Starting phenix.real_space_refine on Mon Dec 30 03:18:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aod_11841/12_2024/7aod_11841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aod_11841/12_2024/7aod_11841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aod_11841/12_2024/7aod_11841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aod_11841/12_2024/7aod_11841.map" model { file = "/net/cci-nas-00/data/ceres_data/7aod_11841/12_2024/7aod_11841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aod_11841/12_2024/7aod_11841.cif" } resolution = 4.5 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 Anisotropic ADP refinement not supported. Converting 1140 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 12 6.06 5 S 328 5.16 5 C 37608 2.51 5 N 10240 2.21 5 O 11068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 449 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 59256 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 10976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1384, 10976 Classifications: {'peptide': 1384} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1317} Chain breaks: 13 Chain: "B" Number of atoms: 9127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9127 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 59, 'TRANS': 1096} Chain breaks: 3 Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1663 Classifications: {'peptide': 207} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 195} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1267 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "J" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "L" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 368 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 10976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1384, 10976 Classifications: {'peptide': 1384} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1317} Chain breaks: 13 Chain: "N" Number of atoms: 9127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9127 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 59, 'TRANS': 1096} Chain breaks: 3 Chain: "O" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "P" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "Q" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1663 Classifications: {'peptide': 207} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 195} Chain: "R" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "S" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1267 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Chain: "T" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "U" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "V" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "W" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "X" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 368 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 483 SG CYS A 63 133.861 103.007 104.136 1.00110.95 S ATOM 501 SG CYS A 66 133.326 105.104 100.919 1.00122.56 S ATOM 565 SG CYS A 73 135.418 103.713 101.118 1.00 95.95 S ATOM 809 SG CYS A 103 175.060 113.810 131.338 1.00150.16 S ATOM 1540 SG CYS A 228 176.932 114.201 131.408 1.00162.65 S ATOM 1562 SG CYS A 231 175.736 116.570 134.919 1.00164.31 S ATOM 19527 SG CYS B1089 144.383 118.948 102.596 1.00114.91 S ATOM 19552 SG CYS B1092 145.828 117.220 103.855 1.00115.80 S ATOM 19708 SG CYS B1115 142.861 116.676 104.612 1.00104.03 S ATOM 27567 SG CYS I 10 214.344 46.920 128.526 1.00178.72 S ATOM 27588 SG CYS I 13 211.550 48.141 129.609 1.00194.95 S ATOM 27693 SG CYS I 27 213.434 49.132 131.602 1.00217.33 S ATOM 27716 SG CYS I 30 212.662 47.936 131.051 1.00214.77 S ATOM 28015 SG CYS J 7 154.125 56.517 48.098 1.00 84.28 S ATOM 28038 SG CYS J 10 156.893 56.951 44.991 1.00106.53 S ATOM 28310 SG CYS J 44 158.227 57.557 45.548 1.00100.24 S ATOM 28316 SG CYS J 45 156.326 55.675 45.139 1.00111.55 S ATOM 29303 SG CYS L 24 137.102 40.422 86.091 1.00 99.09 S ATOM 29322 SG CYS L 27 136.834 38.793 85.789 1.00111.53 S ATOM 29429 SG CYS L 41 135.421 39.107 87.376 1.00102.15 S ATOM 29455 SG CYS L 44 137.764 37.602 87.528 1.00105.50 S ATOM 30105 SG CYS M 63 110.764 56.330 104.007 1.00111.02 S ATOM 30123 SG CYS M 66 111.283 54.233 100.788 1.00124.09 S ATOM 30187 SG CYS M 73 109.197 55.633 100.992 1.00 94.01 S ATOM 30431 SG CYS M 103 69.576 45.687 131.289 1.00151.77 S ATOM 31162 SG CYS M 228 67.702 45.303 131.362 1.00165.63 S ATOM 31184 SG CYS M 231 68.895 42.928 134.870 1.00167.14 S ATOM 49149 SG CYS N1089 100.026 40.506 102.573 1.00117.13 S ATOM 49174 SG CYS N1092 98.589 42.240 103.832 1.00117.43 S ATOM 49330 SG CYS N1115 101.558 42.774 104.585 1.00103.25 S ATOM 57189 SG CYS U 10 30.727 111.437 128.324 1.00173.52 S ATOM 57210 SG CYS U 13 33.331 109.949 129.542 1.00186.06 S ATOM 57315 SG CYS U 27 31.253 109.118 131.411 1.00202.39 S ATOM 57338 SG CYS U 30 32.162 110.243 130.923 1.00200.82 S ATOM 57637 SG CYS V 7 90.146 102.506 48.418 1.00 79.08 S ATOM 57660 SG CYS V 10 87.424 102.121 45.264 1.00 98.08 S ATOM 57932 SG CYS V 44 86.062 101.566 45.803 1.00 93.30 S ATOM 57938 SG CYS V 45 88.030 103.380 45.407 1.00103.69 S ATOM 58925 SG CYS X 24 107.250 119.110 85.915 1.00 99.09 S ATOM 58944 SG CYS X 27 107.563 120.727 85.599 1.00104.70 S ATOM 59051 SG CYS X 41 108.968 120.388 87.189 1.00 99.09 S ATOM 59077 SG CYS X 44 106.667 121.959 87.328 1.00100.30 S Time building chain proxies: 24.20, per 1000 atoms: 0.41 Number of scatterers: 59256 At special positions: 0 Unit cell: (245.669, 160.589, 156.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 12 29.99 S 328 16.00 O 11068 8.00 N 10240 7.00 C 37608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.53 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 76 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 66 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 63 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 73 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 103 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 231 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 228 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1115 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1089 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 27 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 24 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 27 " pdb=" ZN M1701 " pdb="ZN ZN M1701 " - pdb=" NE2 HIS M 76 " pdb="ZN ZN M1701 " - pdb=" SG CYS M 66 " pdb="ZN ZN M1701 " - pdb=" SG CYS M 63 " pdb="ZN ZN M1701 " - pdb=" SG CYS M 73 " pdb=" ZN M1702 " pdb="ZN ZN M1702 " - pdb=" SG CYS M 103 " pdb="ZN ZN M1702 " - pdb=" SG CYS M 231 " pdb="ZN ZN M1702 " - pdb=" SG CYS M 228 " pdb=" ZN N1301 " pdb="ZN ZN N1301 " - pdb=" SG CYS N1115 " pdb="ZN ZN N1301 " - pdb=" SG CYS N1092 " pdb="ZN ZN N1301 " - pdb=" SG CYS N1089 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 13 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 30 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 10 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 27 " pdb=" ZN V 101 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 10 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 7 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 44 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 44 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 24 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 41 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 27 " Number of angles added : 42 14692 Ramachandran restraints generated. 7346 Oldfield, 0 Emsley, 7346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14004 Finding SS restraints... Secondary structure from input PDB file: 256 helices and 86 sheets defined 37.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.87 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.567A pdb=" N VAL A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 112 through 128 removed outlier: 3.873A pdb=" N TYR A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.705A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 223 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.805A pdb=" N PHE A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 4.659A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 386 through 411 Processing helix chain 'A' and resid 422 through 446 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 506 through 513 removed outlier: 3.632A pdb=" N ALA A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 634 through 641 removed outlier: 4.012A pdb=" N ASN A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 666 removed outlier: 3.695A pdb=" N ARG A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 672 Processing helix chain 'A' and resid 686 through 698 Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.876A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 807 through 816 removed outlier: 4.156A pdb=" N SER A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 839 removed outlier: 4.120A pdb=" N ILE A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 865 Processing helix chain 'A' and resid 867 through 878 Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 899 through 925 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 949 through 958 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 1004 through 1022 removed outlier: 3.839A pdb=" N PHE A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1035 Processing helix chain 'A' and resid 1069 through 1074 removed outlier: 3.662A pdb=" N LYS A1072 " --> pdb=" O ASP A1069 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A1074 " --> pdb=" O THR A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1085 removed outlier: 3.890A pdb=" N ASN A1085 " --> pdb=" O PHE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1093 removed outlier: 3.534A pdb=" N GLN A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 4.161A pdb=" N SER A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.857A pdb=" N LYS A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1138 through 1152 removed outlier: 3.774A pdb=" N ASN A1152 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1166 Processing helix chain 'A' and resid 1171 through 1185 Processing helix chain 'A' and resid 1194 through 1209 Proline residue: A1205 - end of helix removed outlier: 4.027A pdb=" N MET A1209 " --> pdb=" O PRO A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1256 through 1268 Processing helix chain 'A' and resid 1273 through 1276 Processing helix chain 'A' and resid 1305 through 1312 removed outlier: 4.214A pdb=" N GLU A1312 " --> pdb=" O GLU A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1344 Processing helix chain 'A' and resid 1504 through 1514 Processing helix chain 'A' and resid 1548 through 1553 Processing helix chain 'A' and resid 1568 through 1575 removed outlier: 3.562A pdb=" N ILE A1572 " --> pdb=" O ASP A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1595 removed outlier: 3.752A pdb=" N ALA A1581 " --> pdb=" O GLY A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1613 removed outlier: 3.855A pdb=" N LEU A1605 " --> pdb=" O ASP A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 Processing helix chain 'A' and resid 1633 through 1638 Processing helix chain 'A' and resid 1640 through 1652 removed outlier: 4.053A pdb=" N PHE A1644 " --> pdb=" O THR A1640 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A1651 " --> pdb=" O GLU A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1666 removed outlier: 3.538A pdb=" N VAL A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1676 Processing helix chain 'B' and resid 4 through 13 Processing helix chain 'B' and resid 22 through 41 removed outlier: 3.707A pdb=" N GLN B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.535A pdb=" N ALA B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 199 through 202 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 299 through 312 removed outlier: 3.708A pdb=" N THR B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.563A pdb=" N GLY B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 361 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 409 removed outlier: 3.883A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 468 through 478 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.637A pdb=" N ALA B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.594A pdb=" N ASN B 596 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 696 through 708 removed outlier: 3.739A pdb=" N ASN B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 746 through 750 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 935 through 939 removed outlier: 3.681A pdb=" N PHE B 939 " --> pdb=" O PRO B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 961 removed outlier: 3.967A pdb=" N PHE B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 959 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 989 Processing helix chain 'B' and resid 1059 through 1068 Processing helix chain 'B' and resid 1069 through 1078 Processing helix chain 'B' and resid 1152 through 1164 removed outlier: 3.631A pdb=" N ASN B1156 " --> pdb=" O PRO B1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.538A pdb=" N ALA C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 79 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.616A pdb=" N VAL C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 4.101A pdb=" N GLU C 184 " --> pdb=" O GLY C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.513A pdb=" N PHE C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.626A pdb=" N ILE C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 33 Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 83 through 88 Processing helix chain 'E' and resid 88 through 97 removed outlier: 4.083A pdb=" N HIS E 92 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.774A pdb=" N LYS E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 76 through 93 removed outlier: 4.103A pdb=" N ALA F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.706A pdb=" N GLN F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 removed outlier: 4.531A pdb=" N ARG G 23 " --> pdb=" O GLY G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 removed outlier: 4.070A pdb=" N ALA G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 71 Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'J' and resid 14 through 17 Processing helix chain 'J' and resid 18 through 26 removed outlier: 4.422A pdb=" N LEU J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 39 removed outlier: 3.888A pdb=" N LYS J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 52 removed outlier: 4.756A pdb=" N ILE J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 43 through 55 removed outlier: 4.596A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 removed outlier: 3.594A pdb=" N VAL K 90 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU K 113 " --> pdb=" O PHE K 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 28 removed outlier: 3.566A pdb=" N VAL M 24 " --> pdb=" O ASP M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 101 Processing helix chain 'M' and resid 112 through 128 removed outlier: 3.873A pdb=" N TYR M 128 " --> pdb=" O LYS M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 136 Processing helix chain 'M' and resid 137 through 139 No H-bonds generated for 'chain 'M' and resid 137 through 139' Processing helix chain 'M' and resid 173 through 195 removed outlier: 3.705A pdb=" N GLN M 195 " --> pdb=" O ALA M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 223 Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.807A pdb=" N PHE M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 339 removed outlier: 4.658A pdb=" N VAL M 328 " --> pdb=" O THR M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 347 Processing helix chain 'M' and resid 357 through 359 No H-bonds generated for 'chain 'M' and resid 357 through 359' Processing helix chain 'M' and resid 386 through 411 Processing helix chain 'M' and resid 422 through 446 Processing helix chain 'M' and resid 463 through 469 Processing helix chain 'M' and resid 506 through 513 removed outlier: 3.632A pdb=" N ALA M 510 " --> pdb=" O PRO M 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 523 through 534 Processing helix chain 'M' and resid 558 through 568 Processing helix chain 'M' and resid 585 through 589 Processing helix chain 'M' and resid 612 through 614 No H-bonds generated for 'chain 'M' and resid 612 through 614' Processing helix chain 'M' and resid 634 through 641 removed outlier: 4.011A pdb=" N ASN M 638 " --> pdb=" O TYR M 634 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER M 639 " --> pdb=" O ALA M 635 " (cutoff:3.500A) Processing helix chain 'M' and resid 656 through 666 removed outlier: 3.695A pdb=" N ARG M 660 " --> pdb=" O SER M 656 " (cutoff:3.500A) Processing helix chain 'M' and resid 668 through 672 Processing helix chain 'M' and resid 686 through 698 Processing helix chain 'M' and resid 704 through 717 Processing helix chain 'M' and resid 717 through 722 removed outlier: 3.875A pdb=" N THR M 721 " --> pdb=" O LYS M 717 " (cutoff:3.500A) Processing helix chain 'M' and resid 742 through 754 Processing helix chain 'M' and resid 771 through 775 Processing helix chain 'M' and resid 807 through 816 removed outlier: 4.156A pdb=" N SER M 811 " --> pdb=" O GLY M 807 " (cutoff:3.500A) Processing helix chain 'M' and resid 816 through 839 removed outlier: 4.121A pdb=" N ILE M 820 " --> pdb=" O TYR M 816 " (cutoff:3.500A) Processing helix chain 'M' and resid 851 through 865 Processing helix chain 'M' and resid 867 through 878 Processing helix chain 'M' and resid 884 through 896 Processing helix chain 'M' and resid 899 through 925 Processing helix chain 'M' and resid 936 through 944 Processing helix chain 'M' and resid 949 through 958 Processing helix chain 'M' and resid 988 through 992 Processing helix chain 'M' and resid 1004 through 1022 removed outlier: 3.839A pdb=" N PHE M1010 " --> pdb=" O GLN M1006 " (cutoff:3.500A) Processing helix chain 'M' and resid 1030 through 1035 Processing helix chain 'M' and resid 1069 through 1074 removed outlier: 3.662A pdb=" N LYS M1072 " --> pdb=" O ASP M1069 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS M1074 " --> pdb=" O THR M1071 " (cutoff:3.500A) Processing helix chain 'M' and resid 1078 through 1085 removed outlier: 3.891A pdb=" N ASN M1085 " --> pdb=" O PHE M1081 " (cutoff:3.500A) Processing helix chain 'M' and resid 1086 through 1093 removed outlier: 3.534A pdb=" N GLN M1091 " --> pdb=" O LYS M1087 " (cutoff:3.500A) Processing helix chain 'M' and resid 1094 through 1102 removed outlier: 4.161A pdb=" N SER M1100 " --> pdb=" O LYS M1096 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA M1101 " --> pdb=" O SER M1097 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL M1102 " --> pdb=" O VAL M1098 " (cutoff:3.500A) Processing helix chain 'M' and resid 1104 through 1116 removed outlier: 3.856A pdb=" N LYS M1112 " --> pdb=" O SER M1108 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS M1113 " --> pdb=" O SER M1109 " (cutoff:3.500A) Processing helix chain 'M' and resid 1123 through 1128 Processing helix chain 'M' and resid 1138 through 1152 removed outlier: 3.774A pdb=" N ASN M1152 " --> pdb=" O TYR M1148 " (cutoff:3.500A) Processing helix chain 'M' and resid 1162 through 1166 Processing helix chain 'M' and resid 1171 through 1185 Processing helix chain 'M' and resid 1194 through 1209 Proline residue: M1205 - end of helix removed outlier: 4.026A pdb=" N MET M1209 " --> pdb=" O PRO M1205 " (cutoff:3.500A) Processing helix chain 'M' and resid 1227 through 1236 Processing helix chain 'M' and resid 1256 through 1268 Processing helix chain 'M' and resid 1273 through 1276 Processing helix chain 'M' and resid 1305 through 1312 removed outlier: 4.214A pdb=" N GLU M1312 " --> pdb=" O GLU M1308 " (cutoff:3.500A) Processing helix chain 'M' and resid 1316 through 1344 Processing helix chain 'M' and resid 1504 through 1514 Processing helix chain 'M' and resid 1548 through 1553 Processing helix chain 'M' and resid 1568 through 1575 removed outlier: 3.562A pdb=" N ILE M1572 " --> pdb=" O ASP M1568 " (cutoff:3.500A) Processing helix chain 'M' and resid 1577 through 1595 removed outlier: 3.753A pdb=" N ALA M1581 " --> pdb=" O GLY M1577 " (cutoff:3.500A) Processing helix chain 'M' and resid 1601 through 1613 removed outlier: 3.856A pdb=" N LEU M1605 " --> pdb=" O ASP M1601 " (cutoff:3.500A) Processing helix chain 'M' and resid 1622 through 1627 Processing helix chain 'M' and resid 1633 through 1638 Processing helix chain 'M' and resid 1640 through 1652 removed outlier: 4.054A pdb=" N PHE M1644 " --> pdb=" O THR M1640 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG M1651 " --> pdb=" O GLU M1647 " (cutoff:3.500A) Processing helix chain 'M' and resid 1659 through 1666 removed outlier: 3.539A pdb=" N VAL M1666 " --> pdb=" O SER M1662 " (cutoff:3.500A) Processing helix chain 'M' and resid 1672 through 1676 Processing helix chain 'N' and resid 4 through 13 Processing helix chain 'N' and resid 22 through 41 removed outlier: 3.707A pdb=" N GLN N 26 " --> pdb=" O PHE N 22 " (cutoff:3.500A) Proline residue: N 31 - end of helix Processing helix chain 'N' and resid 43 through 51 Processing helix chain 'N' and resid 102 through 109 removed outlier: 3.536A pdb=" N ALA N 106 " --> pdb=" O TYR N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 162 Processing helix chain 'N' and resid 199 through 202 Processing helix chain 'N' and resid 252 through 260 Processing helix chain 'N' and resid 263 through 272 Processing helix chain 'N' and resid 278 through 294 Processing helix chain 'N' and resid 299 through 312 removed outlier: 3.708A pdb=" N THR N 303 " --> pdb=" O SER N 299 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 334 removed outlier: 3.563A pdb=" N GLY N 327 " --> pdb=" O ASP N 323 " (cutoff:3.500A) Processing helix chain 'N' and resid 341 through 361 Processing helix chain 'N' and resid 371 through 373 No H-bonds generated for 'chain 'N' and resid 371 through 373' Processing helix chain 'N' and resid 379 through 409 removed outlier: 3.883A pdb=" N LEU N 383 " --> pdb=" O LEU N 379 " (cutoff:3.500A) Processing helix chain 'N' and resid 418 through 429 Processing helix chain 'N' and resid 433 through 444 Processing helix chain 'N' and resid 468 through 478 Processing helix chain 'N' and resid 482 through 487 removed outlier: 3.637A pdb=" N ALA N 486 " --> pdb=" O GLY N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 535 through 543 Processing helix chain 'N' and resid 573 through 596 removed outlier: 3.594A pdb=" N ASN N 596 " --> pdb=" O VAL N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 653 through 657 Processing helix chain 'N' and resid 677 through 682 Processing helix chain 'N' and resid 683 through 688 Processing helix chain 'N' and resid 696 through 708 removed outlier: 3.740A pdb=" N ASN N 700 " --> pdb=" O GLN N 696 " (cutoff:3.500A) Processing helix chain 'N' and resid 740 through 745 Processing helix chain 'N' and resid 746 through 750 Processing helix chain 'N' and resid 775 through 781 Processing helix chain 'N' and resid 821 through 826 Processing helix chain 'N' and resid 935 through 939 removed outlier: 3.681A pdb=" N PHE N 939 " --> pdb=" O PRO N 936 " (cutoff:3.500A) Processing helix chain 'N' and resid 944 through 961 removed outlier: 3.967A pdb=" N PHE N 948 " --> pdb=" O THR N 944 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS N 959 " --> pdb=" O LYS N 955 " (cutoff:3.500A) Processing helix chain 'N' and resid 976 through 989 Processing helix chain 'N' and resid 1059 through 1068 Processing helix chain 'N' and resid 1069 through 1078 Processing helix chain 'N' and resid 1152 through 1164 removed outlier: 3.631A pdb=" N ASN N1156 " --> pdb=" O PRO N1152 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 46 Processing helix chain 'O' and resid 66 through 79 removed outlier: 3.538A pdb=" N ALA O 70 " --> pdb=" O ASP O 66 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 110 removed outlier: 3.616A pdb=" N VAL O 110 " --> pdb=" O ARG O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 186 removed outlier: 4.100A pdb=" N GLU O 184 " --> pdb=" O GLY O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 227 Processing helix chain 'O' and resid 247 through 258 removed outlier: 3.513A pdb=" N PHE O 258 " --> pdb=" O PHE O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 292 Processing helix chain 'O' and resid 293 through 297 Processing helix chain 'O' and resid 319 through 345 removed outlier: 3.627A pdb=" N ILE O 345 " --> pdb=" O SER O 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 33 Processing helix chain 'P' and resid 45 through 58 Processing helix chain 'Q' and resid 6 through 14 Processing helix chain 'Q' and resid 37 through 45 Processing helix chain 'Q' and resid 83 through 88 Processing helix chain 'Q' and resid 88 through 97 removed outlier: 4.083A pdb=" N HIS Q 92 " --> pdb=" O ARG Q 88 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR Q 93 " --> pdb=" O THR Q 89 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU Q 94 " --> pdb=" O PHE Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 122 removed outlier: 3.775A pdb=" N LYS Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE Q 118 " --> pdb=" O ALA Q 114 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 163 Processing helix chain 'Q' and resid 177 through 184 Processing helix chain 'R' and resid 76 through 93 removed outlier: 4.102A pdb=" N ALA R 81 " --> pdb=" O LYS R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 117 removed outlier: 3.706A pdb=" N GLN R 117 " --> pdb=" O LYS R 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 23 removed outlier: 4.531A pdb=" N ARG S 23 " --> pdb=" O GLY S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 37 removed outlier: 4.070A pdb=" N ALA S 28 " --> pdb=" O ASP S 24 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 71 Processing helix chain 'U' and resid 57 through 62 Processing helix chain 'V' and resid 14 through 17 Processing helix chain 'V' and resid 18 through 26 removed outlier: 4.422A pdb=" N LEU V 24 " --> pdb=" O THR V 20 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU V 25 " --> pdb=" O TYR V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 39 removed outlier: 3.888A pdb=" N LYS V 37 " --> pdb=" O GLU V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 52 removed outlier: 4.757A pdb=" N ILE V 49 " --> pdb=" O CYS V 45 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU V 50 " --> pdb=" O ARG V 46 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR V 51 " --> pdb=" O ARG V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 60 Processing helix chain 'W' and resid 43 through 55 removed outlier: 4.596A pdb=" N SER W 49 " --> pdb=" O THR W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 113 removed outlier: 3.594A pdb=" N VAL W 90 " --> pdb=" O THR W 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU W 113 " --> pdb=" O PHE W 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 4.564A pdb=" N SER A 13 " --> pdb=" O GLU B1172 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B1172 " --> pdb=" O SER A 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.249A pdb=" N LYS A 30 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 81 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLN A 363 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N ILE A 84 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N PHE A 361 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.992A pdb=" N ASN A 650 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 494 Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 515 removed outlier: 3.612A pdb=" N HIS A 543 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS A 596 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA A 541 " --> pdb=" O HIS A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 734 through 736 removed outlier: 6.557A pdb=" N ILE H 75 " --> pdb=" O GLN A 735 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 767 removed outlier: 6.918A pdb=" N ASP A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 961 through 962 Processing sheet with id=AB1, first strand: chain 'A' and resid 1524 through 1529 removed outlier: 4.978A pdb=" N ARG A1526 " --> pdb=" O GLU A1545 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A1250 " --> pdb=" O ASN A1562 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN A1562 " --> pdb=" O ARG A1250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1270 through 1271 removed outlier: 7.216A pdb=" N LEU A1270 " --> pdb=" O ILE A1518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1479 through 1482 removed outlier: 3.567A pdb=" N VAL A1281 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR I 46 " --> pdb=" O VAL A1281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1678 through 1679 Processing sheet with id=AB5, first strand: chain 'B' and resid 55 through 57 removed outlier: 6.660A pdb=" N LYS B 120 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 82 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 118 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE B 84 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ARG B 116 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B 138 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 119 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU B 136 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE B 121 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N MET B 134 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.892A pdb=" N LEU B 185 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.356A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 231 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 215 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 226 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS B 242 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.655A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 645 " --> pdb=" O HIS B 640 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.655A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 567 through 572 removed outlier: 5.621A pdb=" N ILE B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 563 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY B 569 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LEU B 625 " --> pdb=" O TRP B 558 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N CYS B 560 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 627 " --> pdb=" O CYS B 560 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLN B 562 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 725 through 729 removed outlier: 4.292A pdb=" N GLN B 885 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 870 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL B 871 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS L 51 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET L 49 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 737 through 738 Processing sheet with id=AC5, first strand: chain 'B' and resid 773 through 774 removed outlier: 3.566A pdb=" N ILE B 933 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ILE B 932 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 757 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 934 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 759 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 773 through 774 removed outlier: 3.566A pdb=" N ILE B 933 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ILE B 932 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 757 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 934 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 759 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 809 through 810 Processing sheet with id=AC8, first strand: chain 'B' and resid 843 through 845 removed outlier: 6.658A pdb=" N GLU B 858 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1085 through 1089 Processing sheet with id=AD1, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 53 removed outlier: 5.547A pdb=" N ILE C 50 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU C 61 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 237 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ASP C 306 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ARG C 235 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N TYR C 308 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 11.035A pdb=" N SER C 233 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N PHE C 310 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N THR C 231 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL C 312 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N VAL C 229 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.325A pdb=" N VAL C 140 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU C 208 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN C 94 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP C 210 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE C 216 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE C 86 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY C 218 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU C 84 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 89 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE L 60 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C 91 " --> pdb=" O VAL L 58 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL L 58 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.507A pdb=" N GLU C 148 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 168 through 170 removed outlier: 6.694A pdb=" N VAL C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 263 through 267 removed outlier: 3.508A pdb=" N GLN C 274 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.611A pdb=" N LYS E 62 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR E 71 " --> pdb=" O HIS E 99 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR E 101 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR E 126 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 102 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.520A pdb=" N LYS E 147 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 9 through 17 removed outlier: 5.256A pdb=" N ASP G 77 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN G 53 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 9 through 17 Processing sheet with id=AE2, first strand: chain 'G' and resid 40 through 41 Processing sheet with id=AE3, first strand: chain 'G' and resid 109 through 114 removed outlier: 7.515A pdb=" N HIS G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL G 96 " --> pdb=" O HIS G 100 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY G 102 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL G 153 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 15 through 17 Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 26 removed outlier: 4.264A pdb=" N THR I 25 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR I 34 " --> pdb=" O THR I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 22 through 24 Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 35 removed outlier: 3.568A pdb=" N VAL K 35 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 11 through 13 removed outlier: 4.450A pdb=" N SER M 13 " --> pdb=" O GLU N1172 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU N1172 " --> pdb=" O SER M 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'M' and resid 16 through 18 Processing sheet with id=AF1, first strand: chain 'M' and resid 30 through 31 removed outlier: 6.249A pdb=" N LYS M 30 " --> pdb=" O HIS M 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL M 81 " --> pdb=" O LYS M 30 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLN M 363 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N ILE M 84 " --> pdb=" O PHE M 361 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N PHE M 361 " --> pdb=" O ILE M 84 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 487 through 490 removed outlier: 3.992A pdb=" N ASN M 650 " --> pdb=" O ASN M 606 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 492 through 494 Processing sheet with id=AF4, first strand: chain 'M' and resid 514 through 515 removed outlier: 3.611A pdb=" N HIS M 543 " --> pdb=" O TYR M 594 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS M 596 " --> pdb=" O ALA M 541 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA M 541 " --> pdb=" O HIS M 596 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 734 through 736 removed outlier: 6.462A pdb=" N ILE T 75 " --> pdb=" O GLN M 735 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 764 through 767 removed outlier: 6.918A pdb=" N ASP M 787 " --> pdb=" O LEU M 791 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU M 791 " --> pdb=" O ASP M 787 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 961 through 962 Processing sheet with id=AF8, first strand: chain 'M' and resid 1524 through 1529 removed outlier: 4.978A pdb=" N ARG M1526 " --> pdb=" O GLU M1545 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG M1250 " --> pdb=" O ASN M1562 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN M1562 " --> pdb=" O ARG M1250 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 1270 through 1271 removed outlier: 7.216A pdb=" N LEU M1270 " --> pdb=" O ILE M1518 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 1479 through 1482 removed outlier: 3.500A pdb=" N THR U 46 " --> pdb=" O VAL M1281 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 1678 through 1679 Processing sheet with id=AG3, first strand: chain 'N' and resid 55 through 57 removed outlier: 6.659A pdb=" N LYS N 120 " --> pdb=" O ASP N 80 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL N 82 " --> pdb=" O VAL N 118 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL N 118 " --> pdb=" O VAL N 82 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE N 84 " --> pdb=" O ARG N 116 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ARG N 116 " --> pdb=" O ILE N 84 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY N 138 " --> pdb=" O LEU N 117 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU N 119 " --> pdb=" O GLU N 136 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU N 136 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE N 121 " --> pdb=" O MET N 134 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N MET N 134 " --> pdb=" O PHE N 121 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 173 through 175 Processing sheet with id=AG5, first strand: chain 'N' and resid 375 through 378 removed outlier: 3.892A pdb=" N LEU N 185 " --> pdb=" O LEU N 378 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 194 through 197 removed outlier: 5.355A pdb=" N TYR N 211 " --> pdb=" O TYR N 231 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR N 231 " --> pdb=" O TYR N 211 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE N 215 " --> pdb=" O ASN N 227 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR N 226 " --> pdb=" O HIS N 242 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS N 242 " --> pdb=" O THR N 226 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 526 through 528 removed outlier: 3.655A pdb=" N ARG N 633 " --> pdb=" O VAL N 528 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU N 645 " --> pdb=" O HIS N 640 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 526 through 528 removed outlier: 3.655A pdb=" N ARG N 633 " --> pdb=" O VAL N 528 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 567 through 572 removed outlier: 5.621A pdb=" N ILE N 567 " --> pdb=" O LEU N 563 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU N 563 " --> pdb=" O ILE N 567 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY N 569 " --> pdb=" O VAL N 561 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LEU N 625 " --> pdb=" O TRP N 558 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N CYS N 560 " --> pdb=" O LEU N 625 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU N 627 " --> pdb=" O CYS N 560 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLN N 562 " --> pdb=" O LEU N 627 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 725 through 729 removed outlier: 4.293A pdb=" N GLN N 885 " --> pdb=" O LEU N 874 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU N 870 " --> pdb=" O LYS N 889 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL N 871 " --> pdb=" O LYS X 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET X 49 " --> pdb=" O LEU N 873 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 737 through 738 Processing sheet with id=AH3, first strand: chain 'N' and resid 773 through 774 removed outlier: 3.565A pdb=" N ILE N 933 " --> pdb=" O ILE N 773 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE N 932 " --> pdb=" O ASN N 755 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL N 757 " --> pdb=" O ILE N 932 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE N 934 " --> pdb=" O VAL N 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA N 759 " --> pdb=" O ILE N 934 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR N1012 " --> pdb=" O VAL N 760 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 773 through 774 removed outlier: 3.565A pdb=" N ILE N 933 " --> pdb=" O ILE N 773 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE N 932 " --> pdb=" O ASN N 755 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL N 757 " --> pdb=" O ILE N 932 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE N 934 " --> pdb=" O VAL N 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA N 759 " --> pdb=" O ILE N 934 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR N1012 " --> pdb=" O VAL N 760 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 809 through 810 Processing sheet with id=AH6, first strand: chain 'N' and resid 843 through 845 removed outlier: 6.658A pdb=" N GLU N 858 " --> pdb=" O ILE N 844 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 1085 through 1089 Processing sheet with id=AH8, first strand: chain 'N' and resid 1098 through 1099 Processing sheet with id=AH9, first strand: chain 'O' and resid 48 through 53 removed outlier: 5.547A pdb=" N ILE O 50 " --> pdb=" O GLU O 61 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU O 61 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU O 237 " --> pdb=" O VAL O 304 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ASP O 306 " --> pdb=" O ARG O 235 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ARG O 235 " --> pdb=" O ASP O 306 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N TYR O 308 " --> pdb=" O SER O 233 " (cutoff:3.500A) removed outlier: 11.035A pdb=" N SER O 233 " --> pdb=" O TYR O 308 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N PHE O 310 " --> pdb=" O THR O 231 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N THR O 231 " --> pdb=" O PHE O 310 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL O 312 " --> pdb=" O VAL O 229 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N VAL O 229 " --> pdb=" O VAL O 312 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 175 through 177 removed outlier: 4.325A pdb=" N VAL O 140 " --> pdb=" O LYS O 177 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU O 208 " --> pdb=" O ASN O 94 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN O 94 " --> pdb=" O GLU O 208 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP O 210 " --> pdb=" O ILE O 92 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE O 216 " --> pdb=" O PHE O 86 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE O 86 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY O 218 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU O 84 " --> pdb=" O GLY O 218 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL O 89 " --> pdb=" O PHE X 60 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE X 60 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE O 91 " --> pdb=" O VAL X 58 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL X 58 " --> pdb=" O ILE O 91 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 148 through 149 removed outlier: 3.507A pdb=" N GLU O 148 " --> pdb=" O VAL O 165 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 168 through 170 removed outlier: 6.694A pdb=" N VAL O 169 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 263 through 267 removed outlier: 3.509A pdb=" N GLN O 274 " --> pdb=" O GLU O 266 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 27 through 28 removed outlier: 4.611A pdb=" N LYS Q 62 " --> pdb=" O GLY Q 28 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR Q 71 " --> pdb=" O HIS Q 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Q 101 " --> pdb=" O THR Q 71 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR Q 126 " --> pdb=" O LYS Q 100 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY Q 102 " --> pdb=" O THR Q 126 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 147 through 149 removed outlier: 3.519A pdb=" N LYS Q 147 " --> pdb=" O VAL Q 194 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'S' and resid 9 through 17 removed outlier: 5.256A pdb=" N ASP S 77 " --> pdb=" O ASN S 53 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN S 53 " --> pdb=" O ASP S 77 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'S' and resid 9 through 17 Processing sheet with id=AI9, first strand: chain 'S' and resid 40 through 41 Processing sheet with id=AJ1, first strand: chain 'S' and resid 109 through 114 removed outlier: 7.514A pdb=" N HIS S 100 " --> pdb=" O VAL S 96 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL S 96 " --> pdb=" O HIS S 100 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY S 102 " --> pdb=" O ASN S 94 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL S 153 " --> pdb=" O THR S 169 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'T' and resid 15 through 17 Processing sheet with id=AJ3, first strand: chain 'U' and resid 25 through 26 removed outlier: 4.264A pdb=" N THR U 25 " --> pdb=" O TYR U 34 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR U 34 " --> pdb=" O THR U 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'W' and resid 22 through 24 Processing sheet with id=AJ5, first strand: chain 'W' and resid 34 through 35 removed outlier: 3.568A pdb=" N VAL W 35 " --> pdb=" O ILE W 79 " (cutoff:3.500A) 2306 hydrogen bonds defined for protein. 6420 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: 35.86 Time building geometry restraints manager: 13.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 19660 1.36 - 1.49: 15236 1.49 - 1.63: 25012 1.63 - 1.76: 0 1.76 - 1.90: 528 Bond restraints: 60436 Sorted by residual: bond pdb=" SD MET F 112 " pdb=" CE MET F 112 " ideal model delta sigma weight residual 1.791 1.899 -0.108 2.50e-02 1.60e+03 1.86e+01 bond pdb=" SD MET R 112 " pdb=" CE MET R 112 " ideal model delta sigma weight residual 1.791 1.898 -0.107 2.50e-02 1.60e+03 1.85e+01 bond pdb=" CB GLN R 109 " pdb=" CG GLN R 109 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.85e+00 bond pdb=" CB GLN F 109 " pdb=" CG GLN F 109 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.80e+00 bond pdb=" C HIS B 192 " pdb=" N PRO B 193 " ideal model delta sigma weight residual 1.332 1.304 0.028 1.12e-02 7.97e+03 6.27e+00 ... (remaining 60431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 80207 2.70 - 5.39: 1300 5.39 - 8.09: 119 8.09 - 10.78: 22 10.78 - 13.48: 6 Bond angle restraints: 81654 Sorted by residual: angle pdb=" C GLY Q 49 " pdb=" N ARG Q 50 " pdb=" CA ARG Q 50 " ideal model delta sigma weight residual 121.70 131.83 -10.13 1.80e+00 3.09e-01 3.17e+01 angle pdb=" C GLY E 49 " pdb=" N ARG E 50 " pdb=" CA ARG E 50 " ideal model delta sigma weight residual 121.70 131.82 -10.12 1.80e+00 3.09e-01 3.16e+01 angle pdb=" N VAL E 91 " pdb=" CA VAL E 91 " pdb=" C VAL E 91 " ideal model delta sigma weight residual 111.62 107.54 4.08 7.90e-01 1.60e+00 2.67e+01 angle pdb=" N VAL Q 91 " pdb=" CA VAL Q 91 " pdb=" C VAL Q 91 " ideal model delta sigma weight residual 111.62 107.55 4.07 7.90e-01 1.60e+00 2.66e+01 angle pdb=" C ASP T 17 " pdb=" N LYS T 18 " pdb=" CA LYS T 18 " ideal model delta sigma weight residual 121.70 130.61 -8.91 1.80e+00 3.09e-01 2.45e+01 ... (remaining 81649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 32610 17.43 - 34.86: 3335 34.86 - 52.29: 590 52.29 - 69.73: 175 69.73 - 87.16: 50 Dihedral angle restraints: 36760 sinusoidal: 15056 harmonic: 21704 Sorted by residual: dihedral pdb=" CA ILE A 84 " pdb=" C ILE A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta harmonic sigma weight residual 180.00 -118.10 -61.90 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ILE M 84 " pdb=" C ILE M 84 " pdb=" N PRO M 85 " pdb=" CA PRO M 85 " ideal model delta harmonic sigma weight residual -180.00 -118.14 -61.86 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ARG E 50 " pdb=" C ARG E 50 " pdb=" N ASN E 51 " pdb=" CA ASN E 51 " ideal model delta harmonic sigma weight residual 180.00 138.02 41.98 0 5.00e+00 4.00e-02 7.05e+01 ... (remaining 36757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 5605 0.037 - 0.074: 2499 0.074 - 0.110: 841 0.110 - 0.147: 157 0.147 - 0.184: 24 Chirality restraints: 9126 Sorted by residual: chirality pdb=" CB ILE R 120 " pdb=" CA ILE R 120 " pdb=" CG1 ILE R 120 " pdb=" CG2 ILE R 120 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CB ILE F 120 " pdb=" CA ILE F 120 " pdb=" CG1 ILE F 120 " pdb=" CG2 ILE F 120 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CB VAL N 605 " pdb=" CA VAL N 605 " pdb=" CG1 VAL N 605 " pdb=" CG2 VAL N 605 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 9123 not shown) Planarity restraints: 10498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 84 " -0.058 5.00e-02 4.00e+02 8.89e-02 1.27e+01 pdb=" N PRO M 85 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO M 85 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO M 85 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 84 " 0.058 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO A 85 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 817 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO N 818 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO N 818 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO N 818 " -0.034 5.00e-02 4.00e+02 ... (remaining 10495 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 629 2.47 - 3.07: 46264 3.07 - 3.68: 94437 3.68 - 4.29: 135700 4.29 - 4.90: 214645 Nonbonded interactions: 491675 Sorted by model distance: nonbonded pdb=" O VAL A1279 " pdb=" OG SER I 48 " model vdw 1.858 3.040 nonbonded pdb=" N CYS M 106 " pdb="ZN ZN M1702 " model vdw 1.888 2.310 nonbonded pdb=" N CYS A 106 " pdb="ZN ZN A1702 " model vdw 1.889 2.310 nonbonded pdb=" OG1 THR V 23 " pdb=" OE2 GLU V 27 " model vdw 1.945 3.040 nonbonded pdb=" OG1 THR J 23 " pdb=" OE2 GLU J 27 " model vdw 1.945 3.040 ... (remaining 491670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 12 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'Q' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'R' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'S' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'T' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'U' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'V' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'W' } pdb_interpretation.ncs_group { reference = chain 'L' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.090 Extract box with map and model: 1.730 Check model and map are aligned: 0.360 Set scattering table: 0.430 Process input model: 127.800 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.007 0.108 60436 Z= 0.424 Angle : 0.892 13.479 81654 Z= 0.508 Chirality : 0.046 0.184 9126 Planarity : 0.005 0.089 10498 Dihedral : 14.842 87.157 22756 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.73 % Favored : 88.95 % Rotamer: Outliers : 1.95 % Allowed : 9.57 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.26 % 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: -4.20 (0.08), residues: 7346 helix: -2.26 (0.08), residues: 2412 sheet: -2.58 (0.14), residues: 1060 loop : -3.27 (0.08), residues: 3874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP Q 15 HIS 0.012 0.002 HIS M 543 PHE 0.024 0.002 PHE B 939 TYR 0.022 0.002 TYR A1031 ARG 0.017 0.001 ARG N 820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14692 Ramachandran restraints generated. 7346 Oldfield, 0 Emsley, 7346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14692 Ramachandran restraints generated. 7346 Oldfield, 0 Emsley, 7346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 SER cc_start: 0.9096 (OUTLIER) cc_final: 0.8864 (t) REVERT: A 568 GLN cc_start: 0.8688 (pt0) cc_final: 0.8286 (tt0) REVERT: A 624 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7793 (tp) REVERT: A 630 ILE cc_start: 0.8523 (pt) cc_final: 0.8044 (pt) REVERT: A 832 PHE cc_start: 0.8990 (m-10) cc_final: 0.8685 (m-10) REVERT: A 845 MET cc_start: 0.7904 (tpt) cc_final: 0.6364 (pmm) REVERT: A 947 LYS cc_start: 0.8341 (tptt) cc_final: 0.7710 (tmtt) REVERT: A 1036 LEU cc_start: 0.8469 (tp) cc_final: 0.8202 (tt) REVERT: A 1038 LYS cc_start: 0.8551 (tmtt) cc_final: 0.7832 (ttmt) outliers start: 11 outliers final: 3 residues processed: 171 average time/residue: 0.2041 time to fit residues: 48.5985 Evaluate side-chains 108 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.956 Evaluate side-chains 154 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.5553 (tmm) cc_final: 0.4621 (tmm) REVERT: B 109 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.6902 (mmt-90) REVERT: B 267 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8786 (mm) REVERT: B 288 MET cc_start: 0.8191 (tmm) cc_final: 0.7962 (tpp) REVERT: B 634 MET cc_start: 0.7493 (mtm) cc_final: 0.7030 (mpp) REVERT: B 708 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7691 (ttpt) REVERT: B 721 ARG cc_start: 0.7819 (mtp85) cc_final: 0.6710 (mmm160) REVERT: B 745 TYR cc_start: 0.8198 (m-80) cc_final: 0.7984 (m-80) REVERT: B 772 MET cc_start: 0.8592 (ptm) cc_final: 0.7828 (ptm) REVERT: B 837 LYS cc_start: 0.8808 (tttt) cc_final: 0.8318 (mptt) REVERT: B 1161 GLU cc_start: 0.8769 (mm-30) cc_final: 0.7631 (tm-30) REVERT: B 1169 MET cc_start: 0.8425 (pmm) cc_final: 0.7526 (tpt) REVERT: B 1170 MET cc_start: 0.8061 (ptp) cc_final: 0.7853 (mpp) outliers start: 12 outliers final: 3 residues processed: 152 average time/residue: 0.1832 time to fit residues: 38.2765 Evaluate side-chains 99 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.786 Evaluate side-chains 48 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.224 Fit side-chains REVERT: C 92 ILE cc_start: 0.7998 (mm) cc_final: 0.7150 (mm) REVERT: C 141 PHE cc_start: 0.8206 (m-80) cc_final: 0.7711 (m-80) REVERT: C 210 ASP cc_start: 0.8476 (t0) cc_final: 0.8192 (t0) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.1403 time to fit residues: 7.3976 Evaluate side-chains 21 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.223 Evaluate side-chains 15 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.032 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.2073 time to fit residues: 3.1950 Evaluate side-chains 6 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.031 Evaluate side-chains 35 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: E 11 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.8828 (p) outliers start: 8 outliers final: 2 residues processed: 34 average time/residue: 0.2075 time to fit residues: 7.6498 Evaluate side-chains 16 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.147 Evaluate side-chains 22 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.059 Fit side-chains revert: symmetry clash REVERT: F 70 THR cc_start: 0.8470 (m) cc_final: 0.8108 (t) outliers start: 3 outliers final: 1 residues processed: 21 average time/residue: 0.0712 time to fit residues: 1.6818 Evaluate side-chains 13 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.059 Evaluate side-chains 23 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.111 Fit side-chains REVERT: G 56 PHE cc_start: 0.8159 (p90) cc_final: 0.7894 (p90) outliers start: 5 outliers final: 0 residues processed: 23 average time/residue: 0.1265 time to fit residues: 3.2745 Evaluate side-chains 7 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.111 Evaluate side-chains 21 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: H 7 LEU cc_start: 0.7845 (mt) cc_final: 0.7624 (mt) REVERT: H 94 TYR cc_start: 0.8282 (m-80) cc_final: 0.7971 (m-80) outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1769 time to fit residues: 3.9934 Evaluate side-chains 12 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.088 Evaluate side-chains 16 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.038 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 16 average time/residue: 0.0664 time to fit residues: 1.1689 Evaluate side-chains 2 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.039 Evaluate side-chains 16 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.051 Fit side-chains REVERT: J 58 LYS cc_start: 0.7999 (tttt) cc_final: 0.7177 (mptt) outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 0.0776 time to fit residues: 1.3852 Evaluate side-chains 9 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 8 time to evaluate : 0.051 Evaluate side-chains 27 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.066 Fit side-chains REVERT: K 41 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8341 (mmtp) REVERT: K 42 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7364 (mm-30) REVERT: K 75 MET cc_start: 0.7267 (ttm) cc_final: 0.6528 (ttm) outliers start: 2 outliers final: 0 residues processed: 27 average time/residue: 0.1129 time to fit residues: 3.2885 Evaluate side-chains 13 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.066 Evaluate side-chains 16 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.2643 time to fit residues: 4.3293 Evaluate side-chains 13 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 619 optimal weight: 2.9990 chunk 556 optimal weight: 0.5980 chunk 308 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 375 optimal weight: 0.0870 chunk 297 optimal weight: 0.0970 chunk 575 optimal weight: 9.9990 chunk 222 optimal weight: 0.0570 chunk 349 optimal weight: 4.9990 chunk 428 optimal weight: 7.9990 chunk 666 optimal weight: 8.9990 overall best weight: 0.7676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 GLN M 60 ASN M 117 HIS M 501 ASN M 533 ASN M 536 HIS ** M 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 546 ASN M 568 GLN M 599 ASN M 655 GLN M 856 ASN M 860 GLN M 889 ASN M 937 HIS ** M 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1073 GLN ** M1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1519 HIS ** M1548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1604 HIS ** M1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS B 98 ASN B 126 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 300 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN B 733 GLN ** B 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 HIS ** B 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN ** B1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 182 GLN O 207 GLN O 214 HIS ** O 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 29 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 60436 Z= 0.269 Angle : 0.792 14.544 81654 Z= 0.405 Chirality : 0.046 0.239 9126 Planarity : 0.006 0.179 10498 Dihedral : 6.209 63.427 8114 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.25 % Favored : 91.70 % Rotamer: Outliers : 0.21 % Allowed : 5.74 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.09), residues: 7346 helix: -0.69 (0.10), residues: 2460 sheet: -2.23 (0.15), residues: 1086 loop : -2.55 (0.09), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 37 HIS 0.012 0.001 HIS W 44 PHE 0.029 0.002 PHE A 247 TYR 0.040 0.002 TYR A1047 ARG 0.034 0.001 ARG X 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11928 Ramachandran restraints generated. 5964 Oldfield, 0 Emsley, 5964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11928 Ramachandran restraints generated. 5964 Oldfield, 0 Emsley, 5964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 70 GLU cc_start: 0.7856 (pm20) cc_final: 0.7534 (mt-10) REVERT: M 476 ARG cc_start: 0.6526 (ttm170) cc_final: 0.6245 (tpp80) REVERT: M 568 GLN cc_start: 0.8233 (pt0) cc_final: 0.7954 (tt0) REVERT: M 649 MET cc_start: 0.8348 (mtm) cc_final: 0.8005 (ptm) REVERT: M 686 ILE cc_start: 0.8751 (pt) cc_final: 0.8416 (pt) REVERT: M 792 LEU cc_start: 0.8670 (mt) cc_final: 0.8138 (tp) REVERT: M 832 PHE cc_start: 0.8819 (m-10) cc_final: 0.8513 (m-10) REVERT: M 845 MET cc_start: 0.7473 (tpt) cc_final: 0.6219 (pmm) REVERT: M 947 LYS cc_start: 0.8343 (tptt) cc_final: 0.7640 (tmtt) REVERT: M 1561 MET cc_start: 0.5136 (tpt) cc_final: 0.4887 (tpt) REVERT: M 1562 ASN cc_start: 0.8720 (t0) cc_final: 0.8449 (t0) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1917 time to fit residues: 44.3925 Evaluate side-chains 109 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.998 Evaluate side-chains 151 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.5379 (tmm) cc_final: 0.4223 (tmm) REVERT: B 109 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.6843 (mmt-90) REVERT: B 772 MET cc_start: 0.8576 (ptm) cc_final: 0.7968 (ptm) REVERT: B 902 PHE cc_start: 0.7343 (m-80) cc_final: 0.6911 (m-10) REVERT: B 1059 MET cc_start: 0.5996 (mmm) cc_final: 0.5767 (mmm) REVERT: B 1161 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7560 (tm-30) REVERT: B 1162 LEU cc_start: 0.8991 (tp) cc_final: 0.8733 (tp) REVERT: B 1169 MET cc_start: 0.8310 (pmm) cc_final: 0.7535 (tpt) REVERT: B 1170 MET cc_start: 0.8084 (ptp) cc_final: 0.7820 (mpp) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.1753 time to fit residues: 37.1057 Evaluate side-chains 98 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.792 Evaluate side-chains 32 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: O 30 TYR cc_start: 0.6320 (m-80) cc_final: 0.5723 (p90) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1289 time to fit residues: 5.0070 Evaluate side-chains 16 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.317 Evaluate side-chains 11 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.031 Fit side-chains REVERT: D 31 GLN cc_start: 0.8913 (mt0) cc_final: 0.8640 (mt0) outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 0.1700 time to fit residues: 1.9473 Evaluate side-chains 5 residues out of total 37 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.040 Evaluate side-chains 24 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.147 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1637 time to fit residues: 4.4246 Evaluate side-chains 11 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.148 Evaluate side-chains 22 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 76 THR cc_start: 0.8914 (p) cc_final: 0.8622 (t) REVERT: R 78 TYR cc_start: 0.7806 (m-10) cc_final: 0.6954 (t80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0893 time to fit residues: 2.1561 Evaluate side-chains 14 residues out of total 70 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.069 Evaluate side-chains 17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 110 ASN cc_start: 0.7718 (m-40) cc_final: 0.7450 (p0) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1205 time to fit residues: 2.3669 Evaluate side-chains 9 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.111 Evaluate side-chains 17 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.8256 (tpt) cc_final: 0.8035 (tpt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1143 time to fit residues: 2.1939 Evaluate side-chains 12 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.089 Evaluate side-chains 8 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.042 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1059 time to fit residues: 0.9318 Evaluate side-chains 0 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.040 Evaluate side-chains 15 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.053 Fit side-chains REVERT: J 58 LYS cc_start: 0.8143 (tttt) cc_final: 0.7224 (mttt) outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.1434 time to fit residues: 2.2884 Evaluate side-chains 10 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.051 Evaluate side-chains 26 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: W 40 GLN cc_start: 0.8574 (tp-100) cc_final: 0.7989 (tp40) REVERT: W 41 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8266 (mmtp) REVERT: W 42 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7692 (mm-30) REVERT: W 51 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8134 (ttm170) REVERT: W 59 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8402 (tt0) REVERT: W 72 GLU cc_start: 0.8568 (pm20) cc_final: 0.8127 (mp0) REVERT: W 103 ASP cc_start: 0.8679 (t0) cc_final: 0.8402 (t0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1065 time to fit residues: 3.0040 Evaluate side-chains 18 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.066 Evaluate side-chains 14 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.035 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.1965 time to fit residues: 2.8452 Evaluate side-chains 8 residues out of total 39 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.0855 > 50: distance: 0 - 1: 16.113 distance: 1 - 2: 9.231 distance: 2 - 3: 6.251 distance: 2 - 4: 16.968 distance: 4 - 5: 11.352 distance: 5 - 6: 18.552 distance: 6 - 7: 26.084 distance: 6 - 8: 4.526 distance: 8 - 9: 13.654 distance: 9 - 10: 28.768 distance: 9 - 12: 23.903 distance: 10 - 11: 16.356 distance: 10 - 19: 14.160 distance: 12 - 13: 6.295 distance: 13 - 14: 6.500 distance: 14 - 16: 4.435 distance: 15 - 17: 6.584 distance: 16 - 18: 6.287 distance: 19 - 20: 7.248 distance: 20 - 21: 12.723 distance: 20 - 23: 6.743 distance: 21 - 22: 13.876 distance: 21 - 27: 9.874 distance: 23 - 24: 10.410 distance: 23 - 25: 11.121 distance: 24 - 26: 8.829 distance: 28 - 29: 4.248 distance: 28 - 31: 10.616 distance: 29 - 30: 20.593 distance: 29 - 32: 4.291 distance: 32 - 33: 11.104 distance: 33 - 34: 5.768 distance: 33 - 36: 7.584 distance: 34 - 35: 13.098 distance: 34 - 38: 14.982 distance: 36 - 37: 28.152 distance: 38 - 39: 12.782 distance: 39 - 40: 11.393 distance: 39 - 42: 11.415 distance: 40 - 41: 24.692 distance: 40 - 49: 17.762 distance: 42 - 43: 28.577 distance: 43 - 44: 27.187 distance: 44 - 45: 26.511 distance: 45 - 46: 10.780 distance: 46 - 47: 8.818 distance: 46 - 48: 16.017 distance: 50 - 51: 7.781 distance: 50 - 53: 9.713 distance: 51 - 52: 5.759 distance: 51 - 60: 14.865 distance: 53 - 54: 10.524 distance: 54 - 55: 10.808 distance: 54 - 56: 5.488 distance: 55 - 57: 7.937 distance: 57 - 59: 10.403 distance: 58 - 59: 10.466 distance: 60 - 61: 6.656 distance: 61 - 62: 11.655 distance: 61 - 64: 10.451 distance: 62 - 63: 6.846 distance: 62 - 68: 6.707 distance: 64 - 65: 16.784 distance: 65 - 66: 11.332 distance: 65 - 67: 20.194 distance: 68 - 69: 6.254 distance: 69 - 70: 4.725 distance: 69 - 72: 3.759 distance: 70 - 71: 7.015 distance: 72 - 73: 3.181 distance: 72 - 74: 5.570