.2335 (mtt) cc_final: 0.1968 (mtt) REVERT: C 433 MET cc_start: 0.7571 (ttp) cc_final: 0.7367 (ttm) REVERT: C 560 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7848 (t) REVERT: C 822 MET cc_start: 0.7303 (mmm) cc_final: 0.6990 (mmm) REVERT: E 284 ILE cc_start: 0.7327 (pt) cc_final: 0.6728 (tp) REVERT: E 314 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7003 (mmt-90) REVERT: d 82 MET cc_start: 0.7600 (ptp) cc_final: 0.7037 (mpp) outliers start: 31 outliers final: 24 residues processed: 276 average time/residue: 0.6996 time to fit residues: 318.4528 Evaluate side-chains 265 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain A residue 1261 ASN Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1707 LEU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 476 CYS Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 557 GLN Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain E residue 248 HIS Chi-restraints excluded: chain E residue 287 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 200 ASP Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain d residue 18 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 329 optimal weight: 7.9990 chunk 224 optimal weight: 0.0980 chunk 5 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 337 optimal weight: 0.0870 chunk 273 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 354 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 overall best weight: 4.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 GLN ** A1469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 32068 Z= 0.337 Angle : 0.613 9.035 44164 Z= 0.334 Chirality : 0.043 0.210 5158 Planarity : 0.005 0.091 5420 Dihedral : 14.838 179.104 5938 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.01 % Allowed : 8.82 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.64 (0.13), residues: 3998 helix: 0.78 (0.14), residues: 1481 sheet: -0.85 (0.19), residues: 718 loop : -1.23 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 293 HIS 0.010 0.002 HIS A 610 PHE 0.027 0.002 PHE A 166 TYR 0.021 0.002 TYR A 431 ARG 0.010 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 3.533 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: A 95 MET cc_start: 0.6919 (tmm) cc_final: 0.6355 (tmm) REVERT: A 99 VAL cc_start: 0.8575 (t) cc_final: 0.8320 (t) REVERT: A 108 MET cc_start: 0.8674 (mmp) cc_final: 0.8410 (mmp) REVERT: A 640 PHE cc_start: 0.8528 (t80) cc_final: 0.8127 (t80) REVERT: A 1009 MET cc_start: 0.8605 (tmm) cc_final: 0.8260 (tmm) REVERT: A 1022 MET cc_start: 0.7861 (mtp) cc_final: 0.7474 (mmm) REVERT: A 1128 TYR cc_start: 0.8085 (t80) cc_final: 0.7544 (t80) REVERT: A 1140 MET cc_start: 0.9301 (ttt) cc_final: 0.9041 (ttt) REVERT: A 1143 MET cc_start: 0.6196 (mmt) cc_final: 0.5812 (mmt) REVERT: A 1189 MET cc_start: 0.7365 (tpp) cc_final: 0.7132 (tpp) REVERT: A 1236 SER cc_start: 0.8603 (m) cc_final: 0.8128 (p) REVERT: A 1652 MET cc_start: 0.2726 (mtt) cc_final: 0.2329 (mmt) REVERT: A 1719 PHE cc_start: 0.1810 (p90) cc_final: 0.1279 (p90) REVERT: A 1730 MET cc_start: 0.7748 (mmp) cc_final: 0.7513 (mmt) REVERT: C 560 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.7955 (t) REVERT: C 822 MET cc_start: 0.7343 (mmm) cc_final: 0.6994 (mmm) REVERT: C 886 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8183 (t0) REVERT: E 284 ILE cc_start: 0.7690 (pt) cc_final: 0.7140 (tp) REVERT: E 298 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6768 (tt) REVERT: E 314 ARG cc_start: 0.7849 (mtt180) cc_final: 0.6841 (mmt-90) REVERT: d 82 MET cc_start: 0.7925 (ptp) cc_final: 0.7105 (mpp) outliers start: 50 outliers final: 37 residues processed: 269 average time/residue: 0.6757 time to fit residues: 303.4420 Evaluate side-chains 248 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain A residue 1261 ASN Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1423 PHE Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1707 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 886 ASP Chi-restraints excluded: chain E residue 248 HIS Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 287 ASN Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain G residue 200 ASP Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain d residue 18 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 133 optimal weight: 10.0000 chunk 356 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 232 optimal weight: 0.0020 chunk 97 optimal weight: 6.9990 chunk 395 optimal weight: 9.9990 chunk 328 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 32068 Z= 0.158 Angle : 0.507 9.601 44164 Z= 0.270 Chirality : 0.041 0.153 5158 Planarity : 0.004 0.087 5420 Dihedral : 14.687 173.877 5938 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.45 % Allowed : 9.63 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.15 (0.14), residues: 3998 helix: 1.31 (0.14), residues: 1476 sheet: -0.74 (0.19), residues: 687 loop : -0.99 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 531 HIS 0.005 0.001 HIS C 642 PHE 0.026 0.001 PHE A 166 TYR 0.014 0.001 TYR C 314 ARG 0.006 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 3.466 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: A 95 MET cc_start: 0.7038 (tmm) cc_final: 0.6361 (tmm) REVERT: A 108 MET cc_start: 0.8746 (mmp) cc_final: 0.8345 (mmp) REVERT: A 147 MET cc_start: 0.9564 (mmp) cc_final: 0.9122 (mmp) REVERT: A 434 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7705 (m-70) REVERT: A 638 LEU cc_start: 0.8846 (mt) cc_final: 0.8507 (tp) REVERT: A 982 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7075 (tp30) REVERT: A 1009 MET cc_start: 0.8623 (tmm) cc_final: 0.8283 (tmm) REVERT: A 1022 MET cc_start: 0.7809 (mtp) cc_final: 0.7243 (tpt) REVERT: A 1128 TYR cc_start: 0.8152 (t80) cc_final: 0.7618 (t80) REVERT: A 1140 MET cc_start: 0.9346 (ttt) cc_final: 0.9044 (ttt) REVERT: A 1143 MET cc_start: 0.6113 (mmt) cc_final: 0.5546 (mmt) REVERT: A 1236 SER cc_start: 0.8549 (m) cc_final: 0.8068 (p) REVERT: A 1474 MET cc_start: 0.7424 (tpp) cc_final: 0.6974 (ttp) REVERT: A 1585 ILE cc_start: 0.7335 (mt) cc_final: 0.6743 (tp) REVERT: A 1652 MET cc_start: 0.2681 (mtt) cc_final: 0.2255 (mmt) REVERT: A 1719 PHE cc_start: 0.1534 (p90) cc_final: 0.1097 (p90) REVERT: C 560 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7880 (t) REVERT: C 822 MET cc_start: 0.7436 (mmm) cc_final: 0.7039 (mmm) REVERT: E 284 ILE cc_start: 0.7546 (pt) cc_final: 0.6949 (tp) REVERT: E 298 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6704 (tt) REVERT: E 314 ARG cc_start: 0.7849 (mtt180) cc_final: 0.6934 (mmt-90) REVERT: d 59 GLU cc_start: 0.5462 (OUTLIER) cc_final: 0.5242 (pp20) REVERT: d 82 MET cc_start: 0.7950 (ptp) cc_final: 0.7115 (mpp) outliers start: 36 outliers final: 26 residues processed: 245 average time/residue: 0.6626 time to fit residues: 273.2963 Evaluate side-chains 240 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1261 ASN Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1442 PHE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1707 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 557 GLN Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain E residue 248 HIS Chi-restraints excluded: chain E residue 287 ASN Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain G residue 200 ASP Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 59 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 381 optimal weight: 9.9990 chunk 44 optimal weight: 0.1980 chunk 225 optimal weight: 3.9990 chunk 288 optimal weight: 30.0000 chunk 223 optimal weight: 0.9990 chunk 333 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 394 optimal weight: 30.0000 chunk 246 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 361 HIS A 723 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.6802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32068 Z= 0.249 Angle : 0.541 7.020 44164 Z= 0.291 Chirality : 0.042 0.156 5158 Planarity : 0.004 0.087 5420 Dihedral : 14.643 173.860 5938 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.69 % Allowed : 9.75 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.26 (0.14), residues: 3998 helix: 1.28 (0.14), residues: 1478 sheet: -0.83 (0.19), residues: 684 loop : -1.10 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.006 0.001 HIS A 610 PHE 0.029 0.002 PHE A 166 TYR 0.017 0.002 TYR A 431 ARG 0.007 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 3.469 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: A 95 MET cc_start: 0.7309 (tmm) cc_final: 0.6812 (tmm) REVERT: A 108 MET cc_start: 0.8885 (mmp) cc_final: 0.8530 (mmp) REVERT: A 434 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7630 (m-70) REVERT: A 759 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6260 (pp20) REVERT: A 1009 MET cc_start: 0.8585 (tmm) cc_final: 0.8276 (tmm) REVERT: A 1022 MET cc_start: 0.7909 (mtp) cc_final: 0.7468 (mmm) REVERT: A 1053 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6306 (tt) REVERT: A 1140 MET cc_start: 0.9326 (ttt) cc_final: 0.9033 (ttt) REVERT: A 1143 MET cc_start: 0.6077 (mmt) cc_final: 0.5554 (mmt) REVERT: A 1189 MET cc_start: 0.7333 (tpp) cc_final: 0.7028 (tpp) REVERT: A 1236 SER cc_start: 0.8674 (m) cc_final: 0.8219 (p) REVERT: A 1585 ILE cc_start: 0.7417 (mt) cc_final: 0.6857 (tp) REVERT: A 1652 MET cc_start: 0.2832 (mtt) cc_final: 0.2306 (mmt) REVERT: A 1719 PHE cc_start: 0.1542 (p90) cc_final: 0.1085 (p90) REVERT: C 560 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7866 (t) REVERT: C 822 MET cc_start: 0.7434 (mmm) cc_final: 0.7056 (mmm) REVERT: C 886 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8117 (t0) REVERT: E 284 ILE cc_start: 0.7691 (pt) cc_final: 0.7118 (tp) REVERT: E 298 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6696 (tt) REVERT: E 314 ARG cc_start: 0.7796 (mtt180) cc_final: 0.6987 (mmt180) REVERT: d 73 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8234 (mt) REVERT: d 82 MET cc_start: 0.8053 (ptp) cc_final: 0.7481 (mpp) outliers start: 42 outliers final: 31 residues processed: 248 average time/residue: 0.6968 time to fit residues: 292.2820 Evaluate side-chains 245 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1261 ASN Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1442 PHE Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1707 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 886 ASP Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain E residue 248 HIS Chi-restraints excluded: chain E residue 287 ASN Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain G residue 200 ASP Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 243 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 268 optimal weight: 30.0000 chunk 194 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 ASN ** d 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32068 Z= 0.226 Angle : 0.529 9.969 44164 Z= 0.284 Chirality : 0.041 0.153 5158 Planarity : 0.004 0.085 5420 Dihedral : 14.621 174.189 5938 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.73 % Allowed : 10.03 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.24 (0.14), residues: 3998 helix: 1.37 (0.14), residues: 1480 sheet: -0.86 (0.19), residues: 687 loop : -1.14 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.006 0.001 HIS C 642 PHE 0.034 0.001 PHE A 640 TYR 0.014 0.001 TYR A 431 ARG 0.007 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 3.396 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: A 61 MET cc_start: 0.5544 (OUTLIER) cc_final: 0.5137 (mtp) REVERT: A 95 MET cc_start: 0.7270 (tmm) cc_final: 0.6817 (tmm) REVERT: A 99 VAL cc_start: 0.8619 (t) cc_final: 0.8360 (t) REVERT: A 108 MET cc_start: 0.8839 (mmp) cc_final: 0.8573 (mmp) REVERT: A 434 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7578 (m-70) REVERT: A 759 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6036 (pp20) REVERT: A 1009 MET cc_start: 0.8637 (tmm) cc_final: 0.8336 (tmm) REVERT: A 1022 MET cc_start: 0.7931 (mtp) cc_final: 0.7440 (mmm) REVERT: A 1053 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6259 (tt) REVERT: A 1140 MET cc_start: 0.9306 (ttt) cc_final: 0.9033 (ttt) REVERT: A 1474 MET cc_start: 0.7719 (tpp) cc_final: 0.7229 (ttp) REVERT: A 1585 ILE cc_start: 0.7566 (mt) cc_final: 0.7007 (tp) REVERT: A 1652 MET cc_start: 0.2989 (mtt) cc_final: 0.2413 (mmt) REVERT: A 1719 PHE cc_start: 0.1419 (p90) cc_final: 0.0967 (p90) REVERT: C 560 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7878 (t) REVERT: C 822 MET cc_start: 0.7374 (mmm) cc_final: 0.6977 (mmm) REVERT: E 284 ILE cc_start: 0.7799 (pt) cc_final: 0.7250 (tp) REVERT: E 298 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6678 (tt) REVERT: E 314 ARG cc_start: 0.7986 (mtt180) cc_final: 0.7059 (mmt-90) REVERT: d 73 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8472 (mt) REVERT: d 82 MET cc_start: 0.8040 (ptp) cc_final: 0.7555 (mpp) outliers start: 43 outliers final: 33 residues processed: 251 average time/residue: 0.6685 time to fit residues: 282.9537 Evaluate side-chains 245 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1261 ASN Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1442 PHE Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1707 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 476 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain E residue 248 HIS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 358 optimal weight: 20.0000 chunk 377 optimal weight: 40.0000 chunk 344 optimal weight: 9.9990 chunk 367 optimal weight: 30.0000 chunk 221 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 288 optimal weight: 40.0000 chunk 112 optimal weight: 8.9990 chunk 331 optimal weight: 8.9990 chunk 347 optimal weight: 9.9990 chunk 366 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 HIS A 244 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS A1293 ASN ** A1332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.8227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.151 32068 Z= 0.500 Angle : 0.757 8.099 44164 Z= 0.413 Chirality : 0.048 0.195 5158 Planarity : 0.006 0.088 5420 Dihedral : 15.097 174.101 5938 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 1.77 % Allowed : 10.64 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.03 % 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: -1.54 (0.13), residues: 3998 helix: 0.10 (0.13), residues: 1466 sheet: -1.26 (0.19), residues: 675 loop : -1.83 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 293 HIS 0.015 0.003 HIS C 642 PHE 0.030 0.003 PHE A 572 TYR 0.032 0.003 TYR A 431 ARG 0.014 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 3.424 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 784 LEU cc_start: 0.8047 (mm) cc_final: 0.7763 (tt) REVERT: A 1009 MET cc_start: 0.8652 (tmm) cc_final: 0.8297 (tmm) REVERT: A 1022 MET cc_start: 0.8123 (mtp) cc_final: 0.7205 (mmm) REVERT: A 1053 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6261 (tt) REVERT: A 1143 MET cc_start: 0.6183 (mmt) cc_final: 0.5700 (mmt) REVERT: A 1351 THR cc_start: 0.6833 (p) cc_final: 0.6478 (t) REVERT: A 1461 ASP cc_start: 0.7132 (m-30) cc_final: 0.6587 (p0) REVERT: A 1474 MET cc_start: 0.7972 (tpp) cc_final: 0.7660 (ttp) REVERT: A 1537 TRP cc_start: 0.7793 (t-100) cc_final: 0.7230 (t-100) REVERT: A 1719 PHE cc_start: 0.1683 (p90) cc_final: 0.1256 (p90) REVERT: C 716 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6540 (mt-10) REVERT: C 822 MET cc_start: 0.7413 (mmm) cc_final: 0.6965 (mmm) REVERT: E 284 ILE cc_start: 0.7835 (pt) cc_final: 0.7364 (tp) REVERT: E 298 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6757 (tt) REVERT: E 314 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7269 (mmp-170) REVERT: d 82 MET cc_start: 0.8166 (ptp) cc_final: 0.7771 (mpp) outliers start: 44 outliers final: 30 residues processed: 240 average time/residue: 0.6741 time to fit residues: 273.5070 Evaluate side-chains 227 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1261 ASN Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1423 PHE Chi-restraints excluded: chain A residue 1442 PHE Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1707 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 ASN Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain E residue 287 ASN Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain d residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 241 optimal weight: 3.9990 chunk 388 optimal weight: 0.5980 chunk 237 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 chunk 270 optimal weight: 10.0000 chunk 407 optimal weight: 50.0000 chunk 375 optimal weight: 50.0000 chunk 324 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.8160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32068 Z= 0.169 Angle : 0.548 8.927 44164 Z= 0.293 Chirality : 0.042 0.159 5158 Planarity : 0.004 0.085 5420 Dihedral : 14.785 175.507 5938 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.25 % Allowed : 11.36 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.03 % 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: -0.72 (0.13), residues: 3998 helix: 1.04 (0.14), residues: 1460 sheet: -1.15 (0.19), residues: 654 loop : -1.45 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 406 HIS 0.007 0.001 HIS C 890 PHE 0.029 0.001 PHE A 640 TYR 0.021 0.001 TYR C 314 ARG 0.004 0.000 ARG A 470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7996 Ramachandran restraints generated. 3998 Oldfield, 0 Emsley, 3998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 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 LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 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 ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue LYS 333 is missing expected H atoms. Skipping. Residue LEU 340 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue LYS 360 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue MET 365 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue ILE 372 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue SER 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue THR 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue SER 392 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 398 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue ILE 424 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue SER 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LEU 449 is missing expected H atoms. Skipping. Residue LEU 450 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue THR 454 is missing expected H atoms. Skipping. Residue THR 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 470 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue LEU 474 is missing expected H atoms. Skipping. Residue THR 477 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Residue ILE 484 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue ILE 489 is missing expected H atoms. Skipping. Residue LYS 490 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 497 is missing expected H atoms. Skipping. Residue THR 499 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 506 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue MET 517 is missing expected H atoms. Skipping. Residue ILE 521 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue ILE 523 is missing expected H atoms. Skipping. Residue THR 525 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue VAL 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue TYR 537 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue VAL 539 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue SER 541 is missing expected H atoms. Skipping. Residue THR 544 is missing expected H atoms. Skipping. Residue TYR 545 is missing expected H atoms. Skipping. Residue VAL 546 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue MET 554 is missing expected H atoms. Skipping. Residue ILE 555 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue VAL 563 is missing expected H atoms. Skipping. Residue LYS 565 is missing expected H atoms. Skipping. Residue ILE 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue MET 570 is missing expected H atoms. Skipping. Residue VAL 572 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue LYS 587 is missing expected H atoms. Skipping. Residue MET 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue SER 594 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue TYR 599 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue MET 604 is missing expected H atoms. Skipping. Residue THR 606 is missing expected H atoms. Skipping. Residue THR 608 is missing expected H atoms. Skipping. Residue MET 609 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue LEU 616 is missing expected H atoms. Skipping. Residue SER 619 is missing expected H atoms. Skipping. Residue TYR 620 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue VAL 626 is missing expected H atoms. Skipping. Residue VAL 627 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue ILE 629 is missing expected H atoms. Skipping. Residue VAL 639 is missing expected H atoms. Skipping. Residue LYS 642 is missing expected H atoms. Skipping. Residue VAL 643 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue MET 646 is missing expected H atoms. Skipping. Residue SER 647 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue LYS 653 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 656 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue LEU 659 is missing expected H atoms. Skipping. Residue ILE 667 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 669 is missing expected H atoms. Skipping. Residue VAL 671 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue VAL 679 is missing expected H atoms. Skipping. Residue LEU 680 is missing expected H atoms. Skipping. Residue LYS 682 is missing expected H atoms. Skipping. Residue SER 683 is missing expected H atoms. Skipping. Residue LEU 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue MET 687 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue LYS 711 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue ILE 717 is missing expected H atoms. Skipping. Residue LEU 718 is missing expected H atoms. Skipping. Residue VAL 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 723 is missing expected H atoms. Skipping. Residue ILE 728 is missing expected H atoms. Skipping. Residue ILE 730 is missing expected H atoms. Skipping. Residue VAL 733 is missing expected H atoms. Skipping. Residue SER 734 is missing expected H atoms. Skipping. Residue MET 735 is missing expected H atoms. Skipping. Residue VAL 736 is missing expected H atoms. Skipping. Residue VAL 737 is missing expected H atoms. Skipping. Residue TYR 739 is missing expected H atoms. Skipping. Residue MET 741 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue TYR 748 is missing expected H atoms. Skipping. Residue ILE 749 is missing expected H atoms. Skipping. Residue ILE 752 is missing expected H atoms. Skipping. Residue THR 755 is missing expected H atoms. Skipping. Residue LYS 760 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue ILE 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue LEU 768 is missing expected H atoms. Skipping. Residue THR 769 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue SER 773 is missing expected H atoms. Skipping. Residue VAL 775 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue LEU 779 is missing expected H atoms. Skipping. Residue LYS 780 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue VAL 788 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Residue SER 790 is missing expected H atoms. Skipping. Residue LEU 795 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 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 LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 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 LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 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 VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 3.354 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: A 140 TYR cc_start: 0.8261 (t80) cc_final: 0.7957 (t80) REVERT: A 147 MET cc_start: 0.9446 (mmp) cc_final: 0.8879 (mmp) REVERT: A 759 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6081 (pp20) REVERT: A 784 LEU cc_start: 0.7976 (mm) cc_final: 0.7756 (tt) REVERT: A 1009 MET cc_start: 0.8450 (tmm) cc_final: 0.8176 (tmm) REVERT: A 1022 MET cc_start: 0.7973 (mtp) cc_final: 0.7047 (mmm) REVERT: A 1053 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6323 (tt) REVERT: A 1351 THR cc_start: 0.6676 (p) cc_final: 0.6332 (t) REVERT: A 1474 MET cc_start: 0.7860 (tpp) cc_final: 0.7535 (ttp) REVERT: A 1585 ILE cc_start: 0.7678 (mt) cc_final: 0.7074 (tp) REVERT: A 1719 PHE cc_start: 0.1501 (p90) cc_final: 0.1064 (p90) REVERT: A 1730 MET cc_start: 0.7700 (mmp) cc_final: 0.7476 (mmt) REVERT: C 822 MET cc_start: 0.7403 (mmm) cc_final: 0.6998 (mmm) REVERT: E 284 ILE cc_start: 0.7718 (pt) cc_final: 0.7245 (tp) REVERT: E 298 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6574 (tt) REVERT: E 314 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7231 (mmp-170) REVERT: d 82 MET cc_start: 0.7962 (ptp) cc_final: 0.7675 (mpp) outliers start: 31 outliers final: 25 residues processed: 235 average time/residue: 0.6980 time to fit residues: 277.2197 Evaluate side-chains 234 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1261 ASN Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1707 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain E residue 248 HIS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain d residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 257 optimal weight: 4.9990 chunk 345 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 299 optimal weight: 30.0000 chunk 47 optimal weight: 0.0770 chunk 90 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 333 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.118989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.095299 restraints weight = 332084.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.094525 restraints weight = 262209.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.094409 restraints weight = 203121.675| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.8363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32068 Z= 0.264 Angle : 0.560 8.325 44164 Z= 0.300 Chirality : 0.042 0.166 5158 Planarity : 0.004 0.087 5420 Dihedral : 14.716 174.659 5938 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.29 % Allowed : 11.44 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.03 % 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: -0.66 (0.14), residues: 3998 helix: 1.13 (0.14), residues: 1468 sheet: -1.19 (0.19), residues: 649 loop : -1.43 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 293 HIS 0.006 0.001 HIS C 642 PHE 0.027 0.002 PHE A 166 TYR 0.017 0.002 TYR A 431 ARG 0.006 0.001 ARG A 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8421.51 seconds wall clock time: 146 minutes 50.72 seconds (8810.72 seconds total)