Starting phenix.real_space_refine on Mon Dec 30 12:29:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w8g_32355/12_2024/7w8g_32355.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w8g_32355/12_2024/7w8g_32355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w8g_32355/12_2024/7w8g_32355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w8g_32355/12_2024/7w8g_32355.map" model { file = "/net/cci-nas-00/data/ceres_data/7w8g_32355/12_2024/7w8g_32355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w8g_32355/12_2024/7w8g_32355.cif" } resolution = 2.52 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 34 5.49 5 Mg 12 5.21 5 S 296 5.16 5 C 39156 2.51 5 N 10892 2.21 5 O 12060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 223 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 62460 Number of models: 1 Model: "" Number of chains: 24 Chain: "2" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "3" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "4" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5323 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5143 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "7" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "B" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "C" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "D" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5323 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5143 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "G" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1302 SG CYS 2 341 93.937 112.773 65.494 1.00 41.70 S ATOM 1325 SG CYS 2 344 97.487 111.810 65.292 1.00 48.39 S ATOM 1483 SG CYS 2 364 95.189 111.375 62.182 1.00 41.74 S ATOM 1504 SG CYS 2 367 95.184 109.051 65.315 1.00 47.57 S ATOM 11400 SG CYS 4 349 52.511 121.934 46.820 1.00 32.99 S ATOM 11421 SG CYS 4 352 50.433 121.108 43.938 1.00 36.68 S ATOM 11568 SG CYS 4 371 48.936 120.575 47.416 1.00 45.62 S ATOM 11610 SG CYS 4 376 51.734 118.271 46.061 1.00 50.96 S ATOM 16593 SG CYS 5 183 85.652 110.748 88.012 1.00 20.28 S ATOM 16618 SG CYS 5 186 87.098 107.038 88.854 1.00 18.51 S ATOM 16805 SG CYS 5 211 88.120 108.926 85.961 1.00 16.94 S ATOM 16923 SG CYS 5 236 84.449 107.869 86.053 1.00 22.39 S ATOM 21671 SG CYS 6 311 71.186 116.912 48.394 1.00 58.41 S ATOM 21693 SG CYS 6 314 71.714 113.877 46.228 1.00 59.59 S ATOM 21850 SG CYS 6 333 68.393 116.244 45.539 1.00 63.23 S ATOM 21884 SG CYS 6 338 68.431 114.006 47.507 1.00 63.25 S ATOM 27404 SG CYS 7 262 41.041 122.709 72.986 1.00 13.73 S ATOM 27427 SG CYS 7 265 39.143 120.848 75.675 1.00 12.99 S ATOM 27581 SG CYS 7 284 42.976 121.416 75.939 1.00 15.58 S ATOM 27618 SG CYS 7 289 41.508 118.877 73.633 1.00 14.86 S ATOM 32339 SG CYS B 341 61.756 112.340 65.511 1.00 39.92 S ATOM 32362 SG CYS B 344 58.204 113.326 65.271 1.00 48.20 S ATOM 32520 SG CYS B 364 60.555 113.775 62.203 1.00 41.24 S ATOM 32541 SG CYS B 367 60.546 116.070 65.348 1.00 46.86 S ATOM 42437 SG CYS D 349 103.267 103.177 46.815 1.00 32.94 S ATOM 42458 SG CYS D 352 105.307 103.974 43.924 1.00 36.84 S ATOM 42605 SG CYS D 371 106.871 104.514 47.414 1.00 45.59 S ATOM 42647 SG CYS D 376 104.063 106.811 46.025 1.00 51.86 S ATOM 47630 SG CYS E 183 70.016 114.400 88.017 1.00 20.09 S ATOM 47655 SG CYS E 186 68.561 118.107 88.849 1.00 17.73 S ATOM 47842 SG CYS E 211 67.592 116.193 85.937 1.00 16.89 S ATOM 47960 SG CYS E 236 71.252 117.267 86.065 1.00 20.40 S ATOM 52708 SG CYS F 311 84.532 108.247 48.394 1.00 58.09 S ATOM 52730 SG CYS F 314 83.995 111.283 46.234 1.00 59.59 S ATOM 52887 SG CYS F 333 87.262 108.882 45.491 1.00 62.93 S ATOM 52921 SG CYS F 338 87.295 111.139 47.520 1.00 61.93 S ATOM 58441 SG CYS G 262 114.667 102.413 72.953 1.00 15.56 S ATOM 58464 SG CYS G 265 116.476 104.272 75.668 1.00 20.28 S ATOM 58618 SG CYS G 284 112.571 103.681 75.746 1.00 14.47 S ATOM 58655 SG CYS G 289 114.126 106.249 73.585 1.00 16.57 S Time building chain proxies: 28.27, per 1000 atoms: 0.45 Number of scatterers: 62460 At special positions: 0 Unit cell: (156.748, 226.18, 149.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 296 16.00 P 34 15.00 Mg 12 11.99 O 12060 8.00 N 10892 7.00 C 39156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.05 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 522 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.05 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 22003 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 364 " pdb=" ZN 42003 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 371 " pdb=" ZN 52003 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 186 " pdb=" ZN 62003 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 311 " pdb=" ZN 72003 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 262 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 344 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 367 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 341 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 364 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 352 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 349 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 376 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 371 " pdb=" ZN E2003 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 211 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 236 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 183 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 186 " pdb=" ZN F2003 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 338 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 314 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 333 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 311 " pdb=" ZN G2003 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 265 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 289 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 284 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 262 " Number of angles added : 60 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14952 Finding SS restraints... Secondary structure from input PDB file: 319 helices and 85 sheets defined 45.9% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 Processing helix chain '2' and resid 193 through 200 Processing helix chain '2' and resid 200 through 218 Processing helix chain '2' and resid 225 through 237 Processing helix chain '2' and resid 246 through 253 Processing helix chain '2' and resid 253 through 263 Processing helix chain '2' and resid 263 through 283 removed outlier: 3.703A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 290 removed outlier: 3.621A pdb=" N ILE 2 289 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 305 through 309 removed outlier: 3.875A pdb=" N LEU 2 309 " --> pdb=" O LEU 2 306 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 Processing helix chain '2' and resid 411 through 415 removed outlier: 3.887A pdb=" N VAL 2 415 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 489 Processing helix chain '2' and resid 492 through 501 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 Processing helix chain '2' and resid 593 through 599 removed outlier: 4.026A pdb=" N VAL 2 597 " --> pdb=" O GLY 2 593 " (cutoff:3.500A) Processing helix chain '2' and resid 608 through 612 removed outlier: 4.007A pdb=" N MET 2 612 " --> pdb=" O PHE 2 609 " (cutoff:3.500A) Processing helix chain '2' and resid 613 through 627 Processing helix chain '2' and resid 652 through 656 removed outlier: 3.869A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 removed outlier: 3.548A pdb=" N VAL 2 667 " --> pdb=" O LEU 2 663 " (cutoff:3.500A) Processing helix chain '2' and resid 670 through 676 removed outlier: 3.515A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 706 Processing helix chain '2' and resid 759 through 774 removed outlier: 3.687A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE 2 774 " --> pdb=" O ALA 2 770 " (cutoff:3.500A) Processing helix chain '2' and resid 779 through 781 No H-bonds generated for 'chain '2' and resid 779 through 781' Processing helix chain '2' and resid 782 through 801 removed outlier: 4.076A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG 2 795 " --> pdb=" O ALA 2 791 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU 2 796 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 3.909A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU 2 818 " --> pdb=" O LEU 2 814 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS 2 822 " --> pdb=" O GLU 2 818 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 848 removed outlier: 3.514A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) Processing helix chain '2' and resid 850 through 861 removed outlier: 3.511A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG 2 859 " --> pdb=" O ARG 2 855 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER 2 860 " --> pdb=" O GLN 2 856 " (cutoff:3.500A) Processing helix chain '2' and resid 861 through 866 Processing helix chain '3' and resid 18 through 35 Processing helix chain '3' and resid 35 through 59 removed outlier: 4.152A pdb=" N ARG 3 39 " --> pdb=" O PHE 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 107 Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 117 through 137 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 161 through 163 No H-bonds generated for 'chain '3' and resid 161 through 163' Processing helix chain '3' and resid 172 through 176 Processing helix chain '3' and resid 279 through 283 removed outlier: 3.686A pdb=" N VAL 3 283 " --> pdb=" O ASP 3 280 " (cutoff:3.500A) Processing helix chain '3' and resid 343 through 355 Processing helix chain '3' and resid 358 through 364 removed outlier: 3.607A pdb=" N SER 3 364 " --> pdb=" O PHE 3 360 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 438 through 443 Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 474 through 478 removed outlier: 3.748A pdb=" N MET 3 478 " --> pdb=" O PHE 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 493 removed outlier: 3.960A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 Processing helix chain '3' and resid 536 through 543 removed outlier: 3.509A pdb=" N PHE 3 543 " --> pdb=" O LEU 3 539 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 569 Processing helix chain '3' and resid 652 through 667 removed outlier: 3.508A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL 3 667 " --> pdb=" O ALA 3 663 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 688 removed outlier: 3.819A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 716 removed outlier: 3.579A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 3.670A pdb=" N PHE 3 735 " --> pdb=" O ASN 3 731 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 3 736 " --> pdb=" O LEU 3 732 " (cutoff:3.500A) Processing helix chain '4' and resid 186 through 201 Processing helix chain '4' and resid 202 through 210 removed outlier: 3.922A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 217 through 222 Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 245 through 251 Processing helix chain '4' and resid 254 through 264 removed outlier: 3.765A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 287 removed outlier: 3.766A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (cutoff:3.500A) Processing helix chain '4' and resid 292 through 299 removed outlier: 3.666A pdb=" N ILE 4 296 " --> pdb=" O ASP 4 292 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS 4 299 " --> pdb=" O GLU 4 295 " (cutoff:3.500A) Processing helix chain '4' and resid 318 through 322 Processing helix chain '4' and resid 422 through 424 No H-bonds generated for 'chain '4' and resid 422 through 424' Processing helix chain '4' and resid 477 through 480 Processing helix chain '4' and resid 481 through 492 Processing helix chain '4' and resid 502 through 513 Processing helix chain '4' and resid 517 through 525 Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 597 through 602 Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 633 through 637 Processing helix chain '4' and resid 638 through 643 Processing helix chain '4' and resid 644 through 652 removed outlier: 4.074A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 700 Processing helix chain '4' and resid 713 through 727 removed outlier: 3.882A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) Processing helix chain '4' and resid 728 through 730 No H-bonds generated for 'chain '4' and resid 728 through 730' Processing helix chain '4' and resid 743 through 758 Processing helix chain '4' and resid 763 through 781 Processing helix chain '4' and resid 794 through 812 removed outlier: 3.588A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 833 removed outlier: 3.519A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '5' and resid 23 through 38 Processing helix chain '5' and resid 44 through 57 Processing helix chain '5' and resid 65 through 72 removed outlier: 3.534A pdb=" N ILE 5 69 " --> pdb=" O MET 5 65 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 82 removed outlier: 3.648A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 105 removed outlier: 3.524A pdb=" N ILE 5 86 " --> pdb=" O GLU 5 82 " (cutoff:3.500A) Proline residue: 5 88 - end of helix removed outlier: 3.722A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 Processing helix chain '5' and resid 152 through 156 Processing helix chain '5' and resid 212 through 217 Processing helix chain '5' and resid 245 through 248 Processing helix chain '5' and resid 281 through 283 No H-bonds generated for 'chain '5' and resid 281 through 283' Processing helix chain '5' and resid 350 through 362 removed outlier: 3.505A pdb=" N ARG 5 362 " --> pdb=" O LEU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 374 Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 486 through 499 Processing helix chain '5' and resid 535 through 540 Processing helix chain '5' and resid 544 through 549 removed outlier: 3.865A pdb=" N SER 5 548 " --> pdb=" O THR 5 544 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 544 through 549' Processing helix chain '5' and resid 561 through 578 Processing helix chain '5' and resid 578 through 591 Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 618 through 641 removed outlier: 3.867A pdb=" N LEU 5 622 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL 5 627 " --> pdb=" O SER 5 623 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE 5 629 " --> pdb=" O ASN 5 625 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG 5 630 " --> pdb=" O PHE 5 626 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 667 removed outlier: 3.639A pdb=" N LEU 5 666 " --> pdb=" O SER 5 662 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 695 removed outlier: 3.588A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA 5 691 " --> pdb=" O SER 5 687 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 122 removed outlier: 3.781A pdb=" N GLU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 147 removed outlier: 3.772A pdb=" N ILE 6 145 " --> pdb=" O GLU 6 141 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 160 Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 198 Processing helix chain '6' and resid 275 through 279 removed outlier: 3.761A pdb=" N ILE 6 279 " --> pdb=" O ILE 6 276 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 407 through 412 removed outlier: 3.598A pdb=" N LEU 6 410 " --> pdb=" O VAL 6 407 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY 6 411 " --> pdb=" O THR 6 408 " (cutoff:3.500A) Processing helix chain '6' and resid 500 through 508 removed outlier: 3.595A pdb=" N SER 6 507 " --> pdb=" O VAL 6 503 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU 6 508 " --> pdb=" O PHE 6 504 " (cutoff:3.500A) Processing helix chain '6' and resid 509 through 521 Processing helix chain '6' and resid 524 through 533 Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 592 removed outlier: 3.608A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 609 Processing helix chain '6' and resid 626 through 631 Processing helix chain '6' and resid 640 through 644 Processing helix chain '6' and resid 645 through 659 removed outlier: 3.950A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 708 removed outlier: 3.910A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 738 Processing helix chain '6' and resid 739 through 742 Processing helix chain '6' and resid 747 through 759 Processing helix chain '6' and resid 766 through 788 removed outlier: 3.720A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 789 through 791 No H-bonds generated for 'chain '6' and resid 789 through 791' Processing helix chain '6' and resid 796 through 814 removed outlier: 3.525A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 3.550A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 28 removed outlier: 3.533A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE 7 18 " --> pdb=" O TYR 7 14 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL 7 26 " --> pdb=" O THR 7 22 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 Processing helix chain '7' and resid 82 through 96 Processing helix chain '7' and resid 101 through 109 Processing helix chain '7' and resid 109 through 124 removed outlier: 3.994A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 165 removed outlier: 3.510A pdb=" N ASN 7 165 " --> pdb=" O ILE 7 161 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 189 Processing helix chain '7' and resid 193 through 197 Processing helix chain '7' and resid 208 through 215 removed outlier: 3.525A pdb=" N ARG 7 214 " --> pdb=" O ASN 7 210 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 231 through 235 Processing helix chain '7' and resid 286 through 292 removed outlier: 3.742A pdb=" N GLN 7 291 " --> pdb=" O GLU 7 287 " (cutoff:3.500A) Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 394 through 408 removed outlier: 3.752A pdb=" N GLU 7 399 " --> pdb=" O SER 7 395 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG 7 400 " --> pdb=" O ASP 7 396 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY 7 408 " --> pdb=" O LEU 7 404 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 417 Processing helix chain '7' and resid 425 through 438 Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 525 through 529 Processing helix chain '7' and resid 530 through 544 removed outlier: 4.166A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 587 through 594 removed outlier: 3.822A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 3.738A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 648 removed outlier: 3.702A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 675 Processing helix chain '7' and resid 685 through 703 removed outlier: 3.540A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 730 removed outlier: 3.944A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 218 Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 263 through 283 removed outlier: 3.672A pdb=" N MET B 267 " --> pdb=" O CYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.623A pdb=" N ILE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.764A pdb=" N LEU B 309 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.849A pdb=" N VAL B 415 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 548 through 560 removed outlier: 3.528A pdb=" N ILE B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 599 removed outlier: 3.992A pdb=" N VAL B 597 " --> pdb=" O GLY B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 612 removed outlier: 3.813A pdb=" N LYS B 611 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET B 612 " --> pdb=" O PHE B 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 608 through 612' Processing helix chain 'B' and resid 613 through 627 Processing helix chain 'B' and resid 652 through 656 removed outlier: 3.841A pdb=" N ARG B 656 " --> pdb=" O ASN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.519A pdb=" N VAL B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.531A pdb=" N ARG B 676 " --> pdb=" O PRO B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 Processing helix chain 'B' and resid 759 through 774 removed outlier: 3.612A pdb=" N LYS B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 774 " --> pdb=" O ALA B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 781 No H-bonds generated for 'chain 'B' and resid 779 through 781' Processing helix chain 'B' and resid 782 through 801 removed outlier: 4.157A pdb=" N VAL B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 787 " --> pdb=" O MET B 783 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 788 " --> pdb=" O ASP B 784 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 795 " --> pdb=" O ALA B 791 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 824 removed outlier: 3.812A pdb=" N LEU B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 822 " --> pdb=" O GLU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 848 Processing helix chain 'B' and resid 850 through 861 removed outlier: 3.508A pdb=" N ARG B 855 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 860 " --> pdb=" O GLN B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'C' and resid 18 through 35 Processing helix chain 'C' and resid 35 through 59 removed outlier: 4.167A pdb=" N ARG C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 117 through 137 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.689A pdb=" N VAL C 283 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 Processing helix chain 'C' and resid 358 through 364 removed outlier: 3.570A pdb=" N SER C 364 " --> pdb=" O PHE C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 414 through 426 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 492 removed outlier: 4.052A pdb=" N GLU C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 534 Processing helix chain 'C' and resid 536 through 543 Processing helix chain 'C' and resid 554 through 569 Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.537A pdb=" N LYS C 658 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 688 removed outlier: 3.866A pdb=" N VAL C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 716 removed outlier: 3.607A pdb=" N GLU C 703 " --> pdb=" O ALA C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 738 removed outlier: 3.670A pdb=" N PHE C 735 " --> pdb=" O ASN C 731 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 202 through 210 removed outlier: 3.919A pdb=" N ARG D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 removed outlier: 3.512A pdb=" N ASP D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 237 Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.755A pdb=" N HIS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 287 removed outlier: 3.764A pdb=" N SER D 270 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 284 " --> pdb=" O MET D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.668A pdb=" N ILE D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 299 " --> pdb=" O GLU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 477 through 480 Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 517 through 525 Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 597 through 602 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 633 through 637 Processing helix chain 'D' and resid 638 through 643 Processing helix chain 'D' and resid 644 through 652 removed outlier: 4.162A pdb=" N VAL D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 693 Processing helix chain 'D' and resid 695 through 700 Processing helix chain 'D' and resid 713 through 726 Processing helix chain 'D' and resid 727 through 730 removed outlier: 4.051A pdb=" N GLU D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 727 through 730' Processing helix chain 'D' and resid 743 through 758 Processing helix chain 'D' and resid 763 through 781 removed outlier: 3.536A pdb=" N GLU D 769 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 812 removed outlier: 3.514A pdb=" N LEU D 798 " --> pdb=" O THR D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 833 removed outlier: 3.718A pdb=" N ILE D 833 " --> pdb=" O ILE D 829 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.597A pdb=" N ILE E 69 " --> pdb=" O MET E 65 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.598A pdb=" N ILE E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 3.786A pdb=" N ARG E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.501A pdb=" N LEU E 151 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'E' and resid 245 through 248 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 350 through 362 removed outlier: 3.612A pdb=" N ARG E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 374 Processing helix chain 'E' and resid 381 through 394 removed outlier: 3.511A pdb=" N MET E 393 " --> pdb=" O VAL E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 433 Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 486 through 499 Processing helix chain 'E' and resid 535 through 540 removed outlier: 3.501A pdb=" N ILE E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 549 removed outlier: 3.877A pdb=" N SER E 548 " --> pdb=" O THR E 544 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG E 549 " --> pdb=" O THR E 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 544 through 549' Processing helix chain 'E' and resid 561 through 578 Processing helix chain 'E' and resid 578 through 591 Processing helix chain 'E' and resid 595 through 610 Processing helix chain 'E' and resid 618 through 641 removed outlier: 3.921A pdb=" N LEU E 622 " --> pdb=" O ALA E 618 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 627 " --> pdb=" O SER E 623 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE E 629 " --> pdb=" O ASN E 625 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG E 630 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 667 removed outlier: 4.018A pdb=" N GLU E 667 " --> pdb=" O LEU E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 695 removed outlier: 3.667A pdb=" N GLU E 679 " --> pdb=" O ARG E 675 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET E 689 " --> pdb=" O GLN E 685 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP E 690 " --> pdb=" O ALA E 686 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 122 removed outlier: 3.721A pdb=" N GLU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 147 removed outlier: 3.608A pdb=" N ILE F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 161 removed outlier: 3.878A pdb=" N ARG F 161 " --> pdb=" O HIS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'F' and resid 173 through 193 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 194 through 199 removed outlier: 4.037A pdb=" N ASN F 198 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 194 through 199' Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.782A pdb=" N ILE F 279 " --> pdb=" O ILE F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 364 through 368 removed outlier: 3.578A pdb=" N ILE F 368 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 407 through 412 removed outlier: 3.618A pdb=" N LEU F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY F 411 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 412 " --> pdb=" O GLN F 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 407 through 412' Processing helix chain 'F' and resid 500 through 508 removed outlier: 3.593A pdb=" N SER F 507 " --> pdb=" O VAL F 503 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 522 Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'F' and resid 540 through 553 Processing helix chain 'F' and resid 580 through 592 removed outlier: 3.532A pdb=" N PHE F 584 " --> pdb=" O SER F 580 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 640 through 644 Processing helix chain 'F' and resid 645 through 659 removed outlier: 3.974A pdb=" N ALA F 655 " --> pdb=" O ALA F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 699 Processing helix chain 'F' and resid 702 through 709 removed outlier: 3.836A pdb=" N ARG F 708 " --> pdb=" O PRO F 704 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE F 709 " --> pdb=" O ILE F 705 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 738 Processing helix chain 'F' and resid 739 through 742 Processing helix chain 'F' and resid 747 through 759 Processing helix chain 'F' and resid 766 through 788 removed outlier: 3.720A pdb=" N SER F 771 " --> pdb=" O LYS F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 791 No H-bonds generated for 'chain 'F' and resid 789 through 791' Processing helix chain 'F' and resid 796 through 814 removed outlier: 3.534A pdb=" N LEU F 800 " --> pdb=" O THR F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 835 removed outlier: 3.597A pdb=" N ILE F 835 " --> pdb=" O LEU F 831 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 28 removed outlier: 3.529A pdb=" N LEU G 17 " --> pdb=" O ASP G 13 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 72 Processing helix chain 'G' and resid 82 through 96 Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 109 through 124 removed outlier: 4.000A pdb=" N GLU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 165 Processing helix chain 'G' and resid 174 through 189 Processing helix chain 'G' and resid 193 through 197 Processing helix chain 'G' and resid 208 through 215 removed outlier: 3.520A pdb=" N ARG G 214 " --> pdb=" O ASN G 210 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR G 215 " --> pdb=" O CYS G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 235 Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 394 through 408 removed outlier: 3.730A pdb=" N GLU G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG G 400 " --> pdb=" O ASP G 396 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY G 408 " --> pdb=" O LEU G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 417 Processing helix chain 'G' and resid 425 through 438 Processing helix chain 'G' and resid 465 through 477 Processing helix chain 'G' and resid 511 through 516 Processing helix chain 'G' and resid 525 through 529 removed outlier: 3.523A pdb=" N MET G 529 " --> pdb=" O PHE G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 544 removed outlier: 4.244A pdb=" N GLU G 542 " --> pdb=" O HIS G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 587 through 594 removed outlier: 3.799A pdb=" N PHE G 594 " --> pdb=" O LEU G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 623 removed outlier: 3.618A pdb=" N GLU G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS G 611 " --> pdb=" O ASP G 607 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 648 removed outlier: 3.563A pdb=" N THR G 647 " --> pdb=" O ALA G 643 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS G 648 " --> pdb=" O TYR G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 675 Processing helix chain 'G' and resid 685 through 703 removed outlier: 3.548A pdb=" N LEU G 689 " --> pdb=" O THR G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 724 removed outlier: 3.888A pdb=" N LYS G 724 " --> pdb=" O VAL G 720 " (cutoff:3.500A) Processing helix chain 'G' and resid 724 through 730 Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 245 removed outlier: 6.385A pdb=" N LEU 2 242 " --> pdb=" O ARG 2 296 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SER 2 298 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL 2 244 " --> pdb=" O SER 2 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 316 through 327 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 316 through 327 current: chain '2' and resid 347 through 352 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 347 through 352 current: chain '2' and resid 405 through 410 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 405 through 410 current: chain '2' and resid 449 through 458 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '2' and resid 525 through 527 Processing sheet with id=AA4, first strand: chain '2' and resid 563 through 567 removed outlier: 6.097A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU 2 542 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 579 through 582 Processing sheet with id=AA6, first strand: chain '2' and resid 628 through 633 Processing sheet with id=AA7, first strand: chain '3' and resid 95 through 99 removed outlier: 6.069A pdb=" N ILE 3 96 " --> pdb=" O SER 3 156 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS 3 158 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '3' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 178 through 189 current: chain '3' and resid 208 through 213 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 208 through 213 current: chain '3' and resid 273 through 278 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 273 through 278 current: chain '3' and resid 318 through 330 Processing sheet with id=AA9, first strand: chain '3' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain '3' and resid 429 through 432 removed outlier: 3.528A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 444 through 448 Processing sheet with id=AB3, first strand: chain '3' and resid 494 through 498 Processing sheet with id=AB4, first strand: chain '4' and resid 240 through 244 removed outlier: 6.408A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR 4 306 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU 4 243 " --> pdb=" O TYR 4 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain '4' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 325 through 335 current: chain '4' and resid 355 through 359 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 355 through 359 current: chain '4' and resid 414 through 420 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 414 through 420 current: chain '4' and resid 458 through 467 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 364 through 367 Processing sheet with id=AB7, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AB8, first strand: chain '4' and resid 550 through 551 Processing sheet with id=AB9, first strand: chain '4' and resid 590 through 592 removed outlier: 6.413A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 603 through 607 Processing sheet with id=AC2, first strand: chain '4' and resid 653 through 657 Processing sheet with id=AC3, first strand: chain '4' and resid 761 through 762 removed outlier: 6.295A pdb=" N ILE 4 761 " --> pdb=" O VAL 4 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '5' and resid 8 through 12 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 8 through 12 current: chain 'G' and resid 238 through 248 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 238 through 248 current: chain 'G' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 267 through 272 current: chain 'G' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 336 current: chain 'G' and resid 372 through 383 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '5' and resid 60 through 64 Processing sheet with id=AC6, first strand: chain '5' and resid 173 through 176 removed outlier: 9.051A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE 5 330 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N ASP 5 279 " --> pdb=" O GLY 5 332 " (cutoff:3.500A) removed outlier: 12.772A pdb=" N GLN 5 334 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 189 through 193 removed outlier: 4.521A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 398 through 399 Processing sheet with id=AC9, first strand: chain '5' and resid 436 through 440 removed outlier: 6.582A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA 5 523 " --> pdb=" O VAL 5 412 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU 5 414 " --> pdb=" O ALA 5 523 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU 5 413 " --> pdb=" O PHE 5 554 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL 5 556 " --> pdb=" O LEU 5 413 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU 5 415 " --> pdb=" O VAL 5 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '5' and resid 452 through 455 removed outlier: 6.767A pdb=" N SER 5 452 " --> pdb=" O GLU 5 465 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '5' and resid 501 through 505 Processing sheet with id=AD3, first strand: chain '5' and resid 613 through 614 removed outlier: 6.533A pdb=" N ARG 5 613 " --> pdb=" O ALA 5 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain '6' and resid 124 through 125 Processing sheet with id=AD5, first strand: chain '6' and resid 150 through 154 removed outlier: 6.467A pdb=" N ILE 6 151 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE 6 153 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '6' and resid 317 through 322 removed outlier: 6.172A pdb=" N ALA 6 307 " --> pdb=" O ASN 6 320 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU 6 322 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N TYR 6 305 " --> pdb=" O GLU 6 322 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA 6 307 " --> pdb=" O ARG 6 350 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ARG 6 350 " --> pdb=" O ALA 6 307 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N PHE 6 309 " --> pdb=" O VAL 6 348 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N VAL 6 348 " --> pdb=" O PHE 6 309 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N CYS 6 311 " --> pdb=" O LEU 6 346 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N LEU 6 346 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) removed outlier: 13.980A pdb=" N THR 6 376 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE 6 452 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASP 6 378 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE 6 454 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG 6 382 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N HIS 6 458 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE 6 452 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL 6 404 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 402 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE 6 402 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA 6 456 " --> pdb=" O VAL 6 400 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL 6 400 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG 6 394 " --> pdb=" O ILE 6 462 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 557 through 558 Processing sheet with id=AD8, first strand: chain '6' and resid 596 through 599 removed outlier: 6.483A pdb=" N ILE 6 571 " --> pdb=" O ALA 6 680 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA 6 682 " --> pdb=" O ILE 6 571 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL 6 573 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS 6 572 " --> pdb=" O PHE 6 713 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE 6 715 " --> pdb=" O CYS 6 572 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL 6 574 " --> pdb=" O ILE 6 715 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 610 through 614 Processing sheet with id=AE1, first strand: chain '6' and resid 660 through 663 Processing sheet with id=AE2, first strand: chain '6' and resid 764 through 765 removed outlier: 7.073A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AE4, first strand: chain '7' and resid 224 through 225 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 248 current: chain '7' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 267 through 272 current: chain '7' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 330 through 336 current: chain '7' and resid 372 through 383 Processing sheet with id=AE5, first strand: chain '7' and resid 442 through 443 Processing sheet with id=AE6, first strand: chain '7' and resid 480 through 483 removed outlier: 6.654A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL 7 456 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA 7 567 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU 7 458 " --> pdb=" O ALA 7 567 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N MET 7 600 " --> pdb=" O CYS 7 457 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET 7 459 " --> pdb=" O MET 7 600 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain '7' and resid 495 through 500 Processing sheet with id=AE8, first strand: chain '7' and resid 545 through 549 Processing sheet with id=AE9, first strand: chain 'B' and resid 241 through 245 Processing sheet with id=AF1, first strand: chain 'B' and resid 316 through 327 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 316 through 327 current: chain 'B' and resid 347 through 352 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 347 through 352 current: chain 'B' and resid 405 through 410 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 405 through 410 current: chain 'B' and resid 449 through 458 No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 525 through 527 Processing sheet with id=AF3, first strand: chain 'B' and resid 563 through 567 removed outlier: 6.146A pdb=" N CYS B 604 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA B 649 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 606 " --> pdb=" O ALA B 649 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 540 " --> pdb=" O CYS B 681 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 683 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 542 " --> pdb=" O VAL B 683 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 579 through 582 Processing sheet with id=AF5, first strand: chain 'B' and resid 628 through 633 Processing sheet with id=AF6, first strand: chain 'C' and resid 95 through 99 removed outlier: 6.095A pdb=" N ILE C 96 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS C 158 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 98 " --> pdb=" O LYS C 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 178 through 189 current: chain 'C' and resid 208 through 213 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 208 through 213 current: chain 'C' and resid 273 through 278 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 278 current: chain 'C' and resid 318 through 330 Processing sheet with id=AF8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF9, first strand: chain 'C' and resid 429 through 432 removed outlier: 6.447A pdb=" N ILE C 430 " --> pdb=" O CYS C 471 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 405 " --> pdb=" O ALA C 514 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA C 516 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET C 407 " --> pdb=" O ALA C 516 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 444 through 448 Processing sheet with id=AG2, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AG3, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.424A pdb=" N LEU D 241 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR D 306 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 243 " --> pdb=" O TYR D 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 325 through 335 current: chain 'D' and resid 355 through 359 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 355 through 359 current: chain 'D' and resid 414 through 420 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 414 through 420 current: chain 'D' and resid 458 through 467 No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'D' and resid 364 through 367 Processing sheet with id=AG6, first strand: chain 'D' and resid 453 through 454 Processing sheet with id=AG7, first strand: chain 'D' and resid 550 through 551 Processing sheet with id=AG8, first strand: chain 'D' and resid 590 through 592 removed outlier: 6.437A pdb=" N ILE D 564 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ALA D 675 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU D 566 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU D 565 " --> pdb=" O TYR D 706 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL D 708 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS D 567 " --> pdb=" O VAL D 708 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 603 through 607 Processing sheet with id=AH1, first strand: chain 'D' and resid 653 through 657 Processing sheet with id=AH2, first strand: chain 'D' and resid 761 through 762 removed outlier: 6.246A pdb=" N ILE D 761 " --> pdb=" O VAL D 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'E' and resid 60 through 64 removed outlier: 5.717A pdb=" N LEU E 61 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASN E 140 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL E 63 " --> pdb=" O ASN E 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'E' and resid 173 through 176 removed outlier: 9.043A pdb=" N ASN E 273 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N ILE E 328 " --> pdb=" O ASN E 273 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR E 275 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE E 330 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR E 277 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY E 332 " --> pdb=" O THR E 277 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N ASP E 279 " --> pdb=" O GLY E 332 " (cutoff:3.500A) removed outlier: 12.710A pdb=" N GLN E 334 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 295 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE E 333 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR E 293 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N SER E 335 " --> pdb=" O ARG E 291 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG E 291 " --> pdb=" O SER E 335 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS E 257 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR E 169 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 255 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 189 through 193 removed outlier: 4.521A pdb=" N SER E 180 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 398 through 399 Processing sheet with id=AH7, first strand: chain 'E' and resid 436 through 440 removed outlier: 6.568A pdb=" N VAL E 437 " --> pdb=" O CYS E 478 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP E 480 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR E 439 " --> pdb=" O ASP E 480 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL E 477 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA E 522 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE E 479 " --> pdb=" O ALA E 522 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL E 412 " --> pdb=" O ALA E 521 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA E 523 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU E 414 " --> pdb=" O ALA E 523 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU E 413 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL E 556 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU E 415 " --> pdb=" O VAL E 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'E' and resid 452 through 455 removed outlier: 6.805A pdb=" N SER E 452 " --> pdb=" O GLU E 465 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 501 through 505 Processing sheet with id=AI1, first strand: chain 'E' and resid 613 through 614 removed outlier: 6.521A pdb=" N ARG E 613 " --> pdb=" O ALA E 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AI3, first strand: chain 'F' and resid 150 through 154 Processing sheet with id=AI4, first strand: chain 'F' and resid 317 through 322 removed outlier: 6.170A pdb=" N ALA F 307 " --> pdb=" O ASN F 320 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU F 322 " --> pdb=" O TYR F 305 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR F 305 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TRP F 356 " --> pdb=" O PRO F 302 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU F 304 " --> pdb=" O LEU F 354 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU F 354 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER F 308 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG F 350 " --> pdb=" O SER F 308 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N THR F 310 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N VAL F 348 " --> pdb=" O THR F 310 " (cutoff:3.500A) removed outlier: 14.021A pdb=" N THR F 376 " --> pdb=" O TYR F 450 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE F 452 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP F 378 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 454 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG F 382 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS F 458 " --> pdb=" O ARG F 382 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE F 452 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL F 404 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE F 454 " --> pdb=" O ILE F 402 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE F 402 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA F 456 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL F 400 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG F 394 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL F 294 " --> pdb=" O GLN F 362 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN F 362 " --> pdb=" O VAL F 294 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 557 through 558 Processing sheet with id=AI6, first strand: chain 'F' and resid 596 through 599 removed outlier: 6.524A pdb=" N ILE F 571 " --> pdb=" O ALA F 680 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA F 682 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL F 573 " --> pdb=" O ALA F 682 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N CYS F 572 " --> pdb=" O PHE F 713 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE F 715 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL F 574 " --> pdb=" O ILE F 715 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 610 through 614 Processing sheet with id=AI8, first strand: chain 'F' and resid 660 through 663 Processing sheet with id=AI9, first strand: chain 'G' and resid 77 through 81 Processing sheet with id=AJ1, first strand: chain 'G' and resid 442 through 443 Processing sheet with id=AJ2, first strand: chain 'G' and resid 480 through 483 removed outlier: 6.656A pdb=" N VAL G 481 " --> pdb=" O CYS G 522 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N CYS G 521 " --> pdb=" O LEU G 564 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA G 566 " --> pdb=" O CYS G 521 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE G 523 " --> pdb=" O ALA G 566 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL G 456 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ALA G 567 " --> pdb=" O VAL G 456 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU G 458 " --> pdb=" O ALA G 567 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS G 457 " --> pdb=" O PHE G 598 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET G 600 " --> pdb=" O CYS G 457 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N MET G 459 " --> pdb=" O MET G 600 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'G' and resid 495 through 500 Processing sheet with id=AJ4, first strand: chain 'G' and resid 545 through 549 2546 hydrogen bonds defined for protein. 7320 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: 26.74 Time building geometry restraints manager: 13.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 20953 1.35 - 1.50: 15433 1.50 - 1.65: 26584 1.65 - 1.80: 241 1.80 - 1.95: 231 Bond restraints: 63442 Sorted by residual: bond pdb=" CG PRO F 745 " pdb=" CD PRO F 745 " ideal model delta sigma weight residual 1.503 1.388 0.115 3.40e-02 8.65e+02 1.15e+01 bond pdb=" CB CYS 7 474 " pdb=" SG CYS 7 474 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.38e+00 bond pdb=" CB CYS G 474 " pdb=" SG CYS G 474 " ideal model delta sigma weight residual 1.808 1.734 0.074 3.30e-02 9.18e+02 4.98e+00 bond pdb=" CB PRO G 632 " pdb=" CG PRO G 632 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.96e+00 bond pdb=" CB PRO F 745 " pdb=" CG PRO F 745 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.90e+00 ... (remaining 63437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 84887 2.88 - 5.76: 866 5.76 - 8.64: 85 8.64 - 11.52: 16 11.52 - 14.40: 2 Bond angle restraints: 85856 Sorted by residual: angle pdb=" N PRO F 745 " pdb=" CD PRO F 745 " pdb=" CG PRO F 745 " ideal model delta sigma weight residual 103.20 94.23 8.97 1.50e+00 4.44e-01 3.58e+01 angle pdb=" CA PRO G 632 " pdb=" N PRO G 632 " pdb=" CD PRO G 632 " ideal model delta sigma weight residual 112.00 104.40 7.60 1.40e+00 5.10e-01 2.95e+01 angle pdb=" CA PRO F 745 " pdb=" N PRO F 745 " pdb=" CD PRO F 745 " ideal model delta sigma weight residual 112.00 105.05 6.95 1.40e+00 5.10e-01 2.46e+01 angle pdb=" N GLN F 833 " pdb=" CA GLN F 833 " pdb=" CB GLN F 833 " ideal model delta sigma weight residual 110.42 117.76 -7.34 1.62e+00 3.81e-01 2.05e+01 angle pdb=" CA GLN F 833 " pdb=" CB GLN F 833 " pdb=" CG GLN F 833 " ideal model delta sigma weight residual 114.10 123.15 -9.05 2.00e+00 2.50e-01 2.05e+01 ... (remaining 85851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 38474 35.44 - 70.87: 625 70.87 - 106.31: 59 106.31 - 141.74: 2 141.74 - 177.18: 2 Dihedral angle restraints: 39162 sinusoidal: 16126 harmonic: 23036 Sorted by residual: dihedral pdb=" O2A ADP 32001 " pdb=" O3A ADP 32001 " pdb=" PA ADP 32001 " pdb=" PB ADP 32001 " ideal model delta sinusoidal sigma weight residual -60.00 67.61 -127.61 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" O2A ADP C2001 " pdb=" O3A ADP C2001 " pdb=" PA ADP C2001 " pdb=" PB ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 67.00 -127.00 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" CA ARG E 5 " pdb=" C ARG E 5 " pdb=" N PRO E 6 " pdb=" CA PRO E 6 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 39159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 9034 0.085 - 0.170: 906 0.170 - 0.255: 21 0.255 - 0.340: 1 0.340 - 0.425: 2 Chirality restraints: 9964 Sorted by residual: chirality pdb=" CB VAL F 403 " pdb=" CA VAL F 403 " pdb=" CG1 VAL F 403 " pdb=" CG2 VAL F 403 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CB VAL 6 403 " pdb=" CA VAL 6 403 " pdb=" CG1 VAL 6 403 " pdb=" CG2 VAL 6 403 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE E 646 " pdb=" CA ILE E 646 " pdb=" CG1 ILE E 646 " pdb=" CG2 ILE E 646 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 9961 not shown) Planarity restraints: 11040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 631 " -0.081 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO G 632 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO G 632 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO G 632 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 744 " 0.073 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO F 745 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO F 745 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 745 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 7 631 " 0.062 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO 7 632 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO 7 632 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO 7 632 " 0.050 5.00e-02 4.00e+02 ... (remaining 11037 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 593 2.61 - 3.19: 52166 3.19 - 3.76: 99508 3.76 - 4.33: 140029 4.33 - 4.90: 226848 Nonbonded interactions: 519144 Sorted by model distance: nonbonded pdb=" O2G AGS 62001 " pdb="MG MG 62002 " model vdw 2.042 2.170 nonbonded pdb=" O2G AGS F2001 " pdb="MG MG F2002 " model vdw 2.052 2.170 nonbonded pdb=" O2G AGS G2001 " pdb="MG MG G2002 " model vdw 2.053 2.170 nonbonded pdb=" OG SER D 575 " pdb="MG MG D2002 " model vdw 2.054 2.170 nonbonded pdb=" OG SER B 550 " pdb="MG MG B2002 " model vdw 2.065 2.170 ... (remaining 519139 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 '2' selection = chain 'B' } ncs_group { reference = chain '3' selection = chain 'C' } ncs_group { reference = chain '4' selection = chain 'D' } ncs_group { reference = chain '5' selection = chain 'E' } ncs_group { reference = chain '6' selection = chain 'F' } ncs_group { reference = chain '7' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.770 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 119.810 Find NCS groups from input model: 4.220 Set up NCS constraints: 0.340 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:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 63442 Z= 0.262 Angle : 0.773 14.399 85856 Z= 0.431 Chirality : 0.048 0.425 9964 Planarity : 0.006 0.118 11040 Dihedral : 13.999 177.179 24204 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.04 % Allowed : 0.17 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.09), residues: 7788 helix: -0.16 (0.09), residues: 3164 sheet: 0.28 (0.13), residues: 1496 loop : -0.24 (0.10), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 2 589 HIS 0.014 0.002 HIS 6 653 PHE 0.026 0.002 PHE 2 351 TYR 0.039 0.002 TYR G 618 ARG 0.019 0.001 ARG 2 705 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1156 time to evaluate : 5.289 Fit side-chains revert: symmetry clash REVERT: 2 423 GLU cc_start: 0.7008 (tt0) cc_final: 0.6751 (tt0) REVERT: 2 488 SER cc_start: 0.6939 (p) cc_final: 0.6705 (p) REVERT: 2 590 THR cc_start: 0.8357 (p) cc_final: 0.8139 (p) REVERT: 2 694 ARG cc_start: 0.5300 (mtm110) cc_final: 0.4998 (mtm-85) REVERT: 2 705 ARG cc_start: 0.6958 (mtm110) cc_final: 0.6664 (mtp180) REVERT: 2 783 MET cc_start: 0.5286 (ttm) cc_final: 0.5000 (ttt) REVERT: 3 43 ARG cc_start: 0.7428 (tpm170) cc_final: 0.7145 (ttm-80) REVERT: 3 720 THR cc_start: 0.8038 (t) cc_final: 0.7804 (m) REVERT: 4 356 MET cc_start: 0.6331 (ptp) cc_final: 0.6124 (ptp) REVERT: 4 483 GLN cc_start: 0.7481 (tp-100) cc_final: 0.7065 (pm20) REVERT: 4 532 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6312 (mm-30) REVERT: 4 610 ASP cc_start: 0.7228 (m-30) cc_final: 0.7015 (m-30) REVERT: 4 718 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7277 (ttm-80) REVERT: 4 811 MET cc_start: 0.7881 (ttp) cc_final: 0.7621 (ttp) REVERT: 5 103 ILE cc_start: 0.7457 (mt) cc_final: 0.7177 (mm) REVERT: 6 313 MET cc_start: 0.3506 (ppp) cc_final: 0.2320 (mmt) REVERT: 6 384 ASP cc_start: 0.6858 (m-30) cc_final: 0.6641 (m-30) REVERT: 6 629 MET cc_start: 0.7574 (mtp) cc_final: 0.7259 (mtm) REVERT: 7 156 ASP cc_start: 0.6839 (m-30) cc_final: 0.6525 (m-30) REVERT: 7 157 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7834 (tpp-160) REVERT: 7 291 GLN cc_start: 0.7574 (mt0) cc_final: 0.7334 (mt0) REVERT: 7 448 MET cc_start: 0.6540 (mmp) cc_final: 0.6161 (ppp) REVERT: 7 573 ARG cc_start: 0.6758 (ttm-80) cc_final: 0.6538 (ttm-80) REVERT: B 488 SER cc_start: 0.7038 (p) cc_final: 0.6778 (p) REVERT: B 783 MET cc_start: 0.4937 (ttm) cc_final: 0.4701 (ttt) REVERT: C 720 THR cc_start: 0.8118 (t) cc_final: 0.7758 (m) REVERT: D 228 LYS cc_start: 0.6908 (tttm) cc_final: 0.6707 (ptmm) REVERT: D 532 GLU cc_start: 0.6462 (mm-30) cc_final: 0.6232 (mm-30) REVERT: D 637 MET cc_start: 0.7883 (ttm) cc_final: 0.7600 (ttm) REVERT: D 811 MET cc_start: 0.7963 (ttp) cc_final: 0.7666 (ttp) REVERT: E 103 ILE cc_start: 0.7248 (mt) cc_final: 0.6959 (mm) REVERT: E 276 MET cc_start: 0.8694 (mtm) cc_final: 0.8282 (mtm) REVERT: E 489 ASP cc_start: 0.7111 (m-30) cc_final: 0.6667 (m-30) REVERT: E 546 ILE cc_start: 0.7855 (mt) cc_final: 0.7649 (mp) REVERT: F 384 ASP cc_start: 0.7100 (m-30) cc_final: 0.6827 (m-30) REVERT: F 629 MET cc_start: 0.7537 (mtp) cc_final: 0.7231 (mtm) REVERT: G 291 GLN cc_start: 0.7417 (mt0) cc_final: 0.7213 (mt0) REVERT: G 402 MET cc_start: 0.5534 (mmp) cc_final: 0.5325 (mpm) REVERT: G 448 MET cc_start: 0.6388 (mmp) cc_final: 0.6076 (ppp) outliers start: 3 outliers final: 5 residues processed: 1159 average time/residue: 1.6009 time to fit residues: 2319.2303 Evaluate side-chains 783 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 778 time to evaluate : 5.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain F residue 276 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 658 optimal weight: 6.9990 chunk 591 optimal weight: 0.7980 chunk 328 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 398 optimal weight: 4.9990 chunk 315 optimal weight: 5.9990 chunk 611 optimal weight: 8.9990 chunk 236 optimal weight: 4.9990 chunk 371 optimal weight: 0.7980 chunk 455 optimal weight: 7.9990 chunk 708 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 340 ASN 2 433 ASN 2 626 GLN 3 365 GLN ** 3 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 4 465 HIS 5 43 GLN 5 334 GLN 5 363 ASN 5 454 GLN 5 561 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 700 ASN 7 109 ASN 7 124 ASN 7 271 GLN 7 554 ASN 7 558 ASN 7 568 ASN B 340 ASN B 391 GLN B 433 ASN B 651 ASN ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN ** C 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN D 380 ASN D 465 HIS E 43 GLN E 363 ASN E 454 GLN E 560 HIS F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 109 ASN G 124 ASN G 554 ASN ** G 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 63442 Z= 0.197 Angle : 0.567 11.310 85856 Z= 0.296 Chirality : 0.043 0.210 9964 Planarity : 0.005 0.058 11040 Dihedral : 7.402 175.022 8836 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.04 % Allowed : 9.49 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.09), residues: 7788 helix: 0.83 (0.09), residues: 3204 sheet: 0.32 (0.13), residues: 1446 loop : -0.04 (0.11), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 2 589 HIS 0.008 0.001 HIS 2 779 PHE 0.022 0.001 PHE 6 142 TYR 0.019 0.001 TYR 5 301 ARG 0.009 0.001 ARG 2 705 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 865 time to evaluate : 5.327 Fit side-chains revert: symmetry clash REVERT: 2 483 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5541 (tm-30) REVERT: 2 850 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7099 (ptpt) REVERT: 3 474 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7005 (mp0) REVERT: 4 189 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6752 (mm-30) REVERT: 4 610 ASP cc_start: 0.7197 (m-30) cc_final: 0.6945 (m-30) REVERT: 4 720 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8010 (tm) REVERT: 4 811 MET cc_start: 0.7879 (ttp) cc_final: 0.7580 (ttp) REVERT: 4 812 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8069 (mtpt) REVERT: 5 370 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6263 (tp) REVERT: 5 546 ILE cc_start: 0.7929 (mt) cc_final: 0.7669 (mp) REVERT: 5 561 ASN cc_start: 0.5465 (m-40) cc_final: 0.5193 (m110) REVERT: 5 583 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5630 (tmm) REVERT: 5 608 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7490 (mp) REVERT: 6 320 ASN cc_start: 0.5721 (m-40) cc_final: 0.5509 (m-40) REVERT: 6 629 MET cc_start: 0.7546 (mtp) cc_final: 0.7284 (mtm) REVERT: 6 654 GLU cc_start: 0.6539 (tm-30) cc_final: 0.6337 (mm-30) REVERT: 6 829 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: 7 156 ASP cc_start: 0.6846 (m-30) cc_final: 0.6550 (m-30) REVERT: 7 167 MET cc_start: 0.3043 (OUTLIER) cc_final: 0.2278 (mtt) REVERT: 7 293 GLN cc_start: 0.7452 (pm20) cc_final: 0.7249 (mp10) REVERT: 7 448 MET cc_start: 0.6484 (mmp) cc_final: 0.6140 (ppp) REVERT: 7 652 MET cc_start: 0.7499 (mmm) cc_final: 0.7161 (mmm) REVERT: B 205 ARG cc_start: 0.6121 (ptp90) cc_final: 0.5774 (ptt90) REVERT: B 452 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: B 488 SER cc_start: 0.7044 (p) cc_final: 0.6807 (p) REVERT: C 43 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.7020 (ttm-80) REVERT: C 286 THR cc_start: 0.7549 (p) cc_final: 0.7316 (p) REVERT: C 474 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: C 478 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.5995 (tpt) REVERT: C 559 ARG cc_start: 0.5723 (tpp-160) cc_final: 0.5484 (mmt180) REVERT: D 285 VAL cc_start: 0.6566 (t) cc_final: 0.6331 (p) REVERT: D 637 MET cc_start: 0.7939 (ttm) cc_final: 0.7650 (ttm) REVERT: D 811 MET cc_start: 0.7819 (ttp) cc_final: 0.7574 (ttp) REVERT: E 370 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6773 (tp) REVERT: E 489 ASP cc_start: 0.7002 (m-30) cc_final: 0.6697 (m-30) REVERT: E 562 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5711 (tm-30) REVERT: E 583 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5643 (tmm) REVERT: E 608 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7439 (mp) REVERT: F 320 ASN cc_start: 0.5676 (m-40) cc_final: 0.5460 (m-40) REVERT: F 629 MET cc_start: 0.7538 (mtp) cc_final: 0.7252 (mtm) REVERT: G 156 ASP cc_start: 0.6834 (m-30) cc_final: 0.6509 (m-30) REVERT: G 448 MET cc_start: 0.6351 (mmp) cc_final: 0.6071 (ppp) REVERT: G 652 MET cc_start: 0.7457 (mmm) cc_final: 0.7201 (mmm) outliers start: 142 outliers final: 53 residues processed: 940 average time/residue: 1.5904 time to fit residues: 1877.3109 Evaluate side-chains 791 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 720 time to evaluate : 5.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 340 ASN Chi-restraints excluded: chain 2 residue 366 ASN Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 434 TYR Chi-restraints excluded: chain 2 residue 483 GLU Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 710 ASN Chi-restraints excluded: chain 2 residue 850 LYS Chi-restraints excluded: chain 3 residue 91 ILE Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 538 SER Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 4 residue 189 GLU Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 342 MET Chi-restraints excluded: chain 4 residue 489 LYS Chi-restraints excluded: chain 4 residue 686 LEU Chi-restraints excluded: chain 4 residue 720 LEU Chi-restraints excluded: chain 4 residue 812 LYS Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 399 ILE Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 799 GLN Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 167 MET Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 562 GLU Chi-restraints excluded: chain E residue 583 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 506 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 393 optimal weight: 0.7980 chunk 219 optimal weight: 0.0020 chunk 589 optimal weight: 0.9980 chunk 482 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 709 optimal weight: 4.9990 chunk 766 optimal weight: 7.9990 chunk 631 optimal weight: 0.8980 chunk 703 optimal weight: 5.9990 chunk 241 optimal weight: 0.0060 chunk 569 optimal weight: 0.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 GLN 2 340 ASN 2 779 HIS 3 52 ASN 3 293 ASN 3 365 GLN 3 417 GLN ** 3 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 670 GLN ** 3 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 4 483 GLN ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 363 ASN 5 454 GLN 5 499 GLN 5 524 ASN 5 625 ASN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 291 GLN 7 518 ASN B 340 ASN ** B 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN C 365 GLN ** C 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN D 413 HIS D 483 GLN E 43 GLN E 235 ASN E 359 GLN E 363 ASN E 524 ASN F 156 GLN F 335 ASN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN G 316 GLN G 518 ASN G 615 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 63442 Z= 0.158 Angle : 0.522 10.935 85856 Z= 0.271 Chirality : 0.042 0.200 9964 Planarity : 0.004 0.045 11040 Dihedral : 7.139 176.638 8832 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.57 % Allowed : 11.12 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.09), residues: 7788 helix: 1.28 (0.09), residues: 3202 sheet: 0.28 (0.13), residues: 1488 loop : 0.04 (0.11), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 111 HIS 0.009 0.001 HIS 6 653 PHE 0.014 0.001 PHE C 421 TYR 0.019 0.001 TYR F 136 ARG 0.009 0.000 ARG F 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 786 time to evaluate : 5.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 269 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7074 (ptmt) REVERT: 2 483 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5477 (tm-30) REVERT: 2 779 HIS cc_start: 0.3853 (OUTLIER) cc_final: 0.3301 (p-80) REVERT: 3 352 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6836 (ptpt) REVERT: 3 462 MET cc_start: 0.7211 (mmt) cc_final: 0.6625 (mmt) REVERT: 3 533 ILE cc_start: 0.6564 (mt) cc_final: 0.6308 (mt) REVERT: 4 189 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6780 (mm-30) REVERT: 4 223 GLU cc_start: 0.6041 (pt0) cc_final: 0.5717 (pt0) REVERT: 4 246 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6495 (tpm-80) REVERT: 4 359 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6507 (mm-30) REVERT: 4 366 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: 4 720 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7957 (tm) REVERT: 4 747 LEU cc_start: 0.8605 (tp) cc_final: 0.8404 (tt) REVERT: 4 811 MET cc_start: 0.7921 (ttp) cc_final: 0.7583 (ttp) REVERT: 5 198 ASN cc_start: 0.4733 (m-40) cc_final: 0.4312 (t0) REVERT: 5 498 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6821 (pt0) REVERT: 5 513 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8194 (pp) REVERT: 5 546 ILE cc_start: 0.7901 (mt) cc_final: 0.7634 (mp) REVERT: 5 561 ASN cc_start: 0.5414 (m-40) cc_final: 0.5158 (m110) REVERT: 6 191 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6347 (ttpt) REVERT: 6 320 ASN cc_start: 0.5797 (m-40) cc_final: 0.5535 (m-40) REVERT: 6 629 MET cc_start: 0.7520 (mtp) cc_final: 0.7261 (mtm) REVERT: 6 734 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7508 (tt) REVERT: 6 829 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6761 (m-30) REVERT: 7 152 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6821 (ttp-110) REVERT: 7 156 ASP cc_start: 0.6862 (m-30) cc_final: 0.6572 (m-30) REVERT: 7 167 MET cc_start: 0.3016 (OUTLIER) cc_final: 0.2325 (mtt) REVERT: 7 187 ASP cc_start: 0.5876 (t70) cc_final: 0.5499 (m-30) REVERT: 7 291 GLN cc_start: 0.7595 (mt0) cc_final: 0.7342 (mt0) REVERT: 7 448 MET cc_start: 0.6457 (mmp) cc_final: 0.6164 (ppp) REVERT: B 269 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.7015 (ptmt) REVERT: B 452 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: B 459 ARG cc_start: 0.5471 (mtp-110) cc_final: 0.5259 (mtp-110) REVERT: B 483 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5408 (tm-30) REVERT: B 488 SER cc_start: 0.7055 (p) cc_final: 0.6814 (p) REVERT: B 662 PRO cc_start: 0.6858 (Cg_endo) cc_final: 0.6596 (Cg_endo) REVERT: B 693 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.6053 (tm-30) REVERT: B 783 MET cc_start: 0.5437 (ttt) cc_final: 0.5153 (ttm) REVERT: C 263 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: C 286 THR cc_start: 0.7546 (p) cc_final: 0.7297 (p) REVERT: C 528 ASP cc_start: 0.4947 (OUTLIER) cc_final: 0.4738 (t70) REVERT: C 559 ARG cc_start: 0.5680 (tpp-160) cc_final: 0.5451 (mmt-90) REVERT: D 246 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6477 (tpm-80) REVERT: D 359 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6529 (mm-30) REVERT: D 366 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7384 (mt0) REVERT: D 500 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6709 (mp-120) REVERT: D 747 LEU cc_start: 0.8606 (tp) cc_final: 0.8391 (tt) REVERT: D 811 MET cc_start: 0.7863 (ttp) cc_final: 0.7642 (ttp) REVERT: E 370 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6419 (tp) REVERT: E 489 ASP cc_start: 0.7087 (m-30) cc_final: 0.6681 (m-30) REVERT: E 583 MET cc_start: 0.6092 (OUTLIER) cc_final: 0.5568 (tmm) REVERT: F 320 ASN cc_start: 0.5813 (m-40) cc_final: 0.5517 (m-40) REVERT: F 629 MET cc_start: 0.7524 (mtp) cc_final: 0.7273 (mtm) REVERT: G 156 ASP cc_start: 0.6933 (m-30) cc_final: 0.6622 (m-30) REVERT: G 448 MET cc_start: 0.6305 (mmp) cc_final: 0.6083 (ppp) outliers start: 179 outliers final: 54 residues processed: 886 average time/residue: 1.5598 time to fit residues: 1747.6856 Evaluate side-chains 804 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 722 time to evaluate : 5.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 434 TYR Chi-restraints excluded: chain 2 residue 483 GLU Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 3 residue 91 ILE Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 352 LYS Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 538 SER Chi-restraints excluded: chain 3 residue 731 ASN Chi-restraints excluded: chain 4 residue 189 GLU Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 342 MET Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 366 GLN Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 720 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 517 THR Chi-restraints excluded: chain 6 residue 191 LYS Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 152 ARG Chi-restraints excluded: chain 7 residue 167 MET Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 702 LEU Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 366 GLN Chi-restraints excluded: chain D residue 500 GLN Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 583 MET Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 624 GLU Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 506 MET Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 702 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 701 optimal weight: 9.9990 chunk 533 optimal weight: 4.9990 chunk 368 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 476 optimal weight: 1.9990 chunk 712 optimal weight: 0.0070 chunk 753 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 674 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 340 ASN 2 710 ASN 3 29 GLN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 365 GLN ** 3 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 4 483 GLN ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 685 GLN 6 156 GLN 6 182 GLN 6 335 ASN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 109 ASN 7 271 GLN 7 518 ASN B 340 ASN B 710 ASN C 29 GLN C 52 ASN C 239 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN C 487 HIS D 483 GLN E 359 GLN E 499 GLN E 524 ASN E 636 ASN E 685 GLN F 156 GLN F 182 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 786 GLN G 109 ASN G 159 ASN G 291 GLN G 518 ASN G 558 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 63442 Z= 0.373 Angle : 0.682 14.225 85856 Z= 0.354 Chirality : 0.048 0.326 9964 Planarity : 0.005 0.092 11040 Dihedral : 7.543 169.947 8832 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.56 % Allowed : 12.30 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.09), residues: 7788 helix: 1.09 (0.09), residues: 3194 sheet: 0.02 (0.13), residues: 1512 loop : -0.05 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 3 153 HIS 0.030 0.002 HIS 2 779 PHE 0.023 0.002 PHE E 3 TYR 0.024 0.002 TYR F 136 ARG 0.011 0.001 ARG 4 642 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 814 time to evaluate : 5.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 483 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5438 (tm-30) REVERT: 2 693 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5932 (tm-30) REVERT: 2 764 MET cc_start: 0.7632 (mtm) cc_final: 0.7220 (mtm) REVERT: 2 779 HIS cc_start: 0.4233 (OUTLIER) cc_final: 0.3913 (p90) REVERT: 2 850 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7117 (ptpt) REVERT: 3 657 ARG cc_start: 0.7419 (ptp90) cc_final: 0.7175 (mtp85) REVERT: 4 359 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6755 (mm-30) REVERT: 4 431 ASP cc_start: 0.8282 (p0) cc_final: 0.8040 (p0) REVERT: 4 608 ASP cc_start: 0.6981 (t70) cc_final: 0.6771 (t0) REVERT: 4 769 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: 5 65 MET cc_start: 0.7895 (mtp) cc_final: 0.7640 (mtm) REVERT: 5 104 LEU cc_start: 0.7617 (mt) cc_final: 0.7375 (mt) REVERT: 5 198 ASN cc_start: 0.5506 (m-40) cc_final: 0.4838 (t0) REVERT: 5 458 MET cc_start: 0.5440 (OUTLIER) cc_final: 0.5186 (mpt) REVERT: 5 498 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: 5 561 ASN cc_start: 0.5722 (m-40) cc_final: 0.5405 (m110) REVERT: 5 583 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5543 (tmm) REVERT: 5 608 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7549 (tp) REVERT: 5 628 THR cc_start: 0.6563 (p) cc_final: 0.6256 (t) REVERT: 5 679 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.5904 (tm-30) REVERT: 6 320 ASN cc_start: 0.5950 (m-40) cc_final: 0.5625 (m-40) REVERT: 6 421 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7541 (mm) REVERT: 6 652 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7287 (tt) REVERT: 6 659 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: 6 829 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: 7 23 ASP cc_start: 0.7714 (t70) cc_final: 0.7437 (t70) REVERT: 7 152 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6915 (ttp-110) REVERT: 7 156 ASP cc_start: 0.6979 (m-30) cc_final: 0.6646 (m-30) REVERT: 7 167 MET cc_start: 0.3404 (OUTLIER) cc_final: 0.2810 (mtt) REVERT: 7 441 ASP cc_start: 0.7481 (t70) cc_final: 0.7033 (p0) REVERT: 7 448 MET cc_start: 0.6528 (mmp) cc_final: 0.6180 (ppp) REVERT: 7 597 LEU cc_start: 0.8792 (tt) cc_final: 0.8404 (tp) REVERT: B 196 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5409 (pt0) REVERT: B 391 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8774 (pt0) REVERT: B 459 ARG cc_start: 0.5715 (mtp-110) cc_final: 0.5344 (mtp85) REVERT: B 483 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5409 (tm-30) REVERT: B 488 SER cc_start: 0.7055 (p) cc_final: 0.6822 (p) REVERT: B 850 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7007 (ptpt) REVERT: C 352 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6942 (ptpt) REVERT: C 474 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: C 559 ARG cc_start: 0.5929 (tpp-160) cc_final: 0.5629 (mtt-85) REVERT: D 359 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: D 366 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: D 431 ASP cc_start: 0.8289 (p0) cc_final: 0.8080 (p0) REVERT: D 608 ASP cc_start: 0.6898 (t0) cc_final: 0.6544 (t0) REVERT: E 489 ASP cc_start: 0.7144 (m-30) cc_final: 0.6747 (m-30) REVERT: E 583 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5462 (tmm) REVERT: E 608 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7509 (tp) REVERT: F 195 GLU cc_start: 0.4980 (OUTLIER) cc_final: 0.4640 (tm-30) REVERT: F 320 ASN cc_start: 0.5971 (m-40) cc_final: 0.5644 (m-40) REVERT: F 505 LEU cc_start: 0.6220 (mt) cc_final: 0.5939 (mp) REVERT: F 654 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6149 (mm-30) REVERT: F 702 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.7006 (t) REVERT: G 156 ASP cc_start: 0.6912 (m-30) cc_final: 0.6594 (m-30) REVERT: G 272 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7605 (mt-10) REVERT: G 448 MET cc_start: 0.6528 (mmp) cc_final: 0.6151 (ppp) outliers start: 248 outliers final: 113 residues processed: 960 average time/residue: 1.5418 time to fit residues: 1871.0238 Evaluate side-chains 876 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 734 time to evaluate : 5.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 321 THR Chi-restraints excluded: chain 2 residue 340 ASN Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 434 TYR Chi-restraints excluded: chain 2 residue 483 GLU Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 693 GLU Chi-restraints excluded: chain 2 residue 706 SER Chi-restraints excluded: chain 2 residue 710 ASN Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 800 THR Chi-restraints excluded: chain 2 residue 850 LYS Chi-restraints excluded: chain 3 residue 91 ILE Chi-restraints excluded: chain 3 residue 352 LYS Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 342 MET Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 489 LYS Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 720 LEU Chi-restraints excluded: chain 4 residue 726 ASN Chi-restraints excluded: chain 4 residue 769 GLU Chi-restraints excluded: chain 4 residue 849 LEU Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 361 SER Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 458 MET Chi-restraints excluded: chain 5 residue 470 VAL Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 5 residue 517 THR Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 5 residue 677 VAL Chi-restraints excluded: chain 5 residue 679 GLU Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 261 ARG Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 624 GLU Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 135 LYS Chi-restraints excluded: chain 7 residue 152 ARG Chi-restraints excluded: chain 7 residue 167 MET Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 418 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 850 LYS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 366 GLN Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 834 LYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 583 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 624 GLU Chi-restraints excluded: chain F residue 628 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 459 MET Chi-restraints excluded: chain G residue 506 MET Chi-restraints excluded: chain G residue 535 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 627 optimal weight: 0.5980 chunk 427 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 561 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 643 optimal weight: 2.9990 chunk 521 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 384 optimal weight: 4.9990 chunk 676 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 340 ASN 2 710 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 365 GLN 3 487 HIS 3 517 ASN 4 366 GLN 4 380 ASN 4 483 GLN 5 235 ASN ** 5 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 669 GLN B 340 ASN B 710 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN C 487 HIS C 517 ASN E 524 ASN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 ASN F 833 GLN G 291 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 63442 Z= 0.275 Angle : 0.611 12.987 85856 Z= 0.316 Chirality : 0.045 0.286 9964 Planarity : 0.005 0.069 11040 Dihedral : 7.369 166.683 8832 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.77 % Allowed : 13.98 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.09), residues: 7788 helix: 1.21 (0.09), residues: 3210 sheet: 0.08 (0.13), residues: 1486 loop : -0.05 (0.11), residues: 3092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 3 111 HIS 0.009 0.001 HIS E 560 PHE 0.018 0.002 PHE G 113 TYR 0.022 0.002 TYR F 136 ARG 0.008 0.001 ARG 4 642 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 772 time to evaluate : 5.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 425 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: 2 483 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.5415 (tm-30) REVERT: 2 693 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5976 (tm-30) REVERT: 2 777 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6393 (mtpt) REVERT: 2 779 HIS cc_start: 0.3981 (OUTLIER) cc_final: 0.3327 (p90) REVERT: 2 850 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7080 (ptpt) REVERT: 3 29 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: 3 97 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8388 (mm) REVERT: 3 306 MET cc_start: 0.7974 (mtp) cc_final: 0.7684 (mtm) REVERT: 4 178 ARG cc_start: 0.5854 (tpt170) cc_final: 0.5491 (tpt170) REVERT: 4 189 GLU cc_start: 0.7063 (tp30) cc_final: 0.6825 (mm-30) REVERT: 4 359 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6739 (mm-30) REVERT: 4 431 ASP cc_start: 0.8277 (p0) cc_final: 0.7980 (p0) REVERT: 4 715 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7070 (pttp) REVERT: 4 720 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8052 (tm) REVERT: 4 769 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: 5 65 MET cc_start: 0.7817 (mtp) cc_final: 0.7593 (mtm) REVERT: 5 104 LEU cc_start: 0.7612 (mt) cc_final: 0.7409 (mt) REVERT: 5 198 ASN cc_start: 0.5572 (m-40) cc_final: 0.4885 (t0) REVERT: 5 498 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6931 (pt0) REVERT: 5 608 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7593 (tp) REVERT: 5 628 THR cc_start: 0.6612 (p) cc_final: 0.6277 (t) REVERT: 6 320 ASN cc_start: 0.5992 (m-40) cc_final: 0.5657 (m-40) REVERT: 6 345 THR cc_start: 0.6338 (t) cc_final: 0.6073 (m) REVERT: 6 421 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7528 (mm) REVERT: 6 462 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.6055 (mp) REVERT: 6 652 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7178 (tt) REVERT: 6 659 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: 7 152 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6872 (ttp-110) REVERT: 7 156 ASP cc_start: 0.6966 (m-30) cc_final: 0.6643 (m-30) REVERT: 7 441 ASP cc_start: 0.7523 (t70) cc_final: 0.7024 (p0) REVERT: 7 448 MET cc_start: 0.6505 (mmp) cc_final: 0.6178 (ppp) REVERT: 7 597 LEU cc_start: 0.8780 (tt) cc_final: 0.8450 (tp) REVERT: B 196 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5384 (pt0) REVERT: B 391 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8764 (pt0) REVERT: B 452 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: B 459 ARG cc_start: 0.5731 (mtp-110) cc_final: 0.5476 (mtp85) REVERT: B 483 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5403 (tm-30) REVERT: B 488 SER cc_start: 0.7034 (p) cc_final: 0.6805 (p) REVERT: B 843 ASP cc_start: 0.6249 (m-30) cc_final: 0.6037 (m-30) REVERT: B 850 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6907 (ptpt) REVERT: C 29 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: C 97 ILE cc_start: 0.8821 (mm) cc_final: 0.8438 (mm) REVERT: C 306 MET cc_start: 0.7986 (mtp) cc_final: 0.7683 (mtm) REVERT: C 352 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6910 (ptpt) REVERT: C 474 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: C 559 ARG cc_start: 0.5978 (tpp-160) cc_final: 0.5689 (mtt-85) REVERT: C 703 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: D 314 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6543 (tpt) REVERT: D 359 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6730 (mm-30) REVERT: D 366 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7313 (mt0) REVERT: D 431 ASP cc_start: 0.8290 (p0) cc_final: 0.8001 (p0) REVERT: D 500 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6758 (mp-120) REVERT: D 608 ASP cc_start: 0.6846 (t0) cc_final: 0.6479 (t0) REVERT: E 139 LEU cc_start: 0.8297 (pp) cc_final: 0.7972 (pt) REVERT: E 489 ASP cc_start: 0.7023 (m-30) cc_final: 0.6671 (m-30) REVERT: E 513 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8295 (pp) REVERT: E 608 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7544 (tp) REVERT: F 116 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6116 (pt0) REVERT: F 195 GLU cc_start: 0.4836 (OUTLIER) cc_final: 0.4472 (tm-30) REVERT: F 320 ASN cc_start: 0.6075 (m-40) cc_final: 0.5715 (m-40) REVERT: F 462 ILE cc_start: 0.6240 (OUTLIER) cc_final: 0.6020 (mp) REVERT: F 505 LEU cc_start: 0.6202 (mt) cc_final: 0.5913 (mp) REVERT: F 657 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6245 (mt-10) REVERT: F 658 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.7017 (mm-40) REVERT: F 700 ASN cc_start: 0.6756 (OUTLIER) cc_final: 0.6327 (m110) REVERT: F 829 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: G 141 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8479 (t) REVERT: G 156 ASP cc_start: 0.6914 (m-30) cc_final: 0.6592 (m-30) REVERT: G 272 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7614 (mt-10) REVERT: G 448 MET cc_start: 0.6515 (mmp) cc_final: 0.6156 (ppp) REVERT: G 627 ASP cc_start: 0.5777 (m-30) cc_final: 0.5495 (m-30) outliers start: 262 outliers final: 127 residues processed: 936 average time/residue: 1.5387 time to fit residues: 1820.4243 Evaluate side-chains 895 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 726 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 340 ASN Chi-restraints excluded: chain 2 residue 425 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 434 TYR Chi-restraints excluded: chain 2 residue 483 GLU Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 693 GLU Chi-restraints excluded: chain 2 residue 706 SER Chi-restraints excluded: chain 2 residue 710 ASN Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 800 THR Chi-restraints excluded: chain 2 residue 850 LYS Chi-restraints excluded: chain 3 residue 29 GLN Chi-restraints excluded: chain 3 residue 91 ILE Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 352 LYS Chi-restraints excluded: chain 3 residue 402 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 538 SER Chi-restraints excluded: chain 3 residue 539 LEU Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 342 MET Chi-restraints excluded: chain 4 residue 356 MET Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 489 LYS Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 639 ASP Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 715 LYS Chi-restraints excluded: chain 4 residue 720 LEU Chi-restraints excluded: chain 4 residue 726 ASN Chi-restraints excluded: chain 4 residue 769 GLU Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 4 residue 849 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 470 VAL Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 593 GLU Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 5 residue 677 VAL Chi-restraints excluded: chain 6 residue 140 ILE Chi-restraints excluded: chain 6 residue 261 ARG Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 423 THR Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 152 ARG Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 418 ILE Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 702 LEU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 850 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 366 GLN Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 500 GLN Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 711 LYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 624 GLU Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 506 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 253 optimal weight: 0.9980 chunk 678 optimal weight: 0.9980 chunk 149 optimal weight: 0.3980 chunk 442 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 754 optimal weight: 1.9990 chunk 626 optimal weight: 2.9990 chunk 349 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 249 optimal weight: 7.9990 chunk 396 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 340 ASN 3 365 GLN 3 487 HIS 3 517 ASN 4 229 GLN ** 4 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 235 ASN 5 359 GLN 5 363 ASN ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 GLN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 518 ASN B 340 ASN B 710 ASN C 293 ASN C 365 GLN C 487 HIS C 493 GLN C 517 ASN E 43 GLN E 145 GLN E 524 ASN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 ASN F 833 GLN G 291 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 63442 Z= 0.184 Angle : 0.551 11.760 85856 Z= 0.284 Chirality : 0.043 0.241 9964 Planarity : 0.004 0.049 11040 Dihedral : 7.127 165.756 8832 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.28 % Allowed : 15.31 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.09), residues: 7788 helix: 1.46 (0.09), residues: 3214 sheet: 0.08 (0.13), residues: 1450 loop : 0.03 (0.11), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 111 HIS 0.010 0.001 HIS 6 653 PHE 0.022 0.001 PHE 6 142 TYR 0.018 0.001 TYR F 136 ARG 0.008 0.000 ARG 4 642 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 780 time to evaluate : 5.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 483 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5489 (tm-30) REVERT: 2 554 LYS cc_start: 0.7833 (mmtp) cc_final: 0.7471 (mmtt) REVERT: 2 693 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.6084 (tm-30) REVERT: 2 777 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6369 (mtpt) REVERT: 2 850 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6992 (ptpt) REVERT: 3 29 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: 3 97 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8226 (mm) REVERT: 3 656 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8198 (tp) REVERT: 4 189 GLU cc_start: 0.7027 (tp30) cc_final: 0.6809 (mm-30) REVERT: 4 359 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6624 (mm-30) REVERT: 4 720 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7996 (tm) REVERT: 4 732 LYS cc_start: 0.5257 (mmmm) cc_final: 0.5031 (mmmm) REVERT: 4 769 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: 5 65 MET cc_start: 0.7790 (mtp) cc_final: 0.7515 (mtm) REVERT: 5 198 ASN cc_start: 0.5378 (m-40) cc_final: 0.4755 (t0) REVERT: 5 249 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7962 (mptt) REVERT: 5 363 ASN cc_start: 0.6117 (t0) cc_final: 0.5834 (m-40) REVERT: 5 366 LEU cc_start: 0.6748 (tp) cc_final: 0.6282 (tm) REVERT: 5 498 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6896 (pt0) REVERT: 5 628 THR cc_start: 0.6513 (p) cc_final: 0.6280 (t) REVERT: 6 320 ASN cc_start: 0.5885 (m-40) cc_final: 0.5591 (m-40) REVERT: 6 345 THR cc_start: 0.6482 (t) cc_final: 0.6214 (m) REVERT: 6 421 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7464 (mm) REVERT: 6 462 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5972 (mp) REVERT: 6 652 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7105 (tt) REVERT: 6 658 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7021 (mm-40) REVERT: 6 659 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: 6 829 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6888 (m-30) REVERT: 7 152 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6874 (ttp-110) REVERT: 7 156 ASP cc_start: 0.6967 (m-30) cc_final: 0.6651 (m-30) REVERT: 7 287 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5895 (mm-30) REVERT: 7 441 ASP cc_start: 0.7354 (t70) cc_final: 0.6908 (p0) REVERT: 7 448 MET cc_start: 0.6507 (mmp) cc_final: 0.6200 (ppp) REVERT: B 196 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.5383 (pt0) REVERT: B 234 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7188 (tt) REVERT: B 425 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: B 452 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: B 483 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5381 (tm-30) REVERT: B 488 SER cc_start: 0.7112 (p) cc_final: 0.6902 (p) REVERT: B 843 ASP cc_start: 0.6215 (m-30) cc_final: 0.5982 (m-30) REVERT: B 850 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6904 (ptpt) REVERT: C 29 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: C 39 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6698 (tmm-80) REVERT: C 136 MET cc_start: 0.7597 (mtt) cc_final: 0.7306 (mtt) REVERT: C 352 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6851 (ptpt) REVERT: C 372 TYR cc_start: 0.7063 (t80) cc_final: 0.6722 (t80) REVERT: C 559 ARG cc_start: 0.5974 (tpp-160) cc_final: 0.5715 (mtt-85) REVERT: C 719 LYS cc_start: 0.7515 (mmmt) cc_final: 0.7142 (mmmt) REVERT: D 359 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6581 (mm-30) REVERT: D 608 ASP cc_start: 0.6694 (t0) cc_final: 0.6322 (t0) REVERT: D 732 LYS cc_start: 0.5317 (mmmm) cc_final: 0.5101 (mmmm) REVERT: E 249 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7963 (mptt) REVERT: E 489 ASP cc_start: 0.6928 (m-30) cc_final: 0.6661 (m-30) REVERT: E 513 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8256 (pp) REVERT: F 116 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.6035 (pt0) REVERT: F 320 ASN cc_start: 0.6015 (m-40) cc_final: 0.5699 (m-40) REVERT: F 505 LEU cc_start: 0.6197 (mt) cc_final: 0.5978 (mp) REVERT: F 657 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6201 (mt-10) REVERT: F 658 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6828 (mm-40) REVERT: G 127 LEU cc_start: 0.8116 (mt) cc_final: 0.7909 (tp) REVERT: G 156 ASP cc_start: 0.6934 (m-30) cc_final: 0.6605 (m-30) REVERT: G 272 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7648 (mt-10) REVERT: G 448 MET cc_start: 0.6484 (mmp) cc_final: 0.6170 (ppp) REVERT: G 498 MET cc_start: 0.4788 (mmp) cc_final: 0.4325 (ttt) REVERT: G 627 ASP cc_start: 0.5760 (m-30) cc_final: 0.5558 (m-30) outliers start: 228 outliers final: 100 residues processed: 930 average time/residue: 1.5937 time to fit residues: 1878.7401 Evaluate side-chains 865 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 730 time to evaluate : 5.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 340 ASN Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 434 TYR Chi-restraints excluded: chain 2 residue 483 GLU Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 693 GLU Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 798 ILE Chi-restraints excluded: chain 2 residue 850 LYS Chi-restraints excluded: chain 3 residue 29 GLN Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 352 LYS Chi-restraints excluded: chain 3 residue 402 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 538 SER Chi-restraints excluded: chain 3 residue 586 LEU Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 342 MET Chi-restraints excluded: chain 4 residue 356 MET Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 489 LYS Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 639 ASP Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 711 LYS Chi-restraints excluded: chain 4 residue 720 LEU Chi-restraints excluded: chain 4 residue 726 ASN Chi-restraints excluded: chain 4 residue 769 GLU Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 4 residue 849 LEU Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 249 LYS Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 5 residue 677 VAL Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 423 THR Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 658 GLN Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 152 ARG Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 287 GLU Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 702 LEU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 850 LYS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 593 GLU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 624 GLU Chi-restraints excluded: chain F residue 653 HIS Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 506 MET Chi-restraints excluded: chain G residue 702 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 727 optimal weight: 0.9980 chunk 85 optimal weight: 0.0980 chunk 429 optimal weight: 1.9990 chunk 551 optimal weight: 0.5980 chunk 427 optimal weight: 0.9980 chunk 635 optimal weight: 0.9990 chunk 421 optimal weight: 5.9990 chunk 751 optimal weight: 6.9990 chunk 470 optimal weight: 1.9990 chunk 458 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 340 ASN 3 487 HIS 3 517 ASN 4 229 GLN 4 366 GLN 5 235 ASN ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 GLN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN B 626 GLN B 710 ASN B 856 GLN C 365 GLN C 487 HIS C 517 ASN E 43 GLN E 524 ASN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 833 GLN G 291 GLN G 669 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 63442 Z= 0.182 Angle : 0.547 12.071 85856 Z= 0.281 Chirality : 0.043 0.232 9964 Planarity : 0.004 0.052 11040 Dihedral : 7.021 165.042 8832 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.28 % Allowed : 15.74 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.09), residues: 7788 helix: 1.56 (0.09), residues: 3214 sheet: 0.08 (0.13), residues: 1450 loop : 0.07 (0.11), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 111 HIS 0.011 0.001 HIS 6 653 PHE 0.014 0.001 PHE G 113 TYR 0.016 0.001 TYR 6 136 ARG 0.008 0.000 ARG 4 642 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 759 time to evaluate : 5.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 483 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5521 (tm-30) REVERT: 2 554 LYS cc_start: 0.7829 (mmtp) cc_final: 0.7530 (mmtt) REVERT: 2 693 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6065 (tm-30) REVERT: 2 777 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6358 (mtpt) REVERT: 2 779 HIS cc_start: 0.3735 (OUTLIER) cc_final: 0.3468 (p-80) REVERT: 2 784 ASP cc_start: 0.6161 (OUTLIER) cc_final: 0.5829 (p0) REVERT: 2 850 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6998 (ptpt) REVERT: 3 29 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: 3 97 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8190 (mm) REVERT: 3 352 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6865 (ptpt) REVERT: 3 372 TYR cc_start: 0.7030 (t80) cc_final: 0.6734 (t80) REVERT: 3 657 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.7207 (mtp-110) REVERT: 4 189 GLU cc_start: 0.7015 (tp30) cc_final: 0.6808 (mm-30) REVERT: 4 359 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6611 (mm-30) REVERT: 4 732 LYS cc_start: 0.5324 (mmmm) cc_final: 0.5122 (mmmm) REVERT: 4 769 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: 5 65 MET cc_start: 0.7766 (mtp) cc_final: 0.7540 (mtm) REVERT: 5 198 ASN cc_start: 0.5382 (m-40) cc_final: 0.4756 (t0) REVERT: 5 249 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7971 (mptt) REVERT: 5 366 LEU cc_start: 0.6745 (tp) cc_final: 0.6252 (tm) REVERT: 5 498 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6848 (pt0) REVERT: 5 583 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5466 (tmm) REVERT: 6 320 ASN cc_start: 0.5929 (m-40) cc_final: 0.5621 (m-40) REVERT: 6 421 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7467 (mm) REVERT: 6 462 ILE cc_start: 0.6243 (OUTLIER) cc_final: 0.5987 (mp) REVERT: 6 652 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7165 (tt) REVERT: 6 658 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6912 (mm-40) REVERT: 6 829 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6280 (m-30) REVERT: 6 833 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.5891 (mp-120) REVERT: 7 16 ASN cc_start: 0.7606 (p0) cc_final: 0.7402 (m110) REVERT: 7 152 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6870 (ttp-110) REVERT: 7 156 ASP cc_start: 0.6986 (m-30) cc_final: 0.6695 (m-30) REVERT: 7 287 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5844 (mm-30) REVERT: 7 441 ASP cc_start: 0.7187 (t70) cc_final: 0.6626 (p0) REVERT: 7 475 LYS cc_start: 0.7752 (tttp) cc_final: 0.7181 (mtmm) REVERT: B 196 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.5317 (pt0) REVERT: B 391 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: B 452 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: B 483 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5370 (tm-30) REVERT: B 488 SER cc_start: 0.7094 (p) cc_final: 0.6869 (p) REVERT: B 850 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6863 (ptpt) REVERT: B 859 ARG cc_start: 0.5542 (mtt180) cc_final: 0.5215 (mtt180) REVERT: C 29 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: C 39 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6687 (tmm-80) REVERT: C 97 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8176 (mm) REVERT: C 136 MET cc_start: 0.7668 (mtt) cc_final: 0.7411 (mtt) REVERT: C 352 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6838 (ptpt) REVERT: C 372 TYR cc_start: 0.7063 (t80) cc_final: 0.6707 (t80) REVERT: C 559 ARG cc_start: 0.5982 (tpp-160) cc_final: 0.5714 (mtt-85) REVERT: C 580 GLU cc_start: 0.5759 (tp30) cc_final: 0.5391 (tp30) REVERT: D 359 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6593 (mm-30) REVERT: D 608 ASP cc_start: 0.6534 (t0) cc_final: 0.6146 (t0) REVERT: D 711 LYS cc_start: 0.6756 (mmmm) cc_final: 0.6391 (tptm) REVERT: D 714 GLU cc_start: 0.5884 (mm-30) cc_final: 0.5618 (tp30) REVERT: E 489 ASP cc_start: 0.6917 (m-30) cc_final: 0.6652 (m-30) REVERT: E 513 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8267 (pp) REVERT: F 116 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.6037 (pt0) REVERT: F 320 ASN cc_start: 0.5953 (m-40) cc_final: 0.5632 (m-40) REVERT: F 462 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.6104 (mp) REVERT: F 505 LEU cc_start: 0.6197 (mt) cc_final: 0.5984 (mp) REVERT: F 657 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6325 (mt-10) REVERT: F 658 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6854 (mm-40) REVERT: F 829 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6882 (m-30) REVERT: G 16 ASN cc_start: 0.7625 (p0) cc_final: 0.7423 (m110) REVERT: G 127 LEU cc_start: 0.8106 (mt) cc_final: 0.7894 (tp) REVERT: G 156 ASP cc_start: 0.6933 (m-30) cc_final: 0.6608 (m-30) REVERT: G 272 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7643 (mt-10) REVERT: G 398 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: G 448 MET cc_start: 0.6482 (mmp) cc_final: 0.6180 (ppp) REVERT: G 498 MET cc_start: 0.4677 (mmp) cc_final: 0.4292 (ttt) outliers start: 228 outliers final: 101 residues processed: 908 average time/residue: 1.5766 time to fit residues: 1803.4224 Evaluate side-chains 850 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 710 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 340 ASN Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 434 TYR Chi-restraints excluded: chain 2 residue 483 GLU Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 693 GLU Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 850 LYS Chi-restraints excluded: chain 3 residue 29 GLN Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 352 LYS Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 538 SER Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 586 LEU Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 342 MET Chi-restraints excluded: chain 4 residue 356 MET Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 489 LYS Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 639 ASP Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 726 ASN Chi-restraints excluded: chain 4 residue 769 GLU Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 4 residue 849 LEU Chi-restraints excluded: chain 5 residue 105 SER Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 249 LYS Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 677 VAL Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 423 THR Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 658 GLN Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 152 ARG Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 287 GLU Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 702 LEU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 850 LYS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 624 GLU Chi-restraints excluded: chain F residue 628 LEU Chi-restraints excluded: chain F residue 653 HIS Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 398 GLU Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 702 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 465 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 449 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 477 optimal weight: 0.0050 chunk 512 optimal weight: 0.6980 chunk 371 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 590 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 340 ASN 3 487 HIS 3 517 ASN 5 235 ASN 5 363 ASN ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 GLN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 365 GLN C 487 HIS C 517 ASN E 43 GLN E 524 ASN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN G 518 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 63442 Z= 0.198 Angle : 0.553 12.224 85856 Z= 0.284 Chirality : 0.043 0.242 9964 Planarity : 0.004 0.062 11040 Dihedral : 7.007 164.032 8832 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.85 % Allowed : 16.59 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.09), residues: 7788 helix: 1.59 (0.09), residues: 3206 sheet: 0.07 (0.13), residues: 1470 loop : 0.08 (0.11), residues: 3112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 111 HIS 0.011 0.001 HIS 6 653 PHE 0.024 0.001 PHE 6 142 TYR 0.019 0.001 TYR 6 136 ARG 0.008 0.000 ARG 2 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 732 time to evaluate : 5.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 483 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5527 (tm-30) REVERT: 2 554 LYS cc_start: 0.7828 (mmtp) cc_final: 0.7528 (mmtt) REVERT: 2 693 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6066 (tm-30) REVERT: 2 777 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6365 (mtpt) REVERT: 2 779 HIS cc_start: 0.3715 (OUTLIER) cc_final: 0.3478 (p-80) REVERT: 2 850 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7012 (ptpt) REVERT: 2 851 VAL cc_start: 0.7601 (p) cc_final: 0.7164 (m) REVERT: 3 29 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: 3 97 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8213 (mm) REVERT: 3 352 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7033 (ptpt) REVERT: 3 372 TYR cc_start: 0.7045 (t80) cc_final: 0.6742 (t80) REVERT: 3 657 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7154 (mtp-110) REVERT: 4 189 GLU cc_start: 0.7019 (tp30) cc_final: 0.6805 (mm-30) REVERT: 4 359 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6612 (mm-30) REVERT: 4 769 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: 5 65 MET cc_start: 0.7770 (mtp) cc_final: 0.7536 (mtm) REVERT: 5 198 ASN cc_start: 0.5539 (m-40) cc_final: 0.4857 (t0) REVERT: 5 249 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7942 (mptt) REVERT: 5 366 LEU cc_start: 0.6752 (tp) cc_final: 0.6262 (tm) REVERT: 5 498 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6841 (pt0) REVERT: 5 583 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5434 (tmm) REVERT: 5 617 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.7043 (mm-40) REVERT: 5 679 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6169 (tm-30) REVERT: 6 320 ASN cc_start: 0.5931 (m-40) cc_final: 0.5618 (m-40) REVERT: 6 421 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7472 (mm) REVERT: 6 462 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.5970 (mp) REVERT: 6 652 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7161 (tt) REVERT: 6 829 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6283 (m-30) REVERT: 6 833 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.5905 (mp-120) REVERT: 7 152 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6872 (ttp-110) REVERT: 7 156 ASP cc_start: 0.6999 (m-30) cc_final: 0.6702 (m-30) REVERT: 7 287 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5833 (mm-30) REVERT: 7 475 LYS cc_start: 0.7867 (tttp) cc_final: 0.7290 (mtmm) REVERT: B 196 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5317 (pt0) REVERT: B 234 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7170 (tt) REVERT: B 391 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8726 (pt0) REVERT: B 452 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: B 483 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5868 (tp30) REVERT: B 488 SER cc_start: 0.7040 (p) cc_final: 0.6822 (p) REVERT: B 783 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.5267 (ttm) REVERT: B 850 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6891 (ptpt) REVERT: B 859 ARG cc_start: 0.5572 (mtt180) cc_final: 0.5211 (mtt180) REVERT: C 29 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: C 39 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6718 (tmm-80) REVERT: C 97 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8218 (mm) REVERT: C 136 MET cc_start: 0.7632 (mtt) cc_final: 0.7365 (mtt) REVERT: C 352 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6828 (ptpt) REVERT: C 372 TYR cc_start: 0.7066 (t80) cc_final: 0.6713 (t80) REVERT: C 478 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.5874 (tpt) REVERT: C 559 ARG cc_start: 0.5980 (tpp-160) cc_final: 0.5690 (mtt-85) REVERT: C 580 GLU cc_start: 0.5805 (tp30) cc_final: 0.5405 (tp30) REVERT: D 359 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6607 (mm-30) REVERT: D 608 ASP cc_start: 0.6405 (t0) cc_final: 0.6013 (t0) REVERT: D 714 GLU cc_start: 0.5970 (mm-30) cc_final: 0.5631 (tp30) REVERT: E 399 ILE cc_start: 0.7966 (mm) cc_final: 0.7243 (mm) REVERT: E 489 ASP cc_start: 0.6909 (m-30) cc_final: 0.6648 (m-30) REVERT: E 513 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8267 (pp) REVERT: F 116 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.6036 (pt0) REVERT: F 320 ASN cc_start: 0.5961 (m-40) cc_final: 0.5633 (m-40) REVERT: F 462 ILE cc_start: 0.6369 (OUTLIER) cc_final: 0.6119 (mp) REVERT: F 505 LEU cc_start: 0.6194 (mt) cc_final: 0.5990 (mp) REVERT: F 657 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6374 (mt-10) REVERT: F 658 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6839 (mm-40) REVERT: F 829 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: G 127 LEU cc_start: 0.8126 (mt) cc_final: 0.7902 (tp) REVERT: G 156 ASP cc_start: 0.6935 (m-30) cc_final: 0.6612 (m-30) REVERT: G 272 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7646 (mt-10) REVERT: G 398 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: G 448 MET cc_start: 0.6484 (mmp) cc_final: 0.6173 (ppp) REVERT: G 459 MET cc_start: 0.7665 (ttm) cc_final: 0.7456 (ttp) REVERT: G 498 MET cc_start: 0.4701 (mmp) cc_final: 0.4344 (ttt) outliers start: 198 outliers final: 106 residues processed: 867 average time/residue: 1.5665 time to fit residues: 1714.7741 Evaluate side-chains 857 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 709 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 340 ASN Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 434 TYR Chi-restraints excluded: chain 2 residue 483 GLU Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 693 GLU Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 850 LYS Chi-restraints excluded: chain 3 residue 29 GLN Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 352 LYS Chi-restraints excluded: chain 3 residue 402 ASP Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 538 SER Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 586 LEU Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 342 MET Chi-restraints excluded: chain 4 residue 356 MET Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 489 LYS Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 639 ASP Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 726 ASN Chi-restraints excluded: chain 4 residue 769 GLU Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 4 residue 849 LEU Chi-restraints excluded: chain 5 residue 105 SER Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 249 LYS Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 5 residue 517 THR Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 617 GLN Chi-restraints excluded: chain 5 residue 677 VAL Chi-restraints excluded: chain 5 residue 679 GLU Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 345 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 423 THR Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 6 residue 773 LEU Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 152 ARG Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 287 GLU Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 702 LEU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 850 LYS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 624 GLU Chi-restraints excluded: chain F residue 628 LEU Chi-restraints excluded: chain F residue 653 HIS Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 398 GLU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 702 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 683 optimal weight: 2.9990 chunk 720 optimal weight: 0.9990 chunk 657 optimal weight: 3.9990 chunk 700 optimal weight: 6.9990 chunk 421 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 550 optimal weight: 0.2980 chunk 214 optimal weight: 1.9990 chunk 633 optimal weight: 8.9990 chunk 662 optimal weight: 0.0040 chunk 698 optimal weight: 0.6980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 340 ASN 3 487 HIS 3 517 ASN ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 145 GLN ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 GLN 6 156 GLN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 316 GLN 7 518 ASN B 282 HIS B 340 ASN B 856 GLN C 487 HIS C 517 ASN E 43 GLN E 524 ASN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 ASN G 291 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 63442 Z= 0.184 Angle : 0.548 12.324 85856 Z= 0.281 Chirality : 0.043 0.234 9964 Planarity : 0.004 0.081 11040 Dihedral : 6.959 163.677 8830 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.76 % Allowed : 16.92 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.09), residues: 7788 helix: 1.63 (0.09), residues: 3208 sheet: 0.08 (0.13), residues: 1470 loop : 0.08 (0.11), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.011 0.001 HIS 6 653 PHE 0.020 0.001 PHE F 142 TYR 0.018 0.001 TYR 6 136 ARG 0.011 0.000 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 727 time to evaluate : 5.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 483 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5327 (tm-30) REVERT: 2 554 LYS cc_start: 0.7818 (mmtp) cc_final: 0.7525 (mmtt) REVERT: 2 592 GLU cc_start: 0.7478 (mp0) cc_final: 0.7248 (mp0) REVERT: 2 693 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.6055 (tm-30) REVERT: 2 777 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6361 (mtpt) REVERT: 2 781 MET cc_start: 0.4360 (pmm) cc_final: 0.3865 (pmt) REVERT: 2 850 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.6996 (ptpt) REVERT: 2 851 VAL cc_start: 0.7574 (p) cc_final: 0.7159 (m) REVERT: 3 29 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: 3 97 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8193 (mm) REVERT: 3 352 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6937 (ptpt) REVERT: 3 372 TYR cc_start: 0.7057 (t80) cc_final: 0.6732 (t80) REVERT: 3 657 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.7056 (mtp-110) REVERT: 4 189 GLU cc_start: 0.7014 (tp30) cc_final: 0.6804 (mm-30) REVERT: 4 359 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6590 (mm-30) REVERT: 4 769 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: 5 65 MET cc_start: 0.7750 (mtp) cc_final: 0.7514 (mtm) REVERT: 5 198 ASN cc_start: 0.5605 (m-40) cc_final: 0.4897 (t0) REVERT: 5 249 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7936 (mptt) REVERT: 5 366 LEU cc_start: 0.6733 (tp) cc_final: 0.6258 (tm) REVERT: 5 498 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6855 (pt0) REVERT: 5 583 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5427 (tmm) REVERT: 5 646 ILE cc_start: 0.5691 (OUTLIER) cc_final: 0.5395 (mp) REVERT: 5 679 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6171 (tm-30) REVERT: 6 282 GLU cc_start: 0.7587 (pm20) cc_final: 0.7131 (pm20) REVERT: 6 320 ASN cc_start: 0.5932 (m-40) cc_final: 0.5616 (m-40) REVERT: 6 421 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7478 (mm) REVERT: 6 462 ILE cc_start: 0.6243 (OUTLIER) cc_final: 0.5988 (mp) REVERT: 6 624 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6486 (pp20) REVERT: 6 652 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7150 (tt) REVERT: 6 829 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6279 (m-30) REVERT: 6 833 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.5888 (mp-120) REVERT: 7 127 LEU cc_start: 0.8117 (mt) cc_final: 0.7902 (tp) REVERT: 7 152 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6893 (ttp-110) REVERT: 7 156 ASP cc_start: 0.7005 (m-30) cc_final: 0.6695 (m-30) REVERT: 7 287 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5822 (mm-30) REVERT: 7 398 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: 7 475 LYS cc_start: 0.7847 (tttp) cc_final: 0.7283 (mtmm) REVERT: B 196 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.5314 (pt0) REVERT: B 234 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7208 (tp) REVERT: B 391 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8722 (pt0) REVERT: B 452 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: B 483 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5863 (tp30) REVERT: B 488 SER cc_start: 0.7070 (p) cc_final: 0.6850 (p) REVERT: B 783 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.5264 (ttm) REVERT: B 850 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6884 (ptpt) REVERT: B 859 ARG cc_start: 0.5553 (mtt180) cc_final: 0.5182 (mtt180) REVERT: C 29 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: C 39 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6669 (tmm-80) REVERT: C 97 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8175 (mm) REVERT: C 136 MET cc_start: 0.7696 (mtt) cc_final: 0.7409 (mtt) REVERT: C 352 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6816 (ptpt) REVERT: C 372 TYR cc_start: 0.7063 (t80) cc_final: 0.6732 (t80) REVERT: C 474 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7404 (mt-10) REVERT: C 478 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.5892 (tpt) REVERT: C 559 ARG cc_start: 0.5954 (tpp-160) cc_final: 0.5674 (mtt-85) REVERT: C 580 GLU cc_start: 0.5821 (tp30) cc_final: 0.5397 (tp30) REVERT: C 703 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7019 (mm-30) REVERT: D 359 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6564 (mm-30) REVERT: D 714 GLU cc_start: 0.5905 (mm-30) cc_final: 0.5578 (tp30) REVERT: E 399 ILE cc_start: 0.7972 (mm) cc_final: 0.7256 (mm) REVERT: E 489 ASP cc_start: 0.6904 (m-30) cc_final: 0.6659 (m-30) REVERT: E 513 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8268 (pp) REVERT: E 646 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5397 (mp) REVERT: F 116 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6061 (pt0) REVERT: F 320 ASN cc_start: 0.5928 (m-40) cc_final: 0.5597 (m-40) REVERT: F 462 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.6114 (mp) REVERT: F 657 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6337 (mt-10) REVERT: F 658 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6817 (mm-40) REVERT: F 829 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: G 127 LEU cc_start: 0.8120 (mt) cc_final: 0.7905 (tp) REVERT: G 156 ASP cc_start: 0.6938 (m-30) cc_final: 0.6615 (m-30) REVERT: G 272 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7629 (mt-10) REVERT: G 398 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: G 448 MET cc_start: 0.6475 (mmp) cc_final: 0.6172 (ppp) REVERT: G 459 MET cc_start: 0.7704 (ttm) cc_final: 0.7485 (ttp) REVERT: G 498 MET cc_start: 0.4611 (mmp) cc_final: 0.4257 (ttt) outliers start: 192 outliers final: 101 residues processed: 857 average time/residue: 1.5810 time to fit residues: 1713.8886 Evaluate side-chains 854 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 708 time to evaluate : 5.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 483 GLU Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 693 GLU Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 850 LYS Chi-restraints excluded: chain 3 residue 29 GLN Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 352 LYS Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 538 SER Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 586 LEU Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 342 MET Chi-restraints excluded: chain 4 residue 356 MET Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 489 LYS Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 639 ASP Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 726 ASN Chi-restraints excluded: chain 4 residue 769 GLU Chi-restraints excluded: chain 5 residue 105 SER Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 249 LYS Chi-restraints excluded: chain 5 residue 361 SER Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 5 residue 517 THR Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 646 ILE Chi-restraints excluded: chain 5 residue 677 VAL Chi-restraints excluded: chain 5 residue 679 GLU Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 345 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 423 THR Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 624 GLU Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 773 LEU Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 152 ARG Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 287 GLU Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 398 GLU Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 702 LEU Chi-restraints excluded: chain 7 residue 714 GLU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 850 LYS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 624 GLU Chi-restraints excluded: chain F residue 628 LEU Chi-restraints excluded: chain F residue 653 HIS Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 398 GLU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 702 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 460 optimal weight: 4.9990 chunk 740 optimal weight: 1.9990 chunk 452 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 chunk 514 optimal weight: 0.3980 chunk 777 optimal weight: 1.9990 chunk 715 optimal weight: 0.5980 chunk 618 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 477 optimal weight: 1.9990 chunk 379 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 779 HIS 3 487 HIS 3 517 ASN 5 145 GLN ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 636 ASN 6 156 GLN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 856 GLN C 487 HIS C 517 ASN E 43 GLN E 145 GLN E 524 ASN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 ASN G 291 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 63442 Z= 0.225 Angle : 0.576 12.471 85856 Z= 0.296 Chirality : 0.044 0.264 9964 Planarity : 0.004 0.074 11040 Dihedral : 7.041 163.466 8830 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.57 % Allowed : 17.19 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.09), residues: 7788 helix: 1.57 (0.09), residues: 3204 sheet: 0.03 (0.13), residues: 1472 loop : 0.03 (0.11), residues: 3112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 2 589 HIS 0.010 0.001 HIS 6 653 PHE 0.026 0.002 PHE 6 142 TYR 0.019 0.002 TYR 6 136 ARG 0.010 0.000 ARG F 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 715 time to evaluate : 5.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 483 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5329 (tm-30) REVERT: 2 554 LYS cc_start: 0.7816 (mmtp) cc_final: 0.7529 (mmtt) REVERT: 2 693 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.6039 (tm-30) REVERT: 2 850 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6978 (ptpt) REVERT: 2 851 VAL cc_start: 0.7620 (p) cc_final: 0.7174 (m) REVERT: 3 29 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: 3 97 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8312 (mm) REVERT: 3 522 GLN cc_start: 0.7463 (mt0) cc_final: 0.7069 (mt0) REVERT: 3 657 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7145 (mtp-110) REVERT: 4 189 GLU cc_start: 0.7036 (tp30) cc_final: 0.6822 (mm-30) REVERT: 4 359 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6675 (mm-30) REVERT: 4 769 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: 5 65 MET cc_start: 0.7788 (mtp) cc_final: 0.7490 (mtm) REVERT: 5 198 ASN cc_start: 0.5654 (m-40) cc_final: 0.4906 (t0) REVERT: 5 209 ARG cc_start: 0.7409 (mpt180) cc_final: 0.7097 (mmt180) REVERT: 5 249 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7964 (mptt) REVERT: 5 498 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: 5 627 VAL cc_start: 0.7747 (t) cc_final: 0.7477 (t) REVERT: 5 646 ILE cc_start: 0.5901 (OUTLIER) cc_final: 0.5644 (mp) REVERT: 5 679 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6189 (tm-30) REVERT: 6 320 ASN cc_start: 0.5975 (m-40) cc_final: 0.5654 (m-40) REVERT: 6 421 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7448 (mm) REVERT: 6 462 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.6002 (mp) REVERT: 6 624 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6515 (pp20) REVERT: 6 652 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7195 (tt) REVERT: 6 829 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6903 (m-30) REVERT: 7 152 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6889 (ttp-110) REVERT: 7 156 ASP cc_start: 0.7010 (m-30) cc_final: 0.6724 (m-30) REVERT: 7 398 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: B 196 GLU cc_start: 0.5706 (OUTLIER) cc_final: 0.5324 (pt0) REVERT: B 234 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7175 (tt) REVERT: B 391 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: B 452 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: B 483 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5835 (tp30) REVERT: B 488 SER cc_start: 0.7017 (p) cc_final: 0.6798 (p) REVERT: B 783 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.5248 (ttm) REVERT: B 850 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6898 (ptpt) REVERT: C 29 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: C 39 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6736 (tmm-80) REVERT: C 97 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8257 (mm) REVERT: C 136 MET cc_start: 0.7647 (mtt) cc_final: 0.7360 (mtt) REVERT: C 352 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6926 (ptpt) REVERT: C 372 TYR cc_start: 0.7037 (t80) cc_final: 0.6719 (t80) REVERT: C 474 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7350 (mt-10) REVERT: C 559 ARG cc_start: 0.5939 (tpp-160) cc_final: 0.5635 (mtt-85) REVERT: C 703 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: D 359 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6653 (mm-30) REVERT: D 442 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8415 (pp) REVERT: E 139 LEU cc_start: 0.8421 (pp) cc_final: 0.8087 (pt) REVERT: E 399 ILE cc_start: 0.7957 (mm) cc_final: 0.7243 (mm) REVERT: E 489 ASP cc_start: 0.7032 (m-30) cc_final: 0.6785 (m-30) REVERT: E 513 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8284 (pp) REVERT: E 646 ILE cc_start: 0.5909 (OUTLIER) cc_final: 0.5607 (mp) REVERT: F 116 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6082 (pt0) REVERT: F 140 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7792 (mt) REVERT: F 320 ASN cc_start: 0.5946 (m-40) cc_final: 0.5610 (m-40) REVERT: F 462 ILE cc_start: 0.6381 (OUTLIER) cc_final: 0.6098 (mp) REVERT: F 657 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6399 (mt-10) REVERT: F 658 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6898 (mm-40) REVERT: F 829 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: G 127 LEU cc_start: 0.8137 (mt) cc_final: 0.7907 (tp) REVERT: G 156 ASP cc_start: 0.6919 (m-30) cc_final: 0.6599 (m-30) REVERT: G 272 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7627 (mt-10) REVERT: G 398 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: G 448 MET cc_start: 0.6501 (mmp) cc_final: 0.6189 (ppp) REVERT: G 498 MET cc_start: 0.4699 (mmp) cc_final: 0.4339 (ttt) outliers start: 179 outliers final: 104 residues processed: 841 average time/residue: 1.5879 time to fit residues: 1690.0605 Evaluate side-chains 848 residues out of total 6964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 703 time to evaluate : 5.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 483 GLU Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 693 GLU Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 850 LYS Chi-restraints excluded: chain 3 residue 29 GLN Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 538 SER Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 342 MET Chi-restraints excluded: chain 4 residue 356 MET Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 489 LYS Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 639 ASP Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 726 ASN Chi-restraints excluded: chain 4 residue 769 GLU Chi-restraints excluded: chain 4 residue 849 LEU Chi-restraints excluded: chain 5 residue 105 SER Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 249 LYS Chi-restraints excluded: chain 5 residue 361 SER Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 5 residue 517 THR Chi-restraints excluded: chain 5 residue 646 ILE Chi-restraints excluded: chain 5 residue 677 VAL Chi-restraints excluded: chain 5 residue 679 GLU Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 345 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 423 THR Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 624 GLU Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 773 LEU Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 152 ARG Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 398 GLU Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 702 LEU Chi-restraints excluded: chain 7 residue 714 GLU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 850 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 624 GLU Chi-restraints excluded: chain F residue 628 LEU Chi-restraints excluded: chain F residue 653 HIS Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 398 GLU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 702 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 491 optimal weight: 0.5980 chunk 659 optimal weight: 0.0870 chunk 189 optimal weight: 0.9990 chunk 570 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 619 optimal weight: 2.9990 chunk 259 optimal weight: 0.0470 chunk 636 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 293 ASN 3 487 HIS 3 517 ASN 4 483 GLN ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 GLN 6 156 GLN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 703 HIS B 856 GLN C 487 HIS ** D 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN E 145 GLN E 524 ASN E 617 GLN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 ASN G 112 HIS G 291 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138982 restraints weight = 65834.977| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.61 r_work: 0.3428 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 63442 Z= 0.156 Angle : 0.532 12.482 85856 Z= 0.272 Chirality : 0.042 0.211 9964 Planarity : 0.004 0.054 11040 Dihedral : 6.811 162.740 8830 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.01 % Allowed : 17.84 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.09), residues: 7788 helix: 1.73 (0.09), residues: 3210 sheet: 0.07 (0.13), residues: 1470 loop : 0.12 (0.11), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 111 HIS 0.012 0.001 HIS 6 653 PHE 0.027 0.001 PHE F 142 TYR 0.017 0.001 TYR 6 136 ARG 0.015 0.000 ARG G 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24213.78 seconds wall clock time: 419 minutes 13.80 seconds (25153.80 seconds total)