Starting phenix.real_space_refine on Thu Dec 26 03:52:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jas_36133/12_2024/8jas_36133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jas_36133/12_2024/8jas_36133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jas_36133/12_2024/8jas_36133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jas_36133/12_2024/8jas_36133.map" model { file = "/net/cci-nas-00/data/ceres_data/8jas_36133/12_2024/8jas_36133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jas_36133/12_2024/8jas_36133.cif" } resolution = 3.54 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4754 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 233 5.16 5 C 25086 2.51 5 N 6680 2.21 5 O 7280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 39287 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4622 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 6, 'TRANS': 565} Chain: "E" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1726 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 1 Chain: "S" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4622 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 6, 'TRANS': 565} Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "G" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 782 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5223 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 618} Chain breaks: 1 Chain: "R" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 661 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "J" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4619 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 565} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "L" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1161 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "M" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "N" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 718 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 1 Chain: "Q" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 722 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 1 Chain: "V" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 666 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5223 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 618} Chain breaks: 1 Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 410 SG CYS A 54 79.387 76.055 82.159 1.00 48.45 S ATOM 8298 SG CYS B 54 82.965 74.924 83.333 1.00 22.68 S ATOM 19558 SG CYS R 53 91.244 85.385 170.851 1.00 95.08 S ATOM 19581 SG CYS R 56 91.965 81.756 169.966 1.00 99.71 S ATOM 19665 SG CYS R 68 92.364 82.919 173.544 1.00104.08 S ATOM 19472 SG CYS R 42 91.989 91.961 174.593 1.00 72.41 S ATOM 19491 SG CYS R 45 88.723 90.255 173.625 1.00 76.06 S ATOM 19786 SG CYS R 83 91.695 89.936 171.305 1.00 90.39 S ATOM 19715 SG CYS R 75 100.483 98.979 178.115 1.00 94.65 S ATOM 19882 SG CYS R 94 98.738 99.483 175.506 1.00 95.50 S ATOM 20411 SG CYS J 54 78.627 127.958 172.425 1.00 31.80 S ATOM 25030 SG CYS K 54 80.731 130.845 170.692 1.00 82.03 S ATOM 33576 SG CYS V 53 74.957 120.453 83.550 1.00 86.52 S ATOM 33599 SG CYS V 56 74.273 124.182 83.750 1.00 93.30 S ATOM 33683 SG CYS V 68 74.867 122.478 80.293 1.00 91.40 S ATOM 33490 SG CYS V 42 77.362 114.544 79.060 1.00 74.59 S ATOM 33509 SG CYS V 45 74.090 114.967 80.805 1.00 75.04 S ATOM 33804 SG CYS V 83 77.046 116.472 82.479 1.00 78.48 S ATOM 33733 SG CYS V 75 87.754 111.147 73.596 1.00 88.96 S ATOM 33900 SG CYS V 94 86.186 110.386 76.387 1.00 78.50 S Time building chain proxies: 21.80, per 1000 atoms: 0.55 Number of scatterers: 39287 At special positions: 0 Unit cell: (151.7, 195.16, 248.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 233 16.00 O 7280 8.00 N 6680 7.00 C 25086 6.00 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: 10.00 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN A 601 " - pdb=" SG CYS B 54 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 54 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 89 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS J 89 " pdb="ZN ZN K 601 " - pdb=" SG CYS J 54 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 54 " pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 53 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb=" ZN V 200 " pdb="ZN ZN V 200 " - pdb=" ND1 HIS V 82 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 53 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 56 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 68 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 80 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 83 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 42 " pdb=" ZN V 202 " pdb="ZN ZN V 202 " - pdb=" SG CYS V 94 " pdb="ZN ZN V 202 " - pdb=" SG CYS V 75 " pdb="ZN ZN V 202 " - pdb=" ND1 HIS V 77 " Number of angles added : 16 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9266 Finding SS restraints... Secondary structure from input PDB file: 233 helices and 19 sheets defined 71.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.686A pdb=" N ILE A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 33' Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.786A pdb=" N PHE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.611A pdb=" N GLU A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.914A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 72 No H-bonds generated for 'chain 'A' and resid 71 through 72' Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.782A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 85 " --> pdb=" O HIS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 133 Processing helix chain 'A' and resid 135 through 152 removed outlier: 3.848A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 176 removed outlier: 3.569A pdb=" N VAL A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.590A pdb=" N HIS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.678A pdb=" N LEU A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 Processing helix chain 'A' and resid 241 through 258 removed outlier: 3.688A pdb=" N VAL A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 280 removed outlier: 3.972A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 303 through 309 removed outlier: 4.515A pdb=" N ALA A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.914A pdb=" N TYR A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.705A pdb=" N ALA A 360 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.814A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.738A pdb=" N GLU A 399 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 443 removed outlier: 3.788A pdb=" N SER A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 463 removed outlier: 4.761A pdb=" N GLU A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 484 removed outlier: 3.505A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.272A pdb=" N GLY A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.823A pdb=" N THR E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 53 through 78 removed outlier: 3.581A pdb=" N LEU E 57 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.909A pdb=" N ARG E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 152 removed outlier: 3.934A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET E 151 " --> pdb=" O TRP E 147 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 168 removed outlier: 4.238A pdb=" N LEU E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE E 160 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 186 removed outlier: 3.759A pdb=" N VAL E 184 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 185 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 Processing helix chain 'E' and resid 200 through 220 removed outlier: 4.909A pdb=" N SER E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Proline residue: E 210 - end of helix removed outlier: 3.897A pdb=" N THR E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS E 220 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 36 removed outlier: 3.510A pdb=" N LEU C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.852A pdb=" N ALA D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 84 Processing helix chain 'D' and resid 100 through 110 Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.715A pdb=" N ASP B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 33 removed outlier: 4.071A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.918A pdb=" N PHE B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 4.254A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 71 removed outlier: 3.663A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.886A pdb=" N HIS B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 139 through 152 removed outlier: 3.600A pdb=" N SER B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 176 Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.689A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 234 Processing helix chain 'B' and resid 241 through 259 removed outlier: 3.597A pdb=" N VAL B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.522A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.619A pdb=" N PHE B 322 " --> pdb=" O ARG B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 350 through 368 removed outlier: 3.547A pdb=" N ALA B 360 " --> pdb=" O HIS B 356 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 3.517A pdb=" N ALA B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 421 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.649A pdb=" N GLU B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 487 through 507 removed outlier: 3.630A pdb=" N GLU B 492 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 527 removed outlier: 4.275A pdb=" N TYR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 550 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 569 through 577 Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.785A pdb=" N LEU G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 removed outlier: 4.542A pdb=" N GLY G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.325A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.628A pdb=" N ASN H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.611A pdb=" N THR I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.511A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 79 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.651A pdb=" N GLU I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 4.277A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 172 removed outlier: 3.618A pdb=" N LEU I 159 " --> pdb=" O LEU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 191 removed outlier: 3.517A pdb=" N PHE I 188 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL I 189 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL I 191 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'I' and resid 201 through 207 removed outlier: 3.577A pdb=" N PHE I 207 " --> pdb=" O TYR I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 230 Processing helix chain 'I' and resid 231 through 254 removed outlier: 3.838A pdb=" N MET I 236 " --> pdb=" O CYS I 232 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP I 245 " --> pdb=" O GLY I 241 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 269 Processing helix chain 'I' and resid 274 through 287 removed outlier: 4.223A pdb=" N HIS I 283 " --> pdb=" O HIS I 279 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE I 285 " --> pdb=" O GLU I 281 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG I 287 " --> pdb=" O HIS I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 304 removed outlier: 3.644A pdb=" N LEU I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA I 303 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL I 304 " --> pdb=" O LEU I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 327 removed outlier: 3.843A pdb=" N MET I 311 " --> pdb=" O GLY I 307 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU I 324 " --> pdb=" O HIS I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 333 No H-bonds generated for 'chain 'I' and resid 331 through 333' Processing helix chain 'I' and resid 334 through 357 removed outlier: 4.105A pdb=" N GLN I 352 " --> pdb=" O GLY I 348 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL I 357 " --> pdb=" O LEU I 353 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 377 Processing helix chain 'I' and resid 386 through 400 removed outlier: 3.550A pdb=" N LEU I 390 " --> pdb=" O LYS I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 423 removed outlier: 3.511A pdb=" N ASP I 413 " --> pdb=" O ASN I 409 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER I 417 " --> pdb=" O ASP I 413 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE I 419 " --> pdb=" O LEU I 415 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR I 420 " --> pdb=" O THR I 416 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL I 421 " --> pdb=" O SER I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 427 through 445 removed outlier: 3.608A pdb=" N PHE I 431 " --> pdb=" O ASP I 427 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS I 445 " --> pdb=" O LYS I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 465 Processing helix chain 'I' and resid 470 through 477 removed outlier: 3.571A pdb=" N ARG I 475 " --> pdb=" O SER I 471 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR I 477 " --> pdb=" O LEU I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 495 removed outlier: 4.051A pdb=" N ASP I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS I 495 " --> pdb=" O ASN I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 530 through 548 removed outlier: 4.399A pdb=" N LYS I 535 " --> pdb=" O GLN I 531 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER I 536 " --> pdb=" O GLU I 532 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE I 540 " --> pdb=" O SER I 536 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU I 541 " --> pdb=" O VAL I 537 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 579 through 591 removed outlier: 3.808A pdb=" N ALA I 583 " --> pdb=" O THR I 579 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL I 584 " --> pdb=" O TYR I 580 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA I 587 " --> pdb=" O ALA I 583 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN I 590 " --> pdb=" O LEU I 586 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER I 591 " --> pdb=" O ALA I 587 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 603 removed outlier: 3.594A pdb=" N ASP I 601 " --> pdb=" O LYS I 597 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR I 603 " --> pdb=" O LEU I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 606 through 620 removed outlier: 4.399A pdb=" N LEU I 610 " --> pdb=" O ASN I 606 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR I 611 " --> pdb=" O GLU I 607 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS I 612 " --> pdb=" O LYS I 608 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE I 614 " --> pdb=" O LEU I 610 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS I 615 " --> pdb=" O THR I 611 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU I 617 " --> pdb=" O THR I 613 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 68 Processing helix chain 'R' and resid 81 through 89 Processing helix chain 'J' and resid 12 through 24 Processing helix chain 'J' and resid 31 through 35 removed outlier: 3.655A pdb=" N SER J 34 " --> pdb=" O ASP J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 50 removed outlier: 4.081A pdb=" N PHE J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 61 removed outlier: 3.935A pdb=" N SER J 58 " --> pdb=" O CYS J 54 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU J 59 " --> pdb=" O GLN J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 71 removed outlier: 4.209A pdb=" N LYS J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 74 No H-bonds generated for 'chain 'J' and resid 72 through 74' Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.578A pdb=" N HIS J 81 " --> pdb=" O HIS J 77 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET J 87 " --> pdb=" O PHE J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 110 removed outlier: 3.577A pdb=" N SER J 106 " --> pdb=" O SER J 102 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU J 110 " --> pdb=" O SER J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 134 Processing helix chain 'J' and resid 135 through 153 removed outlier: 4.263A pdb=" N LYS J 141 " --> pdb=" O SER J 137 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL J 142 " --> pdb=" O ASP J 138 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS J 150 " --> pdb=" O CYS J 146 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS J 153 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 170 removed outlier: 4.021A pdb=" N PHE J 160 " --> pdb=" O MET J 156 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG J 161 " --> pdb=" O LEU J 157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL J 163 " --> pdb=" O TRP J 159 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU J 170 " --> pdb=" O CYS J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 175 removed outlier: 3.671A pdb=" N GLY J 175 " --> pdb=" O HIS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 199 removed outlier: 4.156A pdb=" N GLU J 184 " --> pdb=" O HIS J 180 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE J 186 " --> pdb=" O GLY J 182 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS J 187 " --> pdb=" O GLU J 183 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 219 removed outlier: 4.219A pdb=" N ALA J 214 " --> pdb=" O GLY J 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 235 removed outlier: 3.529A pdb=" N LYS J 227 " --> pdb=" O ASP J 223 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU J 231 " --> pdb=" O LYS J 227 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU J 235 " --> pdb=" O GLU J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 259 removed outlier: 3.656A pdb=" N VAL J 258 " --> pdb=" O LYS J 254 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS J 259 " --> pdb=" O ALA J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 279 removed outlier: 3.520A pdb=" N GLU J 266 " --> pdb=" O PHE J 262 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLN J 267 " --> pdb=" O LYS J 263 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE J 269 " --> pdb=" O ALA J 265 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 301 removed outlier: 3.833A pdb=" N ASN J 300 " --> pdb=" O PHE J 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL J 301 " --> pdb=" O TYR J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 321 removed outlier: 3.545A pdb=" N ALA J 309 " --> pdb=" O CYS J 305 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA J 313 " --> pdb=" O ALA J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 344 removed outlier: 3.581A pdb=" N TYR J 338 " --> pdb=" O GLU J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 368 removed outlier: 3.510A pdb=" N HIS J 366 " --> pdb=" O GLY J 362 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE J 367 " --> pdb=" O ILE J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 393 removed outlier: 3.653A pdb=" N SER J 377 " --> pdb=" O LEU J 373 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL J 381 " --> pdb=" O SER J 377 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA J 390 " --> pdb=" O LEU J 386 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE J 391 " --> pdb=" O GLU J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 422 removed outlier: 3.547A pdb=" N GLU J 399 " --> pdb=" O ASN J 395 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN J 400 " --> pdb=" O LYS J 396 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG J 401 " --> pdb=" O GLU J 397 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU J 403 " --> pdb=" O GLU J 399 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA J 420 " --> pdb=" O LEU J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 442 removed outlier: 3.603A pdb=" N ASN J 434 " --> pdb=" O LYS J 430 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG J 437 " --> pdb=" O GLY J 433 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER J 441 " --> pdb=" O ARG J 437 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET J 442 " --> pdb=" O LEU J 438 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 463 removed outlier: 3.816A pdb=" N GLU J 449 " --> pdb=" O PHE J 445 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS J 452 " --> pdb=" O ALA J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 468 through 484 removed outlier: 3.738A pdb=" N LEU J 472 " --> pdb=" O TYR J 468 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP J 484 " --> pdb=" O LEU J 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 506 removed outlier: 5.159A pdb=" N LYS J 493 " --> pdb=" O GLU J 489 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU J 496 " --> pdb=" O GLU J 492 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER J 498 " --> pdb=" O LEU J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 512 through 526 removed outlier: 3.706A pdb=" N ASP J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 551 removed outlier: 3.830A pdb=" N VAL J 539 " --> pdb=" O GLU J 535 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP J 548 " --> pdb=" O ASN J 544 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG J 549 " --> pdb=" O ARG J 545 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN J 550 " --> pdb=" O LEU J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 562 removed outlier: 3.848A pdb=" N THR J 562 " --> pdb=" O GLU J 558 " (cutoff:3.500A) Processing helix chain 'J' and resid 566 through 578 removed outlier: 4.297A pdb=" N LEU J 575 " --> pdb=" O VAL J 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN J 578 " --> pdb=" O PHE J 574 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 23 Processing helix chain 'K' and resid 28 through 33 removed outlier: 4.152A pdb=" N ARG K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 50 removed outlier: 3.810A pdb=" N ASP K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 61 removed outlier: 3.932A pdb=" N GLU K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS K 61 " --> pdb=" O GLY K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 70 Processing helix chain 'K' and resid 71 through 72 No H-bonds generated for 'chain 'K' and resid 71 through 72' Processing helix chain 'K' and resid 73 through 74 No H-bonds generated for 'chain 'K' and resid 73 through 74' Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.693A pdb=" N HIS K 81 " --> pdb=" O HIS K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 106 removed outlier: 3.698A pdb=" N SER K 106 " --> pdb=" O SER K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 109 No H-bonds generated for 'chain 'K' and resid 107 through 109' Processing helix chain 'K' and resid 112 through 134 removed outlier: 3.829A pdb=" N LYS K 118 " --> pdb=" O ALA K 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA K 119 " --> pdb=" O VAL K 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 120 " --> pdb=" O LYS K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 151 removed outlier: 4.250A pdb=" N LYS K 141 " --> pdb=" O SER K 137 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR K 151 " --> pdb=" O LEU K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 173 removed outlier: 4.066A pdb=" N GLU K 164 " --> pdb=" O PHE K 160 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 199 removed outlier: 3.602A pdb=" N GLU K 183 " --> pdb=" O TYR K 179 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU K 184 " --> pdb=" O HIS K 180 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR K 192 " --> pdb=" O LEU K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 219 removed outlier: 4.105A pdb=" N LEU K 212 " --> pdb=" O LEU K 208 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS K 213 " --> pdb=" O TYR K 209 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA K 214 " --> pdb=" O GLY K 210 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE K 217 " --> pdb=" O CYS K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 235 removed outlier: 3.972A pdb=" N GLU K 235 " --> pdb=" O GLU K 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 259 removed outlier: 3.676A pdb=" N ALA K 255 " --> pdb=" O GLN K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 280 removed outlier: 3.747A pdb=" N GLN K 267 " --> pdb=" O LYS K 263 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS K 271 " --> pdb=" O GLN K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 301 removed outlier: 3.550A pdb=" N ASP K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 322 removed outlier: 3.587A pdb=" N VAL K 308 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA K 309 " --> pdb=" O CYS K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 344 Processing helix chain 'K' and resid 350 through 368 removed outlier: 3.715A pdb=" N LEU K 354 " --> pdb=" O PHE K 350 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE K 364 " --> pdb=" O ALA K 360 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS K 366 " --> pdb=" O GLY K 362 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE K 367 " --> pdb=" O ILE K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 393 removed outlier: 4.016A pdb=" N ALA K 376 " --> pdb=" O HIS K 372 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL K 381 " --> pdb=" O SER K 377 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS K 382 " --> pdb=" O SER K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 422 removed outlier: 3.655A pdb=" N ARG K 401 " --> pdb=" O GLU K 397 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN K 404 " --> pdb=" O GLN K 400 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU K 411 " --> pdb=" O HIS K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 425 through 442 Processing helix chain 'K' and resid 444 through 464 removed outlier: 3.605A pdb=" N LYS K 459 " --> pdb=" O ALA K 455 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU K 460 " --> pdb=" O ILE K 456 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN K 461 " --> pdb=" O GLN K 457 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU K 462 " --> pdb=" O ILE K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 484 removed outlier: 3.934A pdb=" N TYR K 483 " --> pdb=" O SER K 479 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 506 removed outlier: 3.609A pdb=" N ALA K 491 " --> pdb=" O GLN K 487 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS K 493 " --> pdb=" O GLU K 489 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS K 504 " --> pdb=" O ALA K 500 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU K 505 " --> pdb=" O ILE K 501 " (cutoff:3.500A) Processing helix chain 'K' and resid 510 through 527 removed outlier: 4.024A pdb=" N TYR K 515 " --> pdb=" O SER K 511 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY K 519 " --> pdb=" O TYR K 515 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER K 526 " --> pdb=" O LYS K 522 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE K 527 " --> pdb=" O LEU K 523 " (cutoff:3.500A) Processing helix chain 'K' and resid 532 through 551 removed outlier: 3.955A pdb=" N ARG K 547 " --> pdb=" O TRP K 543 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP K 548 " --> pdb=" O ASN K 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN K 550 " --> pdb=" O LEU K 546 " (cutoff:3.500A) Processing helix chain 'K' and resid 556 through 561 removed outlier: 3.536A pdb=" N SER K 561 " --> pdb=" O LEU K 557 " (cutoff:3.500A) Processing helix chain 'K' and resid 566 through 577 removed outlier: 3.741A pdb=" N VAL K 571 " --> pdb=" O THR K 567 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER K 573 " --> pdb=" O GLU K 569 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER K 577 " --> pdb=" O SER K 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 removed outlier: 3.671A pdb=" N THR L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN L 15 " --> pdb=" O ASP L 11 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR L 20 " --> pdb=" O LYS L 16 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE L 21 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL L 25 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 47 removed outlier: 3.525A pdb=" N ARG L 38 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE L 39 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER L 40 " --> pdb=" O ASN L 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL L 47 " --> pdb=" O TYR L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 79 removed outlier: 4.249A pdb=" N ARG L 75 " --> pdb=" O HIS L 71 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU L 77 " --> pdb=" O HIS L 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU L 78 " --> pdb=" O LYS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 105 removed outlier: 4.266A pdb=" N GLU L 93 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 112 Processing helix chain 'L' and resid 138 through 151 removed outlier: 3.706A pdb=" N ALA L 143 " --> pdb=" O ILE L 139 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU L 144 " --> pdb=" O GLY L 140 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET L 146 " --> pdb=" O LEU L 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET L 151 " --> pdb=" O TRP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 156 Processing helix chain 'M' and resid 26 through 36 removed outlier: 4.003A pdb=" N ILE M 30 " --> pdb=" O GLU M 26 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 37 removed outlier: 3.679A pdb=" N LEU N 37 " --> pdb=" O GLU N 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 34 through 37' Processing helix chain 'N' and resid 39 through 47 removed outlier: 3.773A pdb=" N LYS N 43 " --> pdb=" O SER N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 51 removed outlier: 3.596A pdb=" N GLN N 51 " --> pdb=" O GLY N 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 48 through 51' Processing helix chain 'N' and resid 66 through 83 removed outlier: 3.942A pdb=" N LYS N 72 " --> pdb=" O HIS N 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET N 75 " --> pdb=" O SER N 71 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE N 77 " --> pdb=" O VAL N 73 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR N 78 " --> pdb=" O CYS N 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR N 79 " --> pdb=" O MET N 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG N 82 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR N 83 " --> pdb=" O TYR N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 111 removed outlier: 3.511A pdb=" N MET N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 36 removed outlier: 3.824A pdb=" N LEU Q 27 " --> pdb=" O THR Q 23 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS Q 28 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG Q 29 " --> pdb=" O PHE Q 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 39 through 47 Processing helix chain 'T' and resid 48 through 52 removed outlier: 3.603A pdb=" N GLN T 51 " --> pdb=" O GLY T 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE T 52 " --> pdb=" O PRO T 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 48 through 52' Processing helix chain 'T' and resid 66 through 84 removed outlier: 3.547A pdb=" N THR T 78 " --> pdb=" O CYS T 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR T 79 " --> pdb=" O MET T 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL T 81 " --> pdb=" O PHE T 77 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR T 83 " --> pdb=" O TYR T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 111 removed outlier: 4.279A pdb=" N LEU T 101 " --> pdb=" O PRO T 97 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU T 102 " --> pdb=" O GLU T 98 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN T 108 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 3.614A pdb=" N ASN V 59 " --> pdb=" O GLU V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 89 removed outlier: 3.511A pdb=" N LYS V 89 " --> pdb=" O SER V 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 25 removed outlier: 3.693A pdb=" N THR U 13 " --> pdb=" O ASP U 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR U 19 " --> pdb=" O ASN U 15 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA U 23 " --> pdb=" O THR U 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL U 25 " --> pdb=" O ILE U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 47 removed outlier: 4.108A pdb=" N ILE U 42 " --> pdb=" O ARG U 38 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR U 43 " --> pdb=" O PHE U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 79 removed outlier: 3.574A pdb=" N ARG U 70 " --> pdb=" O GLU U 66 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS U 71 " --> pdb=" O ASN U 67 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG U 75 " --> pdb=" O HIS U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 92 Processing helix chain 'U' and resid 94 through 105 Processing helix chain 'U' and resid 105 through 112 Processing helix chain 'U' and resid 138 through 151 removed outlier: 3.609A pdb=" N LEU U 144 " --> pdb=" O GLY U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 155 through 172 removed outlier: 3.534A pdb=" N LEU U 159 " --> pdb=" O LEU U 155 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE U 160 " --> pdb=" O GLN U 156 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG U 161 " --> pdb=" O ALA U 157 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET U 162 " --> pdb=" O ILE U 158 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG U 165 " --> pdb=" O ARG U 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS U 168 " --> pdb=" O LEU U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 186 Processing helix chain 'U' and resid 186 through 191 Processing helix chain 'U' and resid 200 through 207 Processing helix chain 'U' and resid 207 through 230 removed outlier: 3.576A pdb=" N GLN U 228 " --> pdb=" O SER U 224 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU U 229 " --> pdb=" O ASN U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 254 removed outlier: 3.743A pdb=" N MET U 236 " --> pdb=" O CYS U 232 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU U 237 " --> pdb=" O SER U 233 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR U 253 " --> pdb=" O ARG U 249 " (cutoff:3.500A) Processing helix chain 'U' and resid 255 through 257 No H-bonds generated for 'chain 'U' and resid 255 through 257' Processing helix chain 'U' and resid 258 through 269 removed outlier: 3.810A pdb=" N ARG U 269 " --> pdb=" O GLU U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 274 through 281 removed outlier: 3.952A pdb=" N LEU U 278 " --> pdb=" O HIS U 274 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS U 279 " --> pdb=" O LEU U 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 281 through 289 removed outlier: 3.704A pdb=" N ILE U 285 " --> pdb=" O GLU U 281 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE U 286 " --> pdb=" O CYS U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 290 through 304 removed outlier: 3.895A pdb=" N ASN U 296 " --> pdb=" O ASN U 292 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET U 297 " --> pdb=" O ASP U 293 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA U 303 " --> pdb=" O VAL U 299 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL U 304 " --> pdb=" O LEU U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 307 through 329 removed outlier: 3.682A pdb=" N MET U 311 " --> pdb=" O GLY U 307 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG U 325 " --> pdb=" O ASP U 321 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA U 326 " --> pdb=" O GLU U 322 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR U 327 " --> pdb=" O GLY U 323 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN U 329 " --> pdb=" O ARG U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 334 through 357 Processing helix chain 'U' and resid 361 through 377 Processing helix chain 'U' and resid 386 through 400 removed outlier: 3.681A pdb=" N ALA U 392 " --> pdb=" O PRO U 388 " (cutoff:3.500A) Processing helix chain 'U' and resid 401 through 404 removed outlier: 3.845A pdb=" N LYS U 404 " --> pdb=" O LYS U 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 401 through 404' Processing helix chain 'U' and resid 407 through 423 removed outlier: 3.521A pdb=" N GLU U 412 " --> pdb=" O GLU U 408 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP U 413 " --> pdb=" O ASN U 409 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR U 420 " --> pdb=" O THR U 416 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL U 421 " --> pdb=" O SER U 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 427 through 445 removed outlier: 3.851A pdb=" N PHE U 431 " --> pdb=" O ASP U 427 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET U 438 " --> pdb=" O PHE U 434 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS U 441 " --> pdb=" O ARG U 437 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS U 445 " --> pdb=" O LYS U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 450 through 470 removed outlier: 7.303A pdb=" N TYR U 467 " --> pdb=" O GLN U 463 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N GLU U 468 " --> pdb=" O ALA U 464 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE U 469 " --> pdb=" O CYS U 465 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR U 470 " --> pdb=" O GLY U 466 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 477 Processing helix chain 'U' and resid 479 through 496 removed outlier: 3.749A pdb=" N ALA U 484 " --> pdb=" O MET U 480 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP U 485 " --> pdb=" O SER U 481 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS U 489 " --> pdb=" O ASP U 485 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 548 removed outlier: 3.987A pdb=" N LYS U 535 " --> pdb=" O GLN U 531 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER U 536 " --> pdb=" O GLU U 532 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE U 540 " --> pdb=" O SER U 536 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU U 541 " --> pdb=" O VAL U 537 " (cutoff:3.500A) Processing helix chain 'U' and resid 579 through 587 removed outlier: 3.664A pdb=" N VAL U 584 " --> pdb=" O TYR U 580 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 603 removed outlier: 3.540A pdb=" N ASP U 601 " --> pdb=" O LYS U 597 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR U 603 " --> pdb=" O LEU U 599 " (cutoff:3.500A) Processing helix chain 'U' and resid 607 through 620 removed outlier: 4.261A pdb=" N LYS U 612 " --> pdb=" O LYS U 608 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE U 614 " --> pdb=" O LEU U 610 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS U 615 " --> pdb=" O THR U 611 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER U 616 " --> pdb=" O LYS U 612 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU U 617 " --> pdb=" O THR U 613 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL U 620 " --> pdb=" O SER U 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 18 removed outlier: 3.763A pdb=" N THR C 16 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 5 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AA3, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.879A pdb=" N ALA G 73 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL G 75 " --> pdb=" O MET G 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AA7, first strand: chain 'I' and resid 508 through 513 removed outlier: 6.371A pdb=" N GLN I 508 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA R 31 " --> pdb=" O GLN I 508 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR I 510 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N TRP R 33 " --> pdb=" O TYR I 510 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU I 512 " --> pdb=" O TRP R 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'I' and resid 561 through 562 removed outlier: 3.755A pdb=" N VAL I 577 " --> pdb=" O GLY I 562 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL I 574 " --> pdb=" O PHE I 651 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 593 through 595 removed outlier: 3.901A pdb=" N VAL I 594 " --> pdb=" O PHE I 638 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE I 638 " --> pdb=" O VAL I 594 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 70 through 71 Processing sheet with id=AB2, first strand: chain 'M' and resid 16 through 18 removed outlier: 3.723A pdb=" N THR M 16 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU M 5 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE M 4 " --> pdb=" O ALA M 73 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL M 75 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N MET M 6 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU M 77 " --> pdb=" O MET M 6 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG M 8 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 18 through 19 Processing sheet with id=AB4, first strand: chain 'Q' and resid 3 through 5 removed outlier: 3.609A pdb=" N LEU Q 5 " --> pdb=" O THR Q 16 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR Q 16 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 42 through 45 removed outlier: 3.514A pdb=" N ALA Q 78 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 20 through 22 removed outlier: 6.138A pdb=" N LYS T 20 " --> pdb=" O VAL T 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'U' and resid 508 through 513 removed outlier: 3.606A pdb=" N TYR U 510 " --> pdb=" O ALA V 29 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA V 31 " --> pdb=" O TYR U 510 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'V' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'U' and resid 561 through 566 removed outlier: 4.312A pdb=" N VAL U 577 " --> pdb=" O GLY U 562 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL U 564 " --> pdb=" O ALA U 575 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA U 575 " --> pdb=" O VAL U 564 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET U 566 " --> pdb=" O TYR U 573 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 593 through 594 removed outlier: 3.629A pdb=" N VAL U 594 " --> pdb=" O PHE U 638 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE U 638 " --> pdb=" O VAL U 594 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER U 639 " --> pdb=" O ASN U 624 " (cutoff:3.500A) 2191 hydrogen bonds defined for protein. 6510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.07 Time building geometry restraints manager: 11.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12706 1.34 - 1.46: 6569 1.46 - 1.58: 20497 1.58 - 1.70: 0 1.70 - 1.82: 354 Bond restraints: 40126 Sorted by residual: bond pdb=" CA ASP V 51 " pdb=" C ASP V 51 " ideal model delta sigma weight residual 1.528 1.501 0.027 1.34e-02 5.57e+03 3.99e+00 bond pdb=" C MET I 335 " pdb=" N PRO I 336 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.32e+00 bond pdb=" CA ASP R 51 " pdb=" C ASP R 51 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.35e-02 5.49e+03 2.33e+00 bond pdb=" C ASP V 51 " pdb=" O ASP V 51 " ideal model delta sigma weight residual 1.234 1.219 0.015 1.07e-02 8.73e+03 2.02e+00 bond pdb=" CG1 ILE A 385 " pdb=" CD1 ILE A 385 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.66e+00 ... (remaining 40121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 53013 1.57 - 3.14: 978 3.14 - 4.72: 130 4.72 - 6.29: 37 6.29 - 7.86: 9 Bond angle restraints: 54167 Sorted by residual: angle pdb=" N ILE B 39 " pdb=" CA ILE B 39 " pdb=" C ILE B 39 " ideal model delta sigma weight residual 112.96 108.88 4.08 1.00e+00 1.00e+00 1.67e+01 angle pdb=" N VAL U 191 " pdb=" CA VAL U 191 " pdb=" C VAL U 191 " ideal model delta sigma weight residual 112.80 108.12 4.68 1.15e+00 7.56e-01 1.66e+01 angle pdb=" C ASP Q 47 " pdb=" N ASP Q 48 " pdb=" CA ASP Q 48 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N ILE E 206 " pdb=" CA ILE E 206 " pdb=" C ILE E 206 " ideal model delta sigma weight residual 113.53 110.06 3.47 9.80e-01 1.04e+00 1.26e+01 angle pdb=" C LYS C 46 " pdb=" N ASP C 47 " pdb=" CA ASP C 47 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.88e+00 ... (remaining 54162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 21644 17.98 - 35.95: 2013 35.95 - 53.93: 376 53.93 - 71.91: 71 71.91 - 89.88: 48 Dihedral angle restraints: 24152 sinusoidal: 9826 harmonic: 14326 Sorted by residual: dihedral pdb=" CA VAL B 301 " pdb=" C VAL B 301 " pdb=" N ASP B 302 " pdb=" CA ASP B 302 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA MET I 26 " pdb=" C MET I 26 " pdb=" N LEU I 27 " pdb=" CA LEU I 27 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA VAL I 24 " pdb=" C VAL I 24 " pdb=" N VAL I 25 " pdb=" CA VAL I 25 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 24149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4419 0.041 - 0.082: 1265 0.082 - 0.122: 232 0.122 - 0.163: 18 0.163 - 0.204: 5 Chirality restraints: 5939 Sorted by residual: chirality pdb=" CG LEU B 249 " pdb=" CB LEU B 249 " pdb=" CD1 LEU B 249 " pdb=" CD2 LEU B 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE N 30 " pdb=" CA ILE N 30 " pdb=" CG1 ILE N 30 " pdb=" CG2 ILE N 30 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB ILE D 99 " pdb=" CA ILE D 99 " pdb=" CG1 ILE D 99 " pdb=" CG2 ILE D 99 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 5936 not shown) Planarity restraints: 6903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE U 529 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO U 530 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO U 530 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO U 530 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 0 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO F 1 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 1 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 1 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 529 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO I 530 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO I 530 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 530 " 0.028 5.00e-02 4.00e+02 ... (remaining 6900 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 357 2.61 - 3.18: 34247 3.18 - 3.75: 64901 3.75 - 4.33: 87052 4.33 - 4.90: 141351 Nonbonded interactions: 327908 Sorted by model distance: nonbonded pdb=" OD1 ASP R 97 " pdb="ZN ZN R 202 " model vdw 2.033 2.230 nonbonded pdb=" OD1 ASP V 97 " pdb="ZN ZN V 202 " model vdw 2.138 2.230 nonbonded pdb=" OG SER A 566 " pdb=" OE1 GLU A 569 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR M 23 " pdb=" OE1 GLU M 26 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR I 219 " pdb=" OE1 GLU I 246 " model vdw 2.216 3.040 ... (remaining 327903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) selection = (chain 'B' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) selection = (chain 'J' and resid 7 through 577) selection = (chain 'K' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) } ncs_group { reference = (chain 'C' and resid 2 through 100) selection = (chain 'G' and (resid 2 through 79 or resid 88 through 100)) selection = (chain 'M' and resid 2 through 100) } ncs_group { reference = (chain 'D' and (resid 17 through 50 or resid 58 through 112)) selection = (chain 'H' and (resid 17 through 50 or resid 58 through 112)) selection = (chain 'N' and (resid 17 through 50 or resid 58 through 112)) selection = (chain 'T' and (resid 17 through 50 or resid 58 through 112)) } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'R' selection = (chain 'V' and (resid 27 through 107 or resid 200 through 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.050 Extract box with map and model: 1.700 Check model and map are aligned: 0.320 Set scattering table: 0.430 Process input model: 92.470 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 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 : 0.002 0.050 40126 Z= 0.159 Angle : 0.537 7.862 54167 Z= 0.296 Chirality : 0.038 0.204 5939 Planarity : 0.004 0.057 6903 Dihedral : 14.772 89.882 14886 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.02 % Allowed : 0.35 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.12), residues: 4782 helix: -0.56 (0.09), residues: 3080 sheet: -1.34 (0.50), residues: 115 loop : -1.07 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 91 HIS 0.005 0.001 HIS B 410 PHE 0.025 0.001 PHE B 322 TYR 0.025 0.001 TYR D 76 ARG 0.008 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 853 time to evaluate : 4.623 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: A 138 ASP cc_start: 0.8092 (m-30) cc_final: 0.7851 (m-30) REVERT: A 160 PHE cc_start: 0.8171 (m-80) cc_final: 0.7945 (m-80) REVERT: A 194 ASP cc_start: 0.8609 (t70) cc_final: 0.8148 (t70) REVERT: A 263 LYS cc_start: 0.8449 (tptp) cc_final: 0.8220 (mtmt) REVERT: A 407 HIS cc_start: 0.8503 (t-90) cc_final: 0.8282 (t-90) REVERT: A 416 LEU cc_start: 0.8473 (mm) cc_final: 0.8225 (mm) REVERT: E 37 ASP cc_start: 0.7342 (m-30) cc_final: 0.6893 (m-30) REVERT: C 53 ASP cc_start: 0.7112 (t70) cc_final: 0.6815 (t0) REVERT: C 56 THR cc_start: 0.6819 (m) cc_final: 0.6535 (m) REVERT: B 31 ASP cc_start: 0.8397 (t0) cc_final: 0.8159 (m-30) REVERT: B 138 ASP cc_start: 0.7748 (m-30) cc_final: 0.7375 (m-30) REVERT: B 539 VAL cc_start: 0.8010 (t) cc_final: 0.7702 (p) REVERT: G 32 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8057 (tt0) REVERT: I 527 PHE cc_start: 0.6316 (t80) cc_final: 0.6026 (t80) REVERT: I 548 PHE cc_start: 0.7584 (m-80) cc_final: 0.7091 (m-80) REVERT: I 553 LEU cc_start: 0.9134 (mt) cc_final: 0.8863 (mt) REVERT: J 389 ILE cc_start: 0.8267 (mm) cc_final: 0.8058 (mt) REVERT: J 411 LEU cc_start: 0.8008 (mm) cc_final: 0.7770 (pp) REVERT: K 132 ASP cc_start: 0.7755 (m-30) cc_final: 0.7380 (m-30) REVERT: K 387 GLU cc_start: 0.7581 (tt0) cc_final: 0.7170 (tp30) REVERT: K 451 MET cc_start: 0.7858 (mmp) cc_final: 0.7460 (mmm) REVERT: K 468 TYR cc_start: 0.7746 (t80) cc_final: 0.7267 (t80) REVERT: K 469 GLU cc_start: 0.8401 (tp30) cc_final: 0.8036 (mm-30) REVERT: L 86 MET cc_start: 0.0254 (tmm) cc_final: -0.0063 (tmm) REVERT: M 9 ARG cc_start: 0.5948 (tpt90) cc_final: 0.5563 (tpt90) REVERT: M 32 GLU cc_start: 0.7307 (tt0) cc_final: 0.7092 (tp30) REVERT: M 53 ASP cc_start: 0.6748 (m-30) cc_final: 0.6244 (m-30) REVERT: N 65 ILE cc_start: 0.8258 (mp) cc_final: 0.8058 (mp) REVERT: U 141 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7464 (tm-30) REVERT: U 201 LYS cc_start: 0.8397 (tptp) cc_final: 0.8025 (ptmt) REVERT: U 542 LEU cc_start: 0.8223 (mp) cc_final: 0.7635 (tt) outliers start: 1 outliers final: 0 residues processed: 853 average time/residue: 0.5485 time to fit residues: 749.0782 Evaluate side-chains 502 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 401 optimal weight: 0.0980 chunk 360 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 431 optimal weight: 0.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN E 156 GLN E 190 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN J 50 GLN J 427 GLN ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** K 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 525 ASN M 70 GLN N 108 ASN V 76 ASN U 377 ASN U 624 ASN U 625 HIS U 641 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 40126 Z= 0.349 Angle : 0.655 10.429 54167 Z= 0.353 Chirality : 0.042 0.215 5939 Planarity : 0.005 0.069 6903 Dihedral : 4.466 72.404 5292 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.33 % Allowed : 10.64 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.12), residues: 4782 helix: -0.08 (0.09), residues: 3200 sheet: -1.62 (0.45), residues: 113 loop : -1.15 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP U 517 HIS 0.008 0.001 HIS A 279 PHE 0.023 0.002 PHE N 77 TYR 0.027 0.002 TYR U 94 ARG 0.010 0.001 ARG J 318 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 570 time to evaluate : 4.890 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: A 138 ASP cc_start: 0.8203 (m-30) cc_final: 0.7889 (m-30) REVERT: A 263 LYS cc_start: 0.8574 (tptp) cc_final: 0.8294 (mtmt) REVERT: A 411 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 449 GLU cc_start: 0.7878 (tp30) cc_final: 0.7641 (tp30) REVERT: A 568 GLU cc_start: 0.8289 (mp0) cc_final: 0.8052 (mp0) REVERT: E 109 ASN cc_start: 0.8896 (t0) cc_final: 0.8310 (t0) REVERT: B 31 ASP cc_start: 0.8641 (t0) cc_final: 0.7994 (t0) REVERT: B 138 ASP cc_start: 0.7854 (m-30) cc_final: 0.7569 (m-30) REVERT: B 468 TYR cc_start: 0.8199 (t80) cc_final: 0.7843 (t80) REVERT: B 510 TYR cc_start: 0.7427 (t80) cc_final: 0.7126 (t80) REVERT: B 539 VAL cc_start: 0.8001 (t) cc_final: 0.7708 (p) REVERT: G 32 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7999 (tt0) REVERT: I 270 MET cc_start: 0.8717 (tmm) cc_final: 0.8314 (ttt) REVERT: I 378 TYR cc_start: 0.8031 (t80) cc_final: 0.7734 (t80) REVERT: I 548 PHE cc_start: 0.7447 (m-80) cc_final: 0.6962 (m-80) REVERT: I 622 MET cc_start: 0.6384 (tpp) cc_final: 0.6063 (tpp) REVERT: J 228 TRP cc_start: 0.7821 (m100) cc_final: 0.7531 (m100) REVERT: J 233 MET cc_start: 0.8314 (ttp) cc_final: 0.8112 (ttp) REVERT: J 515 TYR cc_start: 0.1675 (OUTLIER) cc_final: 0.0602 (m-80) REVERT: K 132 ASP cc_start: 0.7910 (m-30) cc_final: 0.7582 (m-30) REVERT: K 224 GLU cc_start: 0.8691 (tp30) cc_final: 0.8489 (tp30) REVERT: K 451 MET cc_start: 0.7896 (mmp) cc_final: 0.7553 (mmm) REVERT: K 468 TYR cc_start: 0.8083 (t80) cc_final: 0.7663 (t80) REVERT: K 469 GLU cc_start: 0.8461 (tp30) cc_final: 0.8199 (mm-30) REVERT: K 545 ARG cc_start: 0.8271 (mmp80) cc_final: 0.7974 (mmp80) REVERT: L 22 LYS cc_start: 0.7163 (tptp) cc_final: 0.6725 (tppt) REVERT: L 68 HIS cc_start: 0.5086 (t70) cc_final: 0.4259 (p-80) REVERT: L 70 ARG cc_start: 0.7778 (mmt-90) cc_final: 0.6854 (ppt170) REVERT: M 53 ASP cc_start: 0.6872 (m-30) cc_final: 0.6241 (m-30) REVERT: M 70 GLN cc_start: 0.8133 (mm110) cc_final: 0.6789 (pp30) REVERT: T 64 GLU cc_start: 0.7270 (pm20) cc_final: 0.7060 (pm20) REVERT: T 80 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7958 (ttmm) REVERT: U 141 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7720 (tm-30) REVERT: U 201 LYS cc_start: 0.8389 (tptp) cc_final: 0.8161 (ptmt) REVERT: U 297 MET cc_start: 0.8219 (tmm) cc_final: 0.7927 (tmm) REVERT: U 406 MET cc_start: 0.8152 (mtp) cc_final: 0.7442 (tpp) outliers start: 57 outliers final: 36 residues processed: 611 average time/residue: 0.5289 time to fit residues: 529.5960 Evaluate side-chains 518 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 479 time to evaluate : 4.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 1 THR Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 515 TYR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 55 LYS Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 306 THR Chi-restraints excluded: chain U residue 357 VAL Chi-restraints excluded: chain U residue 546 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 239 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 359 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 432 optimal weight: 2.9990 chunk 466 optimal weight: 0.7980 chunk 384 optimal weight: 20.0000 chunk 428 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN E 156 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN B 153 HIS B 300 ASN B 415 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 HIS K 180 HIS ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 415 GLN L 71 HIS V 76 ASN U 513 GLN U 624 ASN U 641 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 40126 Z= 0.299 Angle : 0.599 11.003 54167 Z= 0.319 Chirality : 0.040 0.197 5939 Planarity : 0.004 0.063 6903 Dihedral : 4.447 76.256 5292 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.73 % Allowed : 13.12 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 4782 helix: 0.12 (0.09), residues: 3206 sheet: -1.74 (0.42), residues: 130 loop : -1.10 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP U 517 HIS 0.006 0.001 HIS K 476 PHE 0.022 0.002 PHE Q 25 TYR 0.052 0.002 TYR K 345 ARG 0.008 0.001 ARG L 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 520 time to evaluate : 5.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: A 138 ASP cc_start: 0.8128 (m-30) cc_final: 0.7841 (m-30) REVERT: A 205 LYS cc_start: 0.8452 (mmtp) cc_final: 0.8163 (mttp) REVERT: A 263 LYS cc_start: 0.8571 (tptp) cc_final: 0.8300 (mtmt) REVERT: A 411 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8081 (mm) REVERT: A 415 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7426 (tp40) REVERT: A 416 LEU cc_start: 0.8399 (mm) cc_final: 0.8067 (mt) REVERT: A 449 GLU cc_start: 0.7876 (tp30) cc_final: 0.7659 (tp30) REVERT: A 568 GLU cc_start: 0.8316 (mp0) cc_final: 0.8073 (mp0) REVERT: E 37 ASP cc_start: 0.7559 (m-30) cc_final: 0.6888 (m-30) REVERT: E 109 ASN cc_start: 0.8879 (t0) cc_final: 0.8322 (t0) REVERT: D 20 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7930 (ptpt) REVERT: D 98 GLU cc_start: 0.7614 (pm20) cc_final: 0.7363 (pm20) REVERT: B 31 ASP cc_start: 0.8695 (t0) cc_final: 0.7984 (t0) REVERT: B 138 ASP cc_start: 0.7829 (m-30) cc_final: 0.7572 (m-30) REVERT: B 156 MET cc_start: 0.6385 (mmp) cc_final: 0.6070 (tmm) REVERT: B 468 TYR cc_start: 0.8190 (t80) cc_final: 0.7765 (t80) REVERT: B 510 TYR cc_start: 0.7468 (t80) cc_final: 0.7202 (t80) REVERT: B 539 VAL cc_start: 0.7977 (t) cc_final: 0.7681 (p) REVERT: G 32 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8064 (tt0) REVERT: I 270 MET cc_start: 0.8720 (tmm) cc_final: 0.8351 (ttt) REVERT: I 378 TYR cc_start: 0.8070 (t80) cc_final: 0.7798 (t80) REVERT: I 527 PHE cc_start: 0.6374 (t80) cc_final: 0.5970 (t80) REVERT: I 548 PHE cc_start: 0.7576 (m-80) cc_final: 0.7089 (m-80) REVERT: I 622 MET cc_start: 0.6503 (tpp) cc_final: 0.6229 (tpp) REVERT: J 228 TRP cc_start: 0.7776 (m100) cc_final: 0.7423 (m100) REVERT: J 233 MET cc_start: 0.8444 (ttp) cc_final: 0.8233 (ttp) REVERT: J 515 TYR cc_start: 0.1620 (OUTLIER) cc_final: 0.0598 (m-80) REVERT: K 132 ASP cc_start: 0.7913 (m-30) cc_final: 0.7552 (m-30) REVERT: K 294 TYR cc_start: 0.8917 (t80) cc_final: 0.8658 (t80) REVERT: K 442 MET cc_start: 0.6791 (mmt) cc_final: 0.6511 (mmt) REVERT: K 451 MET cc_start: 0.7858 (mmp) cc_final: 0.7532 (mmm) REVERT: K 468 TYR cc_start: 0.8161 (t80) cc_final: 0.7780 (t80) REVERT: K 469 GLU cc_start: 0.8473 (tp30) cc_final: 0.8250 (mm-30) REVERT: K 487 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: K 545 ARG cc_start: 0.8322 (mmp80) cc_final: 0.7958 (mmp80) REVERT: L 68 HIS cc_start: 0.4752 (t70) cc_final: 0.4241 (t-170) REVERT: M 53 ASP cc_start: 0.6969 (m-30) cc_final: 0.6426 (m-30) REVERT: N 17 MET cc_start: 0.5622 (tmm) cc_final: 0.4438 (pmm) REVERT: N 18 TYR cc_start: 0.4731 (m-10) cc_final: 0.4374 (m-80) REVERT: T 64 GLU cc_start: 0.7290 (pm20) cc_final: 0.7008 (pm20) REVERT: T 80 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7730 (ttmm) REVERT: U 201 LYS cc_start: 0.8427 (tptp) cc_final: 0.8165 (ptmt) REVERT: U 206 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7372 (mp) REVERT: U 406 MET cc_start: 0.8098 (mtp) cc_final: 0.7490 (tpp) outliers start: 74 outliers final: 44 residues processed: 569 average time/residue: 0.5258 time to fit residues: 492.4496 Evaluate side-chains 515 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 464 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 1 THR Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 515 TYR Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 487 GLN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 542 LEU Chi-restraints excluded: chain U residue 546 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 426 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 290 optimal weight: 7.9990 chunk 433 optimal weight: 0.0020 chunk 459 optimal weight: 2.9990 chunk 226 optimal weight: 20.0000 chunk 411 optimal weight: 0.4980 chunk 123 optimal weight: 0.6980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS A 427 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 550 GLN K 180 HIS K 326 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 70 GLN V 76 ASN U 320 HIS U 624 ASN U 641 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40126 Z= 0.196 Angle : 0.551 10.204 54167 Z= 0.292 Chirality : 0.039 0.178 5939 Planarity : 0.004 0.057 6903 Dihedral : 4.321 79.122 5292 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.89 % Allowed : 14.29 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 4782 helix: 0.36 (0.09), residues: 3208 sheet: -1.64 (0.41), residues: 138 loop : -1.05 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 517 HIS 0.006 0.001 HIS U 73 PHE 0.020 0.001 PHE E 39 TYR 0.022 0.001 TYR K 345 ARG 0.007 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 530 time to evaluate : 4.723 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: A 138 ASP cc_start: 0.8063 (m-30) cc_final: 0.7776 (m-30) REVERT: A 263 LYS cc_start: 0.8555 (tptp) cc_final: 0.8243 (mtmt) REVERT: A 411 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8047 (mm) REVERT: A 415 GLN cc_start: 0.7663 (tp40) cc_final: 0.7407 (tp40) REVERT: A 416 LEU cc_start: 0.8443 (mm) cc_final: 0.8131 (mt) REVERT: A 568 GLU cc_start: 0.8253 (mp0) cc_final: 0.8049 (mp0) REVERT: E 99 ASP cc_start: 0.7570 (m-30) cc_final: 0.7317 (t0) REVERT: E 109 ASN cc_start: 0.8790 (t0) cc_final: 0.8568 (t0) REVERT: E 207 PHE cc_start: 0.7986 (t80) cc_final: 0.7612 (t80) REVERT: B 31 ASP cc_start: 0.8646 (t0) cc_final: 0.7985 (t0) REVERT: B 138 ASP cc_start: 0.7832 (m-30) cc_final: 0.7572 (m-30) REVERT: B 156 MET cc_start: 0.6450 (mmp) cc_final: 0.6175 (tmm) REVERT: B 468 TYR cc_start: 0.8314 (t80) cc_final: 0.7880 (t80) REVERT: B 539 VAL cc_start: 0.7730 (t) cc_final: 0.7269 (p) REVERT: G 32 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8022 (tt0) REVERT: I 270 MET cc_start: 0.8687 (tmm) cc_final: 0.8392 (ttt) REVERT: I 304 VAL cc_start: 0.8236 (t) cc_final: 0.8006 (m) REVERT: I 378 TYR cc_start: 0.8039 (t80) cc_final: 0.7792 (t80) REVERT: I 435 TYR cc_start: 0.9148 (t80) cc_final: 0.8846 (t80) REVERT: I 527 PHE cc_start: 0.6342 (t80) cc_final: 0.5936 (t80) REVERT: I 548 PHE cc_start: 0.7567 (m-80) cc_final: 0.7080 (m-80) REVERT: I 553 LEU cc_start: 0.8953 (mt) cc_final: 0.8438 (mt) REVERT: I 622 MET cc_start: 0.6613 (tpp) cc_final: 0.6262 (tpp) REVERT: J 228 TRP cc_start: 0.7617 (m100) cc_final: 0.7292 (m100) REVERT: K 132 ASP cc_start: 0.7868 (m-30) cc_final: 0.7522 (m-30) REVERT: K 468 TYR cc_start: 0.8151 (t80) cc_final: 0.7780 (t80) REVERT: K 469 GLU cc_start: 0.8472 (tp30) cc_final: 0.8257 (mm-30) REVERT: K 545 ARG cc_start: 0.8301 (mmp80) cc_final: 0.7897 (mmp80) REVERT: M 23 THR cc_start: 0.6983 (t) cc_final: 0.6735 (m) REVERT: M 53 ASP cc_start: 0.6981 (m-30) cc_final: 0.6467 (m-30) REVERT: M 65 GLN cc_start: 0.8314 (pp30) cc_final: 0.8109 (pp30) REVERT: M 70 GLN cc_start: 0.8272 (mm110) cc_final: 0.6612 (pp30) REVERT: N 17 MET cc_start: 0.5466 (tmm) cc_final: 0.4327 (pmm) REVERT: N 18 TYR cc_start: 0.4800 (m-10) cc_final: 0.4388 (m-80) REVERT: T 37 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7664 (mm) REVERT: T 64 GLU cc_start: 0.7262 (pm20) cc_final: 0.6963 (pm20) REVERT: T 80 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7709 (ttmm) REVERT: T 95 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7200 (tp) REVERT: U 201 LYS cc_start: 0.8418 (tptp) cc_final: 0.8113 (ptmt) REVERT: U 206 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7319 (mp) REVERT: U 406 MET cc_start: 0.7935 (mtp) cc_final: 0.7361 (tpp) REVERT: U 622 MET cc_start: 0.7587 (mmm) cc_final: 0.7378 (mmm) outliers start: 81 outliers final: 40 residues processed: 581 average time/residue: 0.5143 time to fit residues: 496.7363 Evaluate side-chains 507 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 462 time to evaluate : 4.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 345 GLU Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 382 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 341 optimal weight: 0.0270 chunk 189 optimal weight: 0.6980 chunk 391 optimal weight: 9.9990 chunk 317 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 412 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 581 GLN ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN J 50 GLN ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 550 GLN K 180 HIS K 300 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN U 156 GLN U 624 ASN U 641 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40126 Z= 0.212 Angle : 0.553 11.050 54167 Z= 0.290 Chirality : 0.039 0.170 5939 Planarity : 0.004 0.057 6903 Dihedral : 4.280 78.574 5292 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.87 % Allowed : 15.76 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 4782 helix: 0.48 (0.09), residues: 3205 sheet: -1.59 (0.42), residues: 131 loop : -1.03 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 517 HIS 0.004 0.001 HIS B 476 PHE 0.033 0.001 PHE N 77 TYR 0.020 0.001 TYR I 558 ARG 0.007 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 496 time to evaluate : 4.693 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: A 105 CYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7010 (p) REVERT: A 138 ASP cc_start: 0.8061 (m-30) cc_final: 0.7768 (m-30) REVERT: A 263 LYS cc_start: 0.8548 (tptp) cc_final: 0.8245 (mtmt) REVERT: A 415 GLN cc_start: 0.7673 (tp40) cc_final: 0.7430 (tp40) REVERT: E 37 ASP cc_start: 0.7457 (m-30) cc_final: 0.6856 (m-30) REVERT: E 109 ASN cc_start: 0.8782 (t0) cc_final: 0.8556 (t0) REVERT: E 207 PHE cc_start: 0.8026 (t80) cc_final: 0.7689 (t80) REVERT: D 98 GLU cc_start: 0.7562 (pm20) cc_final: 0.7312 (pm20) REVERT: B 31 ASP cc_start: 0.8718 (t0) cc_final: 0.8084 (t0) REVERT: B 138 ASP cc_start: 0.7842 (m-30) cc_final: 0.7580 (m-30) REVERT: B 156 MET cc_start: 0.6589 (mmp) cc_final: 0.6201 (tmm) REVERT: G 32 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8014 (tt0) REVERT: I 270 MET cc_start: 0.8720 (tmm) cc_final: 0.8413 (ttt) REVERT: I 304 VAL cc_start: 0.8253 (t) cc_final: 0.8042 (m) REVERT: I 378 TYR cc_start: 0.8072 (t80) cc_final: 0.7806 (t80) REVERT: I 435 TYR cc_start: 0.9182 (t80) cc_final: 0.8801 (t80) REVERT: I 476 MET cc_start: 0.8920 (mmm) cc_final: 0.8325 (mmm) REVERT: I 527 PHE cc_start: 0.6323 (t80) cc_final: 0.5884 (t80) REVERT: I 548 PHE cc_start: 0.7521 (m-80) cc_final: 0.7012 (m-80) REVERT: I 622 MET cc_start: 0.6626 (tpp) cc_final: 0.6293 (tpp) REVERT: J 228 TRP cc_start: 0.7639 (m100) cc_final: 0.7247 (m100) REVERT: K 132 ASP cc_start: 0.7874 (m-30) cc_final: 0.7533 (m-30) REVERT: K 468 TYR cc_start: 0.8273 (t80) cc_final: 0.7786 (t80) REVERT: K 469 GLU cc_start: 0.8520 (tp30) cc_final: 0.8300 (mm-30) REVERT: K 545 ARG cc_start: 0.8337 (mmp80) cc_final: 0.7968 (mmp80) REVERT: M 23 THR cc_start: 0.6982 (t) cc_final: 0.6724 (m) REVERT: M 53 ASP cc_start: 0.6965 (m-30) cc_final: 0.6451 (m-30) REVERT: M 65 GLN cc_start: 0.8314 (pp30) cc_final: 0.8051 (mp10) REVERT: M 70 GLN cc_start: 0.8113 (mm110) cc_final: 0.6574 (pp30) REVERT: Q 27 LEU cc_start: 0.8032 (mm) cc_final: 0.7475 (pp) REVERT: T 37 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7637 (mm) REVERT: T 80 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7724 (ttmm) REVERT: T 95 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7176 (tp) REVERT: V 32 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8804 (mp) REVERT: U 9 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7873 (p0) REVERT: U 201 LYS cc_start: 0.8445 (tptp) cc_final: 0.8115 (ptmt) REVERT: U 206 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7282 (mp) REVERT: U 406 MET cc_start: 0.7745 (mtp) cc_final: 0.7254 (tpp) REVERT: U 622 MET cc_start: 0.7682 (mmm) cc_final: 0.7443 (mmm) outliers start: 80 outliers final: 53 residues processed: 546 average time/residue: 0.5109 time to fit residues: 460.9908 Evaluate side-chains 517 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 457 time to evaluate : 4.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain F residue -1 LYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 154 optimal weight: 5.9990 chunk 413 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 459 optimal weight: 1.9990 chunk 381 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS B 55 GLN B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN Q 49 GLN V 76 ASN U 624 ASN U 641 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40126 Z= 0.216 Angle : 0.555 9.313 54167 Z= 0.291 Chirality : 0.039 0.207 5939 Planarity : 0.004 0.055 6903 Dihedral : 4.267 78.536 5292 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.22 % Allowed : 16.37 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 4782 helix: 0.58 (0.09), residues: 3202 sheet: -1.50 (0.42), residues: 131 loop : -0.99 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP I 517 HIS 0.004 0.001 HIS K 476 PHE 0.021 0.001 PHE N 77 TYR 0.024 0.001 TYR U 94 ARG 0.007 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 490 time to evaluate : 4.775 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: A 105 CYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6974 (p) REVERT: A 138 ASP cc_start: 0.8067 (m-30) cc_final: 0.7765 (m-30) REVERT: A 193 MET cc_start: 0.8296 (mtp) cc_final: 0.8031 (mtp) REVERT: A 263 LYS cc_start: 0.8567 (tptp) cc_final: 0.8283 (mtmt) REVERT: A 415 GLN cc_start: 0.7681 (tp40) cc_final: 0.7423 (tp40) REVERT: E 37 ASP cc_start: 0.7536 (m-30) cc_final: 0.6851 (m-30) REVERT: E 109 ASN cc_start: 0.8774 (t0) cc_final: 0.8537 (t0) REVERT: E 207 PHE cc_start: 0.8010 (t80) cc_final: 0.7622 (t80) REVERT: B 31 ASP cc_start: 0.8727 (t0) cc_final: 0.8080 (t0) REVERT: B 138 ASP cc_start: 0.7842 (m-30) cc_final: 0.7575 (m-30) REVERT: B 156 MET cc_start: 0.6579 (mmp) cc_final: 0.6153 (tmm) REVERT: G 32 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8031 (tt0) REVERT: I 270 MET cc_start: 0.8745 (tmm) cc_final: 0.8436 (ttt) REVERT: I 304 VAL cc_start: 0.8283 (t) cc_final: 0.8077 (m) REVERT: I 378 TYR cc_start: 0.8101 (t80) cc_final: 0.7830 (t80) REVERT: I 435 TYR cc_start: 0.9180 (t80) cc_final: 0.8819 (t80) REVERT: I 527 PHE cc_start: 0.6326 (t80) cc_final: 0.5872 (t80) REVERT: I 548 PHE cc_start: 0.7575 (m-80) cc_final: 0.7069 (m-80) REVERT: I 622 MET cc_start: 0.6696 (tpp) cc_final: 0.6338 (tpp) REVERT: R 50 MET cc_start: 0.8154 (mmm) cc_final: 0.7900 (tpp) REVERT: J 228 TRP cc_start: 0.7586 (m100) cc_final: 0.7124 (m100) REVERT: K 132 ASP cc_start: 0.7910 (m-30) cc_final: 0.7554 (m-30) REVERT: K 468 TYR cc_start: 0.8290 (t80) cc_final: 0.7751 (t80) REVERT: K 469 GLU cc_start: 0.8539 (tp30) cc_final: 0.8331 (mm-30) REVERT: K 485 MET cc_start: 0.7023 (mmt) cc_final: 0.6463 (mtm) REVERT: K 545 ARG cc_start: 0.8347 (mmp80) cc_final: 0.7968 (mmp80) REVERT: M 23 THR cc_start: 0.6930 (t) cc_final: 0.6661 (m) REVERT: M 25 PHE cc_start: 0.7752 (t80) cc_final: 0.7529 (t80) REVERT: M 53 ASP cc_start: 0.7038 (m-30) cc_final: 0.5972 (t0) REVERT: M 65 GLN cc_start: 0.8315 (pp30) cc_final: 0.8108 (mp10) REVERT: N 17 MET cc_start: 0.5087 (tmm) cc_final: 0.4129 (pmm) REVERT: N 19 VAL cc_start: 0.7128 (OUTLIER) cc_final: 0.6924 (m) REVERT: N 98 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6094 (mt-10) REVERT: Q 27 LEU cc_start: 0.8071 (mm) cc_final: 0.7502 (pp) REVERT: T 37 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7639 (mm) REVERT: T 64 GLU cc_start: 0.7154 (pm20) cc_final: 0.6901 (pm20) REVERT: T 80 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7910 (ttmm) REVERT: V 32 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8796 (mp) REVERT: V 50 MET cc_start: 0.8493 (mmm) cc_final: 0.8209 (tpp) REVERT: U 9 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7875 (p0) REVERT: U 206 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7342 (mp) REVERT: U 406 MET cc_start: 0.7670 (mtp) cc_final: 0.7177 (tpp) REVERT: U 622 MET cc_start: 0.7714 (mmm) cc_final: 0.7447 (mmm) outliers start: 95 outliers final: 57 residues processed: 549 average time/residue: 0.5050 time to fit residues: 461.1730 Evaluate side-chains 519 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 454 time to evaluate : 4.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 1 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 410 HIS Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 443 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 335 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 chunk 256 optimal weight: 20.0000 chunk 457 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 457 GLN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 HIS K 180 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 ASN V 48 HIS V 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 40126 Z= 0.491 Angle : 0.701 10.071 54167 Z= 0.368 Chirality : 0.045 0.228 5939 Planarity : 0.004 0.057 6903 Dihedral : 4.576 75.280 5292 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.81 % Allowed : 16.60 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4782 helix: 0.24 (0.09), residues: 3210 sheet: -1.46 (0.46), residues: 124 loop : -1.17 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 517 HIS 0.011 0.001 HIS J 81 PHE 0.031 0.002 PHE I 469 TYR 0.025 0.002 TYR K 338 ARG 0.008 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 468 time to evaluate : 6.128 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: A 105 CYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7217 (p) REVERT: A 138 ASP cc_start: 0.8136 (m-30) cc_final: 0.7819 (m-30) REVERT: A 263 LYS cc_start: 0.8658 (tptp) cc_final: 0.8320 (mtmt) REVERT: A 380 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7374 (ttm170) REVERT: A 415 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7463 (tp40) REVERT: E 109 ASN cc_start: 0.8849 (t0) cc_final: 0.8346 (t0) REVERT: D 98 GLU cc_start: 0.7724 (pm20) cc_final: 0.7415 (pm20) REVERT: B 399 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: B 510 TYR cc_start: 0.6725 (t80) cc_final: 0.6522 (t80) REVERT: G 32 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8119 (tt0) REVERT: H 28 GLU cc_start: 0.8217 (mp0) cc_final: 0.7998 (mp0) REVERT: I 270 MET cc_start: 0.8861 (tmm) cc_final: 0.8450 (ttt) REVERT: I 378 TYR cc_start: 0.8209 (t80) cc_final: 0.7905 (t80) REVERT: I 435 TYR cc_start: 0.9244 (t80) cc_final: 0.8962 (t80) REVERT: I 457 MET cc_start: 0.9060 (tpp) cc_final: 0.8852 (tpp) REVERT: I 548 PHE cc_start: 0.7679 (m-80) cc_final: 0.7137 (m-80) REVERT: I 622 MET cc_start: 0.6716 (tpp) cc_final: 0.6341 (tpp) REVERT: J 228 TRP cc_start: 0.7637 (m100) cc_final: 0.7156 (m100) REVERT: K 132 ASP cc_start: 0.8072 (m-30) cc_final: 0.7501 (m-30) REVERT: K 468 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.8023 (t80) REVERT: K 469 GLU cc_start: 0.8583 (tp30) cc_final: 0.7602 (tp30) REVERT: K 485 MET cc_start: 0.7169 (mmt) cc_final: 0.6849 (mpp) REVERT: K 545 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8192 (mmp80) REVERT: M 53 ASP cc_start: 0.7209 (m-30) cc_final: 0.6124 (t0) REVERT: M 65 GLN cc_start: 0.8311 (pp30) cc_final: 0.8070 (pp30) REVERT: M 70 GLN cc_start: 0.8174 (mm-40) cc_final: 0.6642 (pp30) REVERT: N 75 MET cc_start: 0.5965 (tpt) cc_final: 0.5605 (tpt) REVERT: N 98 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6173 (mt-10) REVERT: Q 27 LEU cc_start: 0.8127 (mm) cc_final: 0.7538 (pp) REVERT: T 37 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7746 (mm) REVERT: T 64 GLU cc_start: 0.7309 (pm20) cc_final: 0.7016 (pm20) REVERT: T 80 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7767 (ttmm) REVERT: V 32 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8923 (mp) REVERT: U 9 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7928 (p0) REVERT: U 206 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7310 (mp) REVERT: U 622 MET cc_start: 0.7809 (mmm) cc_final: 0.7554 (mmm) outliers start: 120 outliers final: 82 residues processed: 545 average time/residue: 0.5232 time to fit residues: 474.4110 Evaluate side-chains 528 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 436 time to evaluate : 4.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 1 THR Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 312 ILE Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 451 MET Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 452 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 410 HIS Chi-restraints excluded: chain K residue 468 TYR Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 297 MET Chi-restraints excluded: chain U residue 306 THR Chi-restraints excluded: chain U residue 411 VAL Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 283 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 273 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 291 optimal weight: 10.0000 chunk 311 optimal weight: 0.9990 chunk 226 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 359 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 300 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN J 81 HIS ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 457 GLN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 40126 Z= 0.212 Angle : 0.591 11.268 54167 Z= 0.307 Chirality : 0.039 0.257 5939 Planarity : 0.004 0.054 6903 Dihedral : 4.429 76.356 5292 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.85 % Allowed : 18.24 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.12), residues: 4782 helix: 0.50 (0.09), residues: 3211 sheet: -1.47 (0.45), residues: 124 loop : -1.06 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 517 HIS 0.004 0.001 HIS D 68 PHE 0.030 0.002 PHE I 469 TYR 0.035 0.001 TYR D 76 ARG 0.008 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 488 time to evaluate : 4.838 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: A 105 CYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7112 (p) REVERT: A 138 ASP cc_start: 0.8124 (m-30) cc_final: 0.7833 (m-30) REVERT: A 263 LYS cc_start: 0.8586 (tptp) cc_final: 0.8274 (mtmt) REVERT: A 415 GLN cc_start: 0.7671 (tp40) cc_final: 0.7425 (tp40) REVERT: E 109 ASN cc_start: 0.8786 (t0) cc_final: 0.8577 (t0) REVERT: D 98 GLU cc_start: 0.7720 (pm20) cc_final: 0.7416 (pm20) REVERT: B 31 ASP cc_start: 0.8704 (t0) cc_final: 0.8100 (t0) REVERT: B 233 MET cc_start: 0.8366 (mtp) cc_final: 0.8119 (mtp) REVERT: B 399 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7765 (tp30) REVERT: G 32 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8038 (tt0) REVERT: I 270 MET cc_start: 0.8785 (tmm) cc_final: 0.8425 (ttt) REVERT: I 304 VAL cc_start: 0.8317 (t) cc_final: 0.8099 (m) REVERT: I 378 TYR cc_start: 0.8112 (t80) cc_final: 0.7806 (t80) REVERT: I 435 TYR cc_start: 0.9216 (t80) cc_final: 0.8944 (t80) REVERT: I 527 PHE cc_start: 0.6033 (t80) cc_final: 0.5544 (t80) REVERT: I 548 PHE cc_start: 0.7661 (m-80) cc_final: 0.7111 (m-80) REVERT: I 622 MET cc_start: 0.6699 (tpp) cc_final: 0.6319 (tpp) REVERT: J 228 TRP cc_start: 0.7629 (m100) cc_final: 0.7090 (m100) REVERT: K 132 ASP cc_start: 0.7938 (m-30) cc_final: 0.7479 (m-30) REVERT: K 469 GLU cc_start: 0.8566 (tp30) cc_final: 0.8256 (mp0) REVERT: K 485 MET cc_start: 0.7193 (mmt) cc_final: 0.6883 (mpp) REVERT: M 15 PHE cc_start: 0.8064 (m-80) cc_final: 0.7802 (m-10) REVERT: M 32 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6744 (tp30) REVERT: M 53 ASP cc_start: 0.7220 (m-30) cc_final: 0.6123 (t0) REVERT: M 70 GLN cc_start: 0.8086 (mm-40) cc_final: 0.6639 (pp30) REVERT: N 75 MET cc_start: 0.5564 (tpt) cc_final: 0.5050 (tpt) REVERT: N 98 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6165 (mt-10) REVERT: Q 27 LEU cc_start: 0.8113 (mm) cc_final: 0.7518 (pp) REVERT: T 37 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7692 (mm) REVERT: T 64 GLU cc_start: 0.7186 (pm20) cc_final: 0.6879 (pm20) REVERT: T 80 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7957 (ttmm) REVERT: V 32 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8838 (mp) REVERT: V 50 MET cc_start: 0.8479 (mmm) cc_final: 0.8178 (tpp) REVERT: U 9 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7852 (p0) REVERT: U 206 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7390 (mp) REVERT: U 476 MET cc_start: 0.8358 (mmt) cc_final: 0.7911 (mtt) REVERT: U 622 MET cc_start: 0.7747 (mmm) cc_final: 0.7503 (mmm) outliers start: 79 outliers final: 57 residues processed: 538 average time/residue: 0.5240 time to fit residues: 465.9509 Evaluate side-chains 517 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 451 time to evaluate : 4.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 410 HIS Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 416 optimal weight: 0.9980 chunk 438 optimal weight: 7.9990 chunk 400 optimal weight: 3.9990 chunk 426 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 335 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 385 optimal weight: 0.9990 chunk 403 optimal weight: 0.9990 chunk 425 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 HIS ** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS K 344 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN V 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40126 Z= 0.219 Angle : 0.602 13.846 54167 Z= 0.310 Chirality : 0.039 0.272 5939 Planarity : 0.004 0.053 6903 Dihedral : 4.390 78.716 5292 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.85 % Allowed : 18.40 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 4782 helix: 0.57 (0.09), residues: 3214 sheet: -1.43 (0.46), residues: 124 loop : -1.03 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 517 HIS 0.005 0.001 HIS D 68 PHE 0.028 0.001 PHE I 469 TYR 0.033 0.001 TYR D 76 ARG 0.008 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 471 time to evaluate : 5.221 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: A 105 CYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7093 (p) REVERT: A 138 ASP cc_start: 0.8114 (m-30) cc_final: 0.7824 (m-30) REVERT: A 263 LYS cc_start: 0.8582 (tptp) cc_final: 0.8269 (mtmt) REVERT: A 415 GLN cc_start: 0.7689 (tp40) cc_final: 0.7441 (tp40) REVERT: E 109 ASN cc_start: 0.8763 (t0) cc_final: 0.8506 (t0) REVERT: D 85 ASN cc_start: 0.8491 (m-40) cc_final: 0.8209 (t0) REVERT: D 98 GLU cc_start: 0.7711 (pm20) cc_final: 0.7471 (pm20) REVERT: B 31 ASP cc_start: 0.8725 (t0) cc_final: 0.8034 (t0) REVERT: B 233 MET cc_start: 0.8385 (mtp) cc_final: 0.8148 (mtp) REVERT: B 399 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: G 32 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8028 (tt0) REVERT: H 34 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7199 (tm-30) REVERT: I 270 MET cc_start: 0.8799 (tmm) cc_final: 0.8450 (ttt) REVERT: I 378 TYR cc_start: 0.8127 (t80) cc_final: 0.7826 (t80) REVERT: I 435 TYR cc_start: 0.9226 (t80) cc_final: 0.8966 (t80) REVERT: I 527 PHE cc_start: 0.6077 (t80) cc_final: 0.5701 (t80) REVERT: I 548 PHE cc_start: 0.7683 (m-80) cc_final: 0.7116 (m-80) REVERT: I 622 MET cc_start: 0.6734 (tpp) cc_final: 0.6353 (tpp) REVERT: J 228 TRP cc_start: 0.7630 (m100) cc_final: 0.7104 (m100) REVERT: K 132 ASP cc_start: 0.7935 (m-30) cc_final: 0.7541 (m-30) REVERT: K 468 TYR cc_start: 0.8135 (t80) cc_final: 0.7881 (t80) REVERT: K 485 MET cc_start: 0.7174 (mmt) cc_final: 0.6907 (mpp) REVERT: K 545 ARG cc_start: 0.8242 (mmp80) cc_final: 0.7960 (mmp80) REVERT: M 15 PHE cc_start: 0.8092 (m-80) cc_final: 0.7843 (m-10) REVERT: M 32 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: M 53 ASP cc_start: 0.7222 (m-30) cc_final: 0.6120 (t0) REVERT: M 70 GLN cc_start: 0.8030 (mm-40) cc_final: 0.6689 (pp30) REVERT: N 75 MET cc_start: 0.5408 (tpt) cc_final: 0.5156 (tpt) REVERT: N 98 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6168 (mt-10) REVERT: Q 27 LEU cc_start: 0.8113 (mm) cc_final: 0.7533 (pp) REVERT: T 37 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7735 (mm) REVERT: T 64 GLU cc_start: 0.7172 (pm20) cc_final: 0.6877 (pm20) REVERT: T 80 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7774 (ttmm) REVERT: V 32 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8833 (mp) REVERT: V 50 MET cc_start: 0.8509 (mmm) cc_final: 0.8225 (tpp) REVERT: U 9 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7862 (p0) REVERT: U 94 TYR cc_start: 0.7770 (t80) cc_final: 0.7485 (t80) REVERT: U 206 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7402 (mp) REVERT: U 476 MET cc_start: 0.8341 (mmt) cc_final: 0.7937 (mtt) REVERT: U 622 MET cc_start: 0.7811 (mmm) cc_final: 0.7532 (mmm) outliers start: 79 outliers final: 61 residues processed: 518 average time/residue: 0.5349 time to fit residues: 462.3860 Evaluate side-chains 515 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 445 time to evaluate : 5.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 1 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 451 MET Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain Q residue 14 ILE Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 297 MET Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 280 optimal weight: 0.7980 chunk 451 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 214 optimal weight: 0.1980 chunk 313 optimal weight: 0.7980 chunk 473 optimal weight: 7.9990 chunk 435 optimal weight: 0.9990 chunk 376 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 600 GLN ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 GLN ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS K 410 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN V 76 ASN U 71 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40126 Z= 0.188 Angle : 0.599 23.329 54167 Z= 0.306 Chirality : 0.039 0.268 5939 Planarity : 0.004 0.074 6903 Dihedral : 4.326 76.965 5292 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.87 % Allowed : 18.52 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 4782 helix: 0.68 (0.09), residues: 3191 sheet: -1.34 (0.44), residues: 134 loop : -0.96 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP U 147 HIS 0.013 0.001 HIS K 410 PHE 0.024 0.001 PHE I 469 TYR 0.031 0.001 TYR D 76 ARG 0.010 0.000 ARG L 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 482 time to evaluate : 4.968 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: A 105 CYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7126 (p) REVERT: A 138 ASP cc_start: 0.8053 (m-30) cc_final: 0.7765 (m-30) REVERT: A 263 LYS cc_start: 0.8564 (tptp) cc_final: 0.8248 (mtmt) REVERT: A 415 GLN cc_start: 0.7718 (tp40) cc_final: 0.7469 (tp40) REVERT: E 109 ASN cc_start: 0.8730 (t0) cc_final: 0.8459 (t0) REVERT: D 85 ASN cc_start: 0.8447 (m-40) cc_final: 0.8210 (t0) REVERT: D 98 GLU cc_start: 0.7687 (pm20) cc_final: 0.7461 (pm20) REVERT: B 31 ASP cc_start: 0.8713 (t0) cc_final: 0.8130 (t0) REVERT: B 233 MET cc_start: 0.8350 (mtp) cc_final: 0.8099 (mtp) REVERT: B 399 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: G 32 GLU cc_start: 0.8606 (tm-30) cc_final: 0.7954 (tt0) REVERT: G 37 ARG cc_start: 0.7252 (mmm-85) cc_final: 0.6909 (mmm-85) REVERT: I 270 MET cc_start: 0.8821 (tmm) cc_final: 0.8399 (ttt) REVERT: I 297 MET cc_start: 0.8195 (mmm) cc_final: 0.7382 (mmm) REVERT: I 378 TYR cc_start: 0.8126 (t80) cc_final: 0.7835 (t80) REVERT: I 435 TYR cc_start: 0.9191 (t80) cc_final: 0.8968 (t80) REVERT: I 527 PHE cc_start: 0.6126 (t80) cc_final: 0.5760 (t80) REVERT: I 548 PHE cc_start: 0.7660 (m-80) cc_final: 0.7111 (m-80) REVERT: I 622 MET cc_start: 0.6749 (tpp) cc_final: 0.6361 (tpp) REVERT: J 228 TRP cc_start: 0.7568 (m100) cc_final: 0.7049 (m100) REVERT: K 132 ASP cc_start: 0.7912 (m-30) cc_final: 0.7553 (m-30) REVERT: K 180 HIS cc_start: 0.7954 (m-70) cc_final: 0.7738 (m90) REVERT: K 294 TYR cc_start: 0.8745 (t80) cc_final: 0.8459 (t80) REVERT: K 545 ARG cc_start: 0.8230 (mmp80) cc_final: 0.7953 (mmp80) REVERT: M 15 PHE cc_start: 0.8092 (m-80) cc_final: 0.7890 (m-10) REVERT: M 32 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: M 53 ASP cc_start: 0.7239 (m-30) cc_final: 0.6149 (t0) REVERT: M 70 GLN cc_start: 0.8051 (mm-40) cc_final: 0.6630 (pp30) REVERT: Q 27 LEU cc_start: 0.8114 (mm) cc_final: 0.7570 (pp) REVERT: T 37 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7667 (mm) REVERT: T 64 GLU cc_start: 0.7143 (pm20) cc_final: 0.6870 (pm20) REVERT: T 80 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7754 (ttmm) REVERT: V 32 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8778 (mp) REVERT: V 50 MET cc_start: 0.8530 (mmm) cc_final: 0.8282 (tpp) REVERT: U 9 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7892 (p0) REVERT: U 94 TYR cc_start: 0.7654 (t80) cc_final: 0.7291 (t80) REVERT: U 206 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7388 (mp) REVERT: U 622 MET cc_start: 0.7788 (mmm) cc_final: 0.7510 (mmm) outliers start: 80 outliers final: 63 residues processed: 530 average time/residue: 0.5661 time to fit residues: 499.4702 Evaluate side-chains 529 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 458 time to evaluate : 5.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 451 MET Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain I residue 600 GLN Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 452 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 410 HIS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 71 HIS Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 297 MET Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 299 optimal weight: 6.9990 chunk 401 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 347 optimal weight: 5.9990 chunk 55 optimal weight: 0.0070 chunk 104 optimal weight: 0.7980 chunk 377 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 387 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS I 600 GLN ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN R 59 ASN ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 HIS K 158 HIS K 410 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.138845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092085 restraints weight = 88880.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091862 restraints weight = 50908.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092811 restraints weight = 34893.637| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40126 Z= 0.190 Angle : 0.605 21.999 54167 Z= 0.308 Chirality : 0.039 0.255 5939 Planarity : 0.004 0.072 6903 Dihedral : 4.308 75.641 5292 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.85 % Allowed : 18.66 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.12), residues: 4782 helix: 0.72 (0.09), residues: 3193 sheet: -1.43 (0.45), residues: 125 loop : -0.96 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP U 517 HIS 0.004 0.001 HIS J 77 PHE 0.026 0.001 PHE B 534 TYR 0.031 0.001 TYR D 76 ARG 0.012 0.000 ARG L 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9593.45 seconds wall clock time: 176 minutes 32.72 seconds (10592.72 seconds total)