Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 23:28:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/10_2023/5w65_8775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/10_2023/5w65_8775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/10_2023/5w65_8775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/10_2023/5w65_8775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/10_2023/5w65_8775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/10_2023/5w65_8775.pdb" } resolution = 4.3 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 102 5.49 5 S 210 5.16 5 C 29683 2.51 5 N 8189 2.21 5 O 9117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "A TYR 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 280": "NH1" <-> "NH2" Residue "O ARG 407": "NH1" <-> "NH2" Residue "O ARG 419": "NH1" <-> "NH2" Residue "O ARG 472": "NH1" <-> "NH2" Residue "O ARG 484": "NH1" <-> "NH2" Residue "O ARG 542": "NH1" <-> "NH2" Residue "O GLU 664": "OE1" <-> "OE2" Residue "P ARG 305": "NH1" <-> "NH2" Residue "P ARG 324": "NH1" <-> "NH2" Residue "P ARG 350": "NH1" <-> "NH2" Residue "P GLU 371": "OE1" <-> "OE2" Residue "P GLU 496": "OE1" <-> "OE2" Residue "Q PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q ARG 17": "NH1" <-> "NH2" Residue "Q ARG 30": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 166": "OE1" <-> "OE2" Residue "Q ARG 302": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 47308 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1461, 11542 Classifications: {'peptide': 1461} Link IDs: {'PTRANS': 59, 'TRANS': 1401} Chain breaks: 7 Chain: "B" Number of atoms: 9351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9351 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 58, 'TRANS': 1119} Chain breaks: 2 Chain: "C" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2431 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1070 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 479 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 841 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "N" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1254 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "O" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5063 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 620} Chain breaks: 4 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 Chain: "P" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3978 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2923 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 2 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "S" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 935 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "T" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1082 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} 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: "P" 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 781 SG CYS A 102 170.512 82.522 85.801 1.00 0.00 S ATOM 806 SG CYS A 105 170.989 79.750 85.913 1.00 0.00 S ATOM 1605 SG CYS A 233 172.206 82.303 88.151 1.00 0.00 S ATOM 1627 SG CYS A 236 172.663 82.108 85.728 1.00 0.00 S ATOM 461 SG CYS A 62 123.339 63.294 87.358 1.00 0.00 S ATOM 480 SG CYS A 65 122.175 60.653 89.288 1.00 0.00 S ATOM 535 SG CYS A 72 122.504 62.741 89.844 1.00 0.00 S ATOM 20196 SG CYS B1104 137.759 55.666 95.347 1.00 0.00 S ATOM 20222 SG CYS B1107 138.386 58.705 95.395 1.00 0.00 S ATOM 20369 SG CYS B1128 136.523 57.073 93.358 1.00 0.00 S ATOM 20397 SG CYS B1131 139.378 55.281 93.520 1.00 0.00 S ATOM 28945 SG CYS I 10 154.612 149.515 92.973 1.00 0.00 S ATOM 28967 SG CYS I 13 152.207 147.753 92.091 1.00 0.00 S ATOM 29087 SG CYS I 30 155.042 147.176 91.289 1.00 0.00 S ATOM 29108 SG CYS I 33 155.476 149.886 91.294 1.00 0.00 S ATOM 29415 SG CYS J 7 84.663 98.083 137.483 1.00 0.00 S ATOM 29438 SG CYS J 10 82.295 96.912 139.106 1.00 0.00 S ATOM 29718 SG CYS J 45 84.845 98.722 140.496 1.00 0.00 S ATOM 29724 SG CYS J 46 81.371 99.662 139.686 1.00 0.00 S ATOM 30790 SG CYS L 31 81.686 103.787 93.493 1.00 0.00 S ATOM 30810 SG CYS L 34 78.814 104.355 93.272 1.00 0.00 S ATOM 30914 SG CYS L 48 80.307 103.469 91.088 1.00 0.00 S ATOM 30937 SG CYS L 51 81.767 105.502 91.057 1.00 0.00 S ATOM 38332 SG CYS P 10 104.321 53.867 99.656 1.00 0.00 S ATOM 38365 SG CYS P 15 100.113 53.658 99.493 1.00 0.00 S ATOM 38485 SG CYS P 29 100.749 55.952 100.683 1.00 0.00 S Time building chain proxies: 22.74, per 1000 atoms: 0.48 Number of scatterers: 47308 At special positions: 0 Unit cell: (206.7, 191.1, 204.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 210 16.00 P 102 15.00 O 9117 8.00 N 8189 7.00 C 29683 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 - 3.50 Amino acid : False - 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: 20.00 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " 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 33 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN J 101 " 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 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb=" ZN P 601 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 15 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 29 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 10 " Number of angles added : 33 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10714 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 61 sheets defined 42.7% alpha, 16.6% beta 36 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 16.19 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 87 through 101 removed outlier: 4.533A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.513A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 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 174 through 199 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.679A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.464A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.948A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 407 Processing helix chain 'A' and resid 416 through 439 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.825A pdb=" N ARG A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.654A pdb=" N ILE A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 802 through 825 Processing helix chain 'A' and resid 829 through 834 removed outlier: 3.667A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.675A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 885 through 916 Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 923 through 931 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1028 removed outlier: 3.837A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A1015 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 4.312A pdb=" N SER A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N HIS A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A1064 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1081 through 1085 removed outlier: 3.763A pdb=" N ALA A1084 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1108 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.770A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1177 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1298 through 1306 Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1320 through 1337 Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1525 through 1531 removed outlier: 3.563A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.692A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.683A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1605 removed outlier: 4.392A pdb=" N THR A1605 " --> pdb=" O GLN A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 Processing helix chain 'A' and resid 1617 through 1629 Processing helix chain 'A' and resid 1636 through 1643 Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 3.573A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.914A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.907A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.577A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.186A pdb=" N LYS B 174 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 175 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.811A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.718A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 322 through 339 removed outlier: 5.220A pdb=" N VAL B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.561A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.691A pdb=" N ASP B 477 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.993A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.514A pdb=" N SER B 524 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 559 No H-bonds generated for 'chain 'B' and resid 557 through 559' Processing helix chain 'B' and resid 560 through 569 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.822A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.610A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.035A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 815 through 819 removed outlier: 4.282A pdb=" N ASP B 819 " --> pdb=" O ASN B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 839 Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.500A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.783A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1173 through 1185 Proline residue: B1179 - end of helix Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.634A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.592A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.631A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.291A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.739A pdb=" N ASN D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.586A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.527A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.594A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.548A pdb=" N TYR G 53 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'I' and resid 37 through 41 removed outlier: 4.171A pdb=" N SER I 40 " --> pdb=" O TYR I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.839A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.504A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.576A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 4.236A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 98 Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 104 through 107 removed outlier: 3.742A pdb=" N ASN M 107 " --> pdb=" O SER M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 107' Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 93 through 97 Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'N' and resid 176 through 180 Processing helix chain 'O' and resid 294 through 298 removed outlier: 3.783A pdb=" N ILE O 297 " --> pdb=" O PHE O 294 " (cutoff:3.500A) Processing helix chain 'O' and resid 571 through 577 Processing helix chain 'O' and resid 582 through 614 Processing helix chain 'O' and resid 618 through 644 removed outlier: 3.601A pdb=" N TRP O 641 " --> pdb=" O LEU O 637 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 686 Processing helix chain 'O' and resid 695 through 704 removed outlier: 4.047A pdb=" N LEU O 699 " --> pdb=" O GLY O 695 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU O 700 " --> pdb=" O PHE O 696 " (cutoff:3.500A) Processing helix chain 'O' and resid 712 through 724 removed outlier: 3.574A pdb=" N ASN O 716 " --> pdb=" O ASP O 712 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN O 720 " --> pdb=" O ASN O 716 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP O 722 " --> pdb=" O LEU O 718 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU O 724 " --> pdb=" O GLN O 720 " (cutoff:3.500A) Processing helix chain 'O' and resid 732 through 744 removed outlier: 3.650A pdb=" N VAL O 737 " --> pdb=" O THR O 733 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE O 740 " --> pdb=" O ILE O 736 " (cutoff:3.500A) Processing helix chain 'O' and resid 752 through 764 Processing helix chain 'O' and resid 765 through 777 Processing helix chain 'P' and resid 80 through 89 Processing helix chain 'P' and resid 97 through 124 removed outlier: 3.524A pdb=" N LEU P 103 " --> pdb=" O GLU P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 147 removed outlier: 3.693A pdb=" N GLU P 130 " --> pdb=" O PRO P 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR P 143 " --> pdb=" O LYS P 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP P 146 " --> pdb=" O LYS P 142 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN P 147 " --> pdb=" O THR P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 173 removed outlier: 4.069A pdb=" N THR P 161 " --> pdb=" O HIS P 157 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE P 162 " --> pdb=" O MET P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 188 Processing helix chain 'P' and resid 201 through 206 Processing helix chain 'P' and resid 211 through 215 Processing helix chain 'P' and resid 225 through 238 removed outlier: 3.847A pdb=" N LYS P 229 " --> pdb=" O GLN P 225 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 243 Processing helix chain 'P' and resid 249 through 260 removed outlier: 4.151A pdb=" N LEU P 253 " --> pdb=" O CYS P 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS P 260 " --> pdb=" O LEU P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 278 Processing helix chain 'P' and resid 301 through 319 Processing helix chain 'P' and resid 327 through 339 removed outlier: 4.146A pdb=" N LEU P 332 " --> pdb=" O LEU P 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER P 333 " --> pdb=" O LYS P 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 355 Processing helix chain 'P' and resid 362 through 369 Processing helix chain 'P' and resid 371 through 385 Processing helix chain 'P' and resid 402 through 417 removed outlier: 4.160A pdb=" N GLN P 406 " --> pdb=" O MET P 402 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS P 407 " --> pdb=" O THR P 403 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE P 408 " --> pdb=" O ILE P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 437 through 449 Processing helix chain 'P' and resid 470 through 491 Processing helix chain 'P' and resid 496 through 510 removed outlier: 3.593A pdb=" N LEU P 510 " --> pdb=" O LYS P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 34 Processing helix chain 'Q' and resid 122 through 132 Processing helix chain 'Q' and resid 159 through 167 Processing helix chain 'Q' and resid 168 through 179 removed outlier: 3.906A pdb=" N ILE Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) Proline residue: Q 176 - end of helix removed outlier: 3.894A pdb=" N HIS Q 179 " --> pdb=" O ILE Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 192 Processing helix chain 'Q' and resid 207 through 225 removed outlier: 3.713A pdb=" N HIS Q 212 " --> pdb=" O TYR Q 208 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE Q 213 " --> pdb=" O ARG Q 209 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL Q 214 " --> pdb=" O THR Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 242 removed outlier: 4.340A pdb=" N LYS Q 234 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 261 removed outlier: 3.625A pdb=" N GLY Q 254 " --> pdb=" O LEU Q 250 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU Q 256 " --> pdb=" O GLY Q 252 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU Q 258 " --> pdb=" O GLY Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 278 Processing helix chain 'Q' and resid 306 through 322 removed outlier: 3.640A pdb=" N ILE Q 310 " --> pdb=" O ALA Q 306 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS Q 322 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 351 Processing helix chain 'Q' and resid 362 through 382 removed outlier: 3.539A pdb=" N TYR Q 368 " --> pdb=" O VAL Q 364 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU Q 379 " --> pdb=" O LYS Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 421 Processing helix chain 'Q' and resid 427 through 443 removed outlier: 3.800A pdb=" N ILE Q 431 " --> pdb=" O PRO Q 427 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG Q 441 " --> pdb=" O SER Q 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 245 removed outlier: 4.616A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA7, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA8, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 5.517A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.977A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 751 removed outlier: 6.129A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 826 through 827 removed outlier: 7.706A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.568A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB6, first strand: chain 'A' and resid 1030 through 1032 removed outlier: 6.653A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 4.074A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.476A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AC1, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.758A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 15.453A pdb=" N HIS G 119 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 16.851A pdb=" N GLU G 102 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.758A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TRP G 117 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE G 89 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS G 119 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU G 87 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.289A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP B 143 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N PHE B 153 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B 145 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN B 151 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC5, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC6, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.582A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.524A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC9, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD1, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.456A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.558A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.558A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD5, first strand: chain 'B' and resid 857 through 863 removed outlier: 3.727A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD7, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD8, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD9, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AE1, first strand: chain 'C' and resid 41 through 47 removed outlier: 5.251A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.258A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.325A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE5, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.348A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE8, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE9, first strand: chain 'G' and resid 132 through 141 removed outlier: 3.891A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.357A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF4, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF5, first strand: chain 'M' and resid 10 through 11 Processing sheet with id=AF6, first strand: chain 'M' and resid 14 through 16 removed outlier: 3.754A pdb=" N LYS M 92 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 30 through 31 removed outlier: 4.065A pdb=" N VAL M 52 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR M 65 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 57 through 60 removed outlier: 3.550A pdb=" N TYR O 548 " --> pdb=" O VAL O 539 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP O 536 " --> pdb=" O THR O 510 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR O 510 " --> pdb=" O ASP O 536 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU O 538 " --> pdb=" O ILE O 508 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE O 508 " --> pdb=" O LEU O 538 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS O 540 " --> pdb=" O THR O 506 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 201 through 205 removed outlier: 4.268A pdb=" N GLU O 201 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.629A pdb=" N ILE O 264 " --> pdb=" O LYS O 243 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 305 through 306 Processing sheet with id=AG3, first strand: chain 'O' and resid 361 through 365 removed outlier: 3.731A pdb=" N GLU O 382 " --> pdb=" O THR O 391 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 402 through 405 removed outlier: 6.879A pdb=" N THR O 417 " --> pdb=" O ARG O 403 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 452 through 457 Processing sheet with id=AG6, first strand: chain 'O' and resid 452 through 457 Processing sheet with id=AG7, first strand: chain 'P' and resid 18 through 21 2006 hydrogen bonds defined for protein. 5490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 27.86 Time building geometry restraints manager: 21.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8738 1.32 - 1.45: 13720 1.45 - 1.58: 25422 1.58 - 1.71: 247 1.71 - 1.84: 333 Bond restraints: 48460 Sorted by residual: bond pdb=" CA LEU P 199 " pdb=" C LEU P 199 " ideal model delta sigma weight residual 1.524 1.675 -0.151 1.26e-02 6.30e+03 1.44e+02 bond pdb=" N PRO B 78 " pdb=" CD PRO B 78 " ideal model delta sigma weight residual 1.473 1.608 -0.135 1.40e-02 5.10e+03 9.28e+01 bond pdb=" CA ASP O 353 " pdb=" C ASP O 353 " ideal model delta sigma weight residual 1.524 1.639 -0.115 1.26e-02 6.30e+03 8.40e+01 bond pdb=" CA ILE O 736 " pdb=" C ILE O 736 " ideal model delta sigma weight residual 1.523 1.638 -0.115 1.27e-02 6.20e+03 8.17e+01 bond pdb=" CA SER P 319 " pdb=" C SER P 319 " ideal model delta sigma weight residual 1.526 1.636 -0.110 1.23e-02 6.61e+03 8.04e+01 ... (remaining 48455 not shown) Histogram of bond angle deviations from ideal: 76.90 - 93.39: 11 93.39 - 109.88: 10299 109.88 - 126.37: 54667 126.37 - 142.86: 959 142.86 - 159.35: 1 Bond angle restraints: 65937 Sorted by residual: angle pdb=" C LYS B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta sigma weight residual 120.66 89.99 30.67 1.09e+00 8.42e-01 7.92e+02 angle pdb=" N ASN P 49 " pdb=" CA ASN P 49 " pdb=" C ASN P 49 " ideal model delta sigma weight residual 110.50 76.90 33.60 1.41e+00 5.03e-01 5.68e+02 angle pdb=" N VAL P 356 " pdb=" CA VAL P 356 " pdb=" C VAL P 356 " ideal model delta sigma weight residual 112.17 91.83 20.34 9.50e-01 1.11e+00 4.58e+02 angle pdb=" N HIS O 705 " pdb=" CA HIS O 705 " pdb=" C HIS O 705 " ideal model delta sigma weight residual 113.21 91.01 22.20 1.15e+00 7.56e-01 3.73e+02 angle pdb=" N ASN O 346 " pdb=" CA ASN O 346 " pdb=" CB ASN O 346 " ideal model delta sigma weight residual 110.49 83.11 27.38 1.69e+00 3.50e-01 2.62e+02 ... (remaining 65932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 28356 35.21 - 70.41: 715 70.41 - 105.62: 36 105.62 - 140.82: 1 140.82 - 176.03: 1 Dihedral angle restraints: 29109 sinusoidal: 12586 harmonic: 16523 Sorted by residual: dihedral pdb=" C ILE P 56 " pdb=" N ILE P 56 " pdb=" CA ILE P 56 " pdb=" CB ILE P 56 " ideal model delta harmonic sigma weight residual -122.00 -163.66 41.66 0 2.50e+00 1.60e-01 2.78e+02 dihedral pdb=" N ILE P 56 " pdb=" C ILE P 56 " pdb=" CA ILE P 56 " pdb=" CB ILE P 56 " ideal model delta harmonic sigma weight residual 123.40 159.46 -36.06 0 2.50e+00 1.60e-01 2.08e+02 dihedral pdb=" C GLN Q 147 " pdb=" N GLN Q 147 " pdb=" CA GLN Q 147 " pdb=" CB GLN Q 147 " ideal model delta harmonic sigma weight residual -122.60 -153.16 30.56 0 2.50e+00 1.60e-01 1.49e+02 ... (remaining 29106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.325: 7241 0.325 - 0.650: 118 0.650 - 0.974: 11 0.974 - 1.299: 1 1.299 - 1.624: 2 Chirality restraints: 7373 Sorted by residual: chirality pdb=" CA ILE P 56 " pdb=" N ILE P 56 " pdb=" C ILE P 56 " pdb=" CB ILE P 56 " both_signs ideal model delta sigma weight residual False 2.43 0.81 1.62 2.00e-01 2.50e+01 6.59e+01 chirality pdb=" CA GLN Q 147 " pdb=" N GLN Q 147 " pdb=" C GLN Q 147 " pdb=" CB GLN Q 147 " both_signs ideal model delta sigma weight residual False 2.51 1.13 1.38 2.00e-01 2.50e+01 4.74e+01 chirality pdb=" CA SER Q 145 " pdb=" N SER Q 145 " pdb=" C SER Q 145 " pdb=" CB SER Q 145 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.82e+01 ... (remaining 7370 not shown) Planarity restraints: 8112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG T 2 " 0.437 2.00e-02 2.50e+03 2.01e-01 1.21e+03 pdb=" N9 DG T 2 " -0.061 2.00e-02 2.50e+03 pdb=" C8 DG T 2 " -0.268 2.00e-02 2.50e+03 pdb=" N7 DG T 2 " -0.208 2.00e-02 2.50e+03 pdb=" C5 DG T 2 " -0.077 2.00e-02 2.50e+03 pdb=" C6 DG T 2 " 0.067 2.00e-02 2.50e+03 pdb=" O6 DG T 2 " 0.328 2.00e-02 2.50e+03 pdb=" N1 DG T 2 " 0.033 2.00e-02 2.50e+03 pdb=" C2 DG T 2 " -0.013 2.00e-02 2.50e+03 pdb=" N2 DG T 2 " -0.229 2.00e-02 2.50e+03 pdb=" N3 DG T 2 " 0.038 2.00e-02 2.50e+03 pdb=" C4 DG T 2 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 3 " 0.358 2.00e-02 2.50e+03 1.86e-01 8.64e+02 pdb=" N1 DT T 3 " -0.107 2.00e-02 2.50e+03 pdb=" C2 DT T 3 " -0.196 2.00e-02 2.50e+03 pdb=" O2 DT T 3 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DT T 3 " -0.170 2.00e-02 2.50e+03 pdb=" C4 DT T 3 " -0.015 2.00e-02 2.50e+03 pdb=" O4 DT T 3 " 0.339 2.00e-02 2.50e+03 pdb=" C5 DT T 3 " -0.070 2.00e-02 2.50e+03 pdb=" C7 DT T 3 " -0.033 2.00e-02 2.50e+03 pdb=" C6 DT T 3 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 1 " -0.288 2.00e-02 2.50e+03 1.48e-01 5.49e+02 pdb=" N1 DT T 1 " 0.067 2.00e-02 2.50e+03 pdb=" C2 DT T 1 " 0.161 2.00e-02 2.50e+03 pdb=" O2 DT T 1 " 0.042 2.00e-02 2.50e+03 pdb=" N3 DT T 1 " 0.111 2.00e-02 2.50e+03 pdb=" C4 DT T 1 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT T 1 " -0.281 2.00e-02 2.50e+03 pdb=" C5 DT T 1 " 0.030 2.00e-02 2.50e+03 pdb=" C7 DT T 1 " 0.090 2.00e-02 2.50e+03 pdb=" C6 DT T 1 " 0.065 2.00e-02 2.50e+03 ... (remaining 8109 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 151 1.85 - 2.61: 2357 2.61 - 3.38: 69610 3.38 - 4.14: 121611 4.14 - 4.90: 209817 Nonbonded interactions: 403546 Sorted by model distance: nonbonded pdb=" CD2 HIS P 294 " pdb=" N6 DA T 48 " model vdw 1.089 3.340 nonbonded pdb=" CG PRO O 727 " pdb=" OE2 GLU P 265 " model vdw 1.127 3.440 nonbonded pdb=" O ARG B1105 " pdb=" CG LEU B1196 " model vdw 1.154 3.470 nonbonded pdb=" O HIS O 701 " pdb=" CD2 LEU O 704 " model vdw 1.161 3.460 nonbonded pdb=" NE2 HIS O 571 " pdb=" NZ LYS P 495 " model vdw 1.169 3.200 ... (remaining 403541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 4.330 Check model and map are aligned: 0.690 Set scattering table: 0.450 Process input model: 145.060 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 0.009 0.151 48460 Z= 0.605 Angle : 1.649 34.351 65937 Z= 1.035 Chirality : 0.100 1.624 7373 Planarity : 0.013 0.201 8112 Dihedral : 14.730 176.029 18395 Min Nonbonded Distance : 1.089 Molprobity Statistics. All-atom Clashscore : 88.79 Ramachandran Plot: Outliers : 4.78 % Allowed : 8.88 % Favored : 86.34 % Rotamer: Outliers : 4.61 % Allowed : 4.93 % Favored : 90.46 % Cbeta Deviations : 1.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.09), residues: 5527 helix: -1.91 (0.09), residues: 1945 sheet: -1.62 (0.17), residues: 753 loop : -2.89 (0.10), residues: 2829 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1877 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1645 time to evaluate : 5.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 232 outliers final: 94 residues processed: 1833 average time/residue: 0.6194 time to fit residues: 1843.3650 Evaluate side-chains 1031 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 937 time to evaluate : 5.295 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 10 residues processed: 94 average time/residue: 0.4879 time to fit residues: 88.8818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 477 optimal weight: 5.9990 chunk 429 optimal weight: 7.9990 chunk 238 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 443 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 chunk 330 optimal weight: 2.9990 chunk 513 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 60 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 489 ASN A 553 GLN A 580 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN A 998 HIS A1108 HIS A1320 GLN ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 128 GLN B 183 HIS B 231 HIS B 254 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS B 462 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN B1010 ASN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN B1163 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 335 GLN E 3 GLN E 113 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS G 237 HIS H 134 ASN H 137 GLN L 53 HIS N 51 GLN ** N 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 267 ASN O 301 GLN O 401 ASN ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 ASN O 613 HIS O 617 HIS O 624 GLN ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 701 HIS ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 42 ASN P 145 ASN P 259 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 301 HIS ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 GLN P 511 HIS Q 160 HIS ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 221 HIS ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 260 ASN Q 287 ASN ** Q 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 48460 Z= 0.309 Angle : 0.962 19.685 65937 Z= 0.498 Chirality : 0.053 0.392 7373 Planarity : 0.007 0.155 8112 Dihedral : 13.654 158.295 7160 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 1.56 % Allowed : 7.56 % Favored : 90.88 % Rotamer: Outliers : 0.60 % Allowed : 4.49 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.11), residues: 5527 helix: -0.30 (0.11), residues: 1973 sheet: -0.98 (0.17), residues: 728 loop : -1.98 (0.11), residues: 2826 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1374 time to evaluate : 5.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 6 residues processed: 1398 average time/residue: 0.5927 time to fit residues: 1378.5085 Evaluate side-chains 937 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 931 time to evaluate : 5.335 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4364 time to fit residues: 12.0938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 285 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 427 optimal weight: 40.0000 chunk 349 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 514 optimal weight: 0.3980 chunk 556 optimal weight: 5.9990 chunk 458 optimal weight: 30.0000 chunk 510 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 413 optimal weight: 20.0000 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 425 ASN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN A 636 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1320 GLN ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1647 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN B 469 ASN B 547 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN B 999 GLN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN G 65 HIS G 237 HIS I 27 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 250 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 GLN ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 276 GLN Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 48460 Z= 0.348 Angle : 0.862 17.631 65937 Z= 0.446 Chirality : 0.049 0.389 7373 Planarity : 0.007 0.173 8112 Dihedral : 13.610 161.677 7160 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.32 % Favored : 90.43 % Rotamer: Outliers : 0.26 % Allowed : 3.80 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.11), residues: 5527 helix: 0.17 (0.11), residues: 1974 sheet: -0.80 (0.18), residues: 731 loop : -1.77 (0.12), residues: 2822 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1193 time to evaluate : 5.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 1202 average time/residue: 0.5776 time to fit residues: 1165.3938 Evaluate side-chains 842 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 839 time to evaluate : 5.653 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4092 time to fit residues: 9.9559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4472 > 50: distance: 21 - 25: 10.520 distance: 25 - 26: 16.221 distance: 26 - 27: 32.659 distance: 26 - 29: 21.460 distance: 27 - 28: 28.576 distance: 27 - 33: 11.531 distance: 29 - 30: 21.063 distance: 30 - 31: 13.139 distance: 31 - 32: 13.650 distance: 33 - 34: 19.065 distance: 34 - 35: 25.746 distance: 34 - 37: 23.003 distance: 35 - 36: 19.374 distance: 35 - 42: 40.648 distance: 37 - 38: 18.674 distance: 38 - 39: 26.219 distance: 39 - 41: 6.174 distance: 42 - 43: 32.294 distance: 42 - 48: 34.946 distance: 43 - 44: 37.603 distance: 43 - 46: 23.601 distance: 44 - 45: 43.643 distance: 46 - 47: 12.335 distance: 47 - 48: 10.058 distance: 49 - 50: 26.608 distance: 50 - 51: 14.778 distance: 50 - 53: 27.887 distance: 51 - 52: 30.944 distance: 51 - 56: 41.272 distance: 53 - 55: 29.486 distance: 56 - 57: 19.002 distance: 57 - 58: 18.167 distance: 57 - 60: 23.089 distance: 58 - 59: 33.883 distance: 58 - 65: 16.405 distance: 60 - 61: 7.622 distance: 61 - 62: 47.108 distance: 62 - 63: 20.877 distance: 62 - 64: 6.874 distance: 65 - 66: 12.590 distance: 66 - 67: 5.303 distance: 66 - 69: 32.587 distance: 69 - 70: 23.561 distance: 70 - 71: 12.629 distance: 70 - 72: 22.150 distance: 73 - 74: 46.537 distance: 74 - 75: 29.805 distance: 74 - 77: 30.155 distance: 75 - 76: 20.922 distance: 75 - 81: 18.330 distance: 76 - 106: 32.370 distance: 77 - 78: 15.351 distance: 78 - 79: 38.742 distance: 82 - 85: 11.809 distance: 83 - 84: 39.818 distance: 83 - 89: 18.446 distance: 84 - 114: 32.176 distance: 85 - 86: 16.883 distance: 86 - 87: 43.737 distance: 86 - 88: 33.275 distance: 89 - 90: 14.155 distance: 90 - 91: 23.732 distance: 90 - 93: 15.513 distance: 91 - 92: 29.790 distance: 91 - 97: 16.906 distance: 92 - 122: 22.750 distance: 93 - 94: 29.319 distance: 94 - 96: 36.491 distance: 97 - 98: 11.604 distance: 98 - 99: 16.881 distance: 98 - 101: 9.492 distance: 99 - 100: 14.791 distance: 99 - 106: 5.871 distance: 100 - 130: 20.447 distance: 101 - 102: 18.611 distance: 102 - 103: 12.344 distance: 103 - 104: 27.941 distance: 103 - 105: 25.251