Starting phenix.real_space_refine on Sun Nov 17 21:16:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/11_2024/5w65_8775.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/11_2024/5w65_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_8775/11_2024/5w65_8775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/11_2024/5w65_8775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/11_2024/5w65_8775.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/11_2024/5w65_8775.cif" } 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. Time to flip 30 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 25.18, per 1000 atoms: 0.53 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 - 3.00 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: 14.71 Conformation dependent library (CDL) restraints added in 6.4 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: 17.21 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: 29.66 Time building geometry restraints manager: 16.72 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: 0.00 - 6.87: 65364 6.87 - 13.74: 505 13.74 - 20.61: 56 20.61 - 27.48: 9 27.48 - 34.35: 3 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: 28454 35.21 - 70.41: 731 70.41 - 105.62: 38 105.62 - 140.82: 1 140.82 - 176.03: 1 Dihedral angle restraints: 29225 sinusoidal: 12702 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 29222 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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.290 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: 1.870 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 134.900 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.160 ------------------------------------------------------------------------------- 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 : 14.853 176.029 18511 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP Q 273 HIS 0.017 0.003 HIS O 368 PHE 0.099 0.004 PHE Q 188 TYR 0.097 0.006 TYR Q 443 ARG 0.087 0.010 ARG J 69 *********************** 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 to be fit. rotamer outliers: 232 poor density : 1645 time to evaluate : 5.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8501 (tp) cc_final: 0.8279 (tp) REVERT: A 217 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8053 (mttm) REVERT: A 388 LYS cc_start: 0.8148 (tttt) cc_final: 0.7376 (tptm) REVERT: A 472 MET cc_start: 0.8745 (mmp) cc_final: 0.8526 (mmp) REVERT: A 500 VAL cc_start: 0.9300 (p) cc_final: 0.8916 (t) REVERT: A 600 MET cc_start: 0.8112 (ttt) cc_final: 0.7798 (ttt) REVERT: A 635 MET cc_start: 0.7681 (ttp) cc_final: 0.7323 (ttp) REVERT: A 640 ASN cc_start: 0.7957 (t0) cc_final: 0.6939 (m-40) REVERT: A 780 ILE cc_start: 0.8933 (pt) cc_final: 0.8516 (pt) REVERT: A 947 LEU cc_start: 0.7740 (mp) cc_final: 0.7474 (mp) REVERT: A 960 MET cc_start: 0.7998 (mtm) cc_final: 0.7656 (mtp) REVERT: A 995 TYR cc_start: 0.8163 (t80) cc_final: 0.7881 (t80) REVERT: A 1007 ILE cc_start: 0.9149 (mt) cc_final: 0.8723 (mm) REVERT: A 1170 MET cc_start: 0.7986 (mmm) cc_final: 0.7575 (tpp) REVERT: A 1238 MET cc_start: 0.7812 (ttp) cc_final: 0.7282 (ttp) REVERT: A 1588 MET cc_start: 0.7995 (tpt) cc_final: 0.7666 (tpp) REVERT: B 38 LEU cc_start: 0.8645 (tp) cc_final: 0.8434 (tp) REVERT: B 72 VAL cc_start: 0.8453 (t) cc_final: 0.7902 (p) REVERT: B 163 VAL cc_start: 0.8638 (m) cc_final: 0.8328 (t) REVERT: B 242 ASP cc_start: 0.7980 (p0) cc_final: 0.7630 (p0) REVERT: B 270 LEU cc_start: 0.8579 (tp) cc_final: 0.8046 (mt) REVERT: B 378 ILE cc_start: 0.9035 (mt) cc_final: 0.8814 (mm) REVERT: B 411 MET cc_start: 0.8139 (mtp) cc_final: 0.7812 (mtp) REVERT: B 472 SER cc_start: 0.9016 (p) cc_final: 0.8710 (p) REVERT: B 494 TYR cc_start: 0.6722 (m-10) cc_final: 0.6258 (m-10) REVERT: B 521 LEU cc_start: 0.8634 (mt) cc_final: 0.8376 (mm) REVERT: B 531 VAL cc_start: 0.8755 (m) cc_final: 0.8529 (p) REVERT: B 647 SER cc_start: 0.9288 (m) cc_final: 0.9006 (p) REVERT: B 716 MET cc_start: 0.7835 (mtm) cc_final: 0.7550 (mtp) REVERT: B 717 TYR cc_start: 0.7250 (m-10) cc_final: 0.6357 (m-10) REVERT: B 782 ASP cc_start: 0.7292 (p0) cc_final: 0.6857 (p0) REVERT: B 783 MET cc_start: 0.6288 (mtt) cc_final: 0.5910 (mtt) REVERT: B 787 MET cc_start: 0.8685 (ptm) cc_final: 0.8257 (ppp) REVERT: B 788 ILE cc_start: 0.8860 (mm) cc_final: 0.8269 (mm) REVERT: B 791 LYS cc_start: 0.7340 (tttm) cc_final: 0.6996 (tttm) REVERT: B 795 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6739 (mm-30) REVERT: B 918 SER cc_start: 0.8196 (t) cc_final: 0.7893 (t) REVERT: B 959 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8554 (p) REVERT: B 1089 GLN cc_start: 0.7842 (tt0) cc_final: 0.7617 (tt0) REVERT: B 1102 SER cc_start: 0.7598 (m) cc_final: 0.7285 (m) REVERT: B 1117 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8759 (t) REVERT: C 72 ILE cc_start: 0.9016 (mt) cc_final: 0.8771 (mt) REVERT: C 136 LEU cc_start: 0.8257 (tt) cc_final: 0.7971 (tp) REVERT: C 188 ASP cc_start: 0.7144 (m-30) cc_final: 0.6921 (m-30) REVERT: C 220 SER cc_start: 0.9374 (m) cc_final: 0.8912 (p) REVERT: C 313 ILE cc_start: 0.8951 (mt) cc_final: 0.8601 (mt) REVERT: F 130 ILE cc_start: 0.8123 (mt) cc_final: 0.7822 (mt) REVERT: F 142 SER cc_start: 0.8323 (m) cc_final: 0.8034 (p) REVERT: G 96 SER cc_start: 0.3765 (OUTLIER) cc_final: 0.2950 (p) REVERT: G 237 HIS cc_start: 0.5306 (m-70) cc_final: 0.4947 (m-70) REVERT: G 245 VAL cc_start: 0.7149 (t) cc_final: 0.6747 (t) REVERT: I 16 LEU cc_start: 0.7800 (tp) cc_final: 0.7504 (tp) REVERT: J 21 TYR cc_start: 0.8363 (t80) cc_final: 0.8154 (t80) REVERT: J 66 LEU cc_start: 0.7305 (mt) cc_final: 0.7007 (tt) REVERT: K 76 LEU cc_start: 0.8013 (tp) cc_final: 0.7785 (tt) REVERT: K 98 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6519 (mt-10) REVERT: L 46 VAL cc_start: 0.7835 (t) cc_final: 0.7617 (p) REVERT: L 54 ARG cc_start: 0.6149 (mtm180) cc_final: 0.5567 (mtm180) REVERT: M 19 PRO cc_start: 0.7306 (Cg_exo) cc_final: 0.7085 (Cg_endo) REVERT: M 48 LYS cc_start: 0.0671 (OUTLIER) cc_final: -0.0428 (ptmm) REVERT: M 52 VAL cc_start: 0.8327 (t) cc_final: 0.7675 (p) REVERT: M 74 ASN cc_start: 0.7144 (t0) cc_final: 0.6056 (t0) REVERT: M 100 VAL cc_start: 0.7603 (t) cc_final: 0.7299 (m) REVERT: O 463 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6615 (pp) REVERT: P 12 THR cc_start: 0.5525 (p) cc_final: 0.4941 (p) REVERT: P 58 ARG cc_start: 0.1299 (OUTLIER) cc_final: 0.0965 (ttm170) REVERT: P 60 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5475 (mt) REVERT: P 147 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: P 150 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: P 321 ASP cc_start: 0.0311 (OUTLIER) cc_final: -0.0106 (t0) REVERT: P 400 MET cc_start: 0.6318 (mpm) cc_final: 0.4598 (mpp) REVERT: P 419 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6189 (pt) REVERT: P 512 ARG cc_start: 0.3569 (OUTLIER) cc_final: 0.1714 (mtm-85) REVERT: Q 147 GLN cc_start: 0.5818 (OUTLIER) cc_final: 0.4541 (pp30) REVERT: Q 153 ASN cc_start: 0.6990 (OUTLIER) cc_final: 0.6625 (p0) REVERT: Q 202 THR cc_start: 0.7676 (m) cc_final: 0.6883 (t) REVERT: Q 216 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8487 (mp) REVERT: Q 238 THR cc_start: 0.8097 (p) cc_final: 0.7671 (p) REVERT: Q 239 LEU cc_start: 0.7544 (tp) cc_final: 0.7343 (tp) REVERT: Q 290 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5684 (m-10) outliers start: 232 outliers final: 94 residues processed: 1833 average time/residue: 0.6487 time to fit residues: 1944.3310 Evaluate side-chains 1065 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 955 time to evaluate : 5.618 ------------------------------------------------------------------------------- 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: 2.9990 chunk 429 optimal weight: 20.0000 chunk 238 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 229 optimal weight: 0.9980 chunk 443 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 513 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN A 425 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 553 GLN A 580 HIS A 639 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 785 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS A1108 HIS A1191 GLN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 128 GLN B 183 HIS B 231 HIS B 254 ASN B 339 GLN B 399 HIS B 462 GLN B 499 HIS ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 575 HIS B 999 GLN B1010 ASN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 H 134 ASN L 53 HIS N 51 GLN O 267 ASN O 301 GLN ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 615 ASN O 617 HIS O 624 GLN O 701 HIS ** P 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 42 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 ASN P 206 GLN ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 368 GLN ** 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 260 ASN Q 276 GLN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 48460 Z= 0.323 Angle : 0.989 20.402 65937 Z= 0.514 Chirality : 0.054 0.388 7373 Planarity : 0.007 0.158 8112 Dihedral : 13.815 149.521 7276 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 1.52 % Allowed : 7.71 % Favored : 90.77 % Rotamer: Outliers : 0.60 % Allowed : 3.96 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -1.93 (0.11), residues: 5527 helix: -0.38 (0.11), residues: 1987 sheet: -1.07 (0.17), residues: 735 loop : -2.03 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP O 399 HIS 0.025 0.002 HIS P 294 PHE 0.048 0.003 PHE P 110 TYR 0.035 0.003 TYR A 723 ARG 0.012 0.001 ARG O 229 *********************** 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 1431 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 1401 time to evaluate : 5.674 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: A 94 LEU cc_start: 0.8128 (pp) cc_final: 0.7746 (pp) REVERT: A 217 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8056 (mttm) REVERT: A 356 PHE cc_start: 0.6576 (m-10) cc_final: 0.6155 (m-10) REVERT: A 424 MET cc_start: 0.7130 (mmm) cc_final: 0.6550 (mmm) REVERT: A 589 MET cc_start: 0.8285 (mmm) cc_final: 0.8009 (mmm) REVERT: A 618 TYR cc_start: 0.8151 (m-80) cc_final: 0.7576 (m-80) REVERT: A 640 ASN cc_start: 0.7423 (t0) cc_final: 0.7167 (m-40) REVERT: A 669 LEU cc_start: 0.9150 (mp) cc_final: 0.8930 (mp) REVERT: A 820 TYR cc_start: 0.8393 (t80) cc_final: 0.8060 (t80) REVERT: A 907 VAL cc_start: 0.8676 (t) cc_final: 0.8344 (p) REVERT: A 947 LEU cc_start: 0.7995 (mp) cc_final: 0.7746 (mp) REVERT: A 960 MET cc_start: 0.7978 (mtm) cc_final: 0.7601 (mtp) REVERT: A 994 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8222 (mt-10) REVERT: A 1024 THR cc_start: 0.8338 (m) cc_final: 0.7743 (t) REVERT: A 1170 MET cc_start: 0.8051 (mmm) cc_final: 0.7552 (tpp) REVERT: A 1176 ARG cc_start: 0.8016 (mmp-170) cc_final: 0.7794 (mmp80) REVERT: A 1238 MET cc_start: 0.7614 (ttp) cc_final: 0.6721 (ttm) REVERT: A 1491 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6536 (mm-30) REVERT: A 1588 MET cc_start: 0.8112 (tpt) cc_final: 0.7721 (tpp) REVERT: A 1613 MET cc_start: 0.7143 (ttm) cc_final: 0.6259 (ttm) REVERT: A 1633 GLN cc_start: 0.7244 (mm-40) cc_final: 0.7004 (mm-40) REVERT: B 72 VAL cc_start: 0.8120 (t) cc_final: 0.7825 (p) REVERT: B 166 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7738 (mm-40) REVERT: B 242 ASP cc_start: 0.7872 (p0) cc_final: 0.7297 (p0) REVERT: B 270 LEU cc_start: 0.8350 (tp) cc_final: 0.7816 (mt) REVERT: B 378 ILE cc_start: 0.9079 (mt) cc_final: 0.8778 (mm) REVERT: B 380 LYS cc_start: 0.8166 (tttt) cc_final: 0.7653 (ttmm) REVERT: B 494 TYR cc_start: 0.6789 (m-10) cc_final: 0.6378 (m-80) REVERT: B 496 PHE cc_start: 0.8266 (t80) cc_final: 0.7989 (t80) REVERT: B 504 HIS cc_start: 0.8242 (t70) cc_final: 0.8037 (t70) REVERT: B 531 VAL cc_start: 0.9109 (m) cc_final: 0.8728 (p) REVERT: B 595 TRP cc_start: 0.8458 (m100) cc_final: 0.8211 (m100) REVERT: B 671 TYR cc_start: 0.7757 (m-80) cc_final: 0.7495 (m-80) REVERT: B 791 LYS cc_start: 0.7392 (tttm) cc_final: 0.6836 (tttm) REVERT: B 900 THR cc_start: 0.8305 (m) cc_final: 0.7895 (p) REVERT: B 918 SER cc_start: 0.7736 (t) cc_final: 0.7458 (t) REVERT: B 986 PHE cc_start: 0.7726 (m-80) cc_final: 0.7079 (m-10) REVERT: B 1031 VAL cc_start: 0.8679 (t) cc_final: 0.8462 (p) REVERT: B 1077 ASP cc_start: 0.6291 (m-30) cc_final: 0.5955 (m-30) REVERT: B 1093 LEU cc_start: 0.8208 (tp) cc_final: 0.7843 (tp) REVERT: C 101 ILE cc_start: 0.9237 (mt) cc_final: 0.8994 (mm) REVERT: C 191 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8612 (mp) REVERT: C 220 SER cc_start: 0.9171 (m) cc_final: 0.8687 (p) REVERT: D 14 THR cc_start: 0.8260 (p) cc_final: 0.7883 (p) REVERT: F 82 THR cc_start: 0.8407 (t) cc_final: 0.8201 (p) REVERT: F 97 ARG cc_start: 0.8343 (tpt170) cc_final: 0.7840 (tpt-90) REVERT: F 114 GLU cc_start: 0.7650 (tp30) cc_final: 0.7423 (tp30) REVERT: F 142 SER cc_start: 0.8320 (m) cc_final: 0.8041 (p) REVERT: J 49 MET cc_start: 0.8729 (tpp) cc_final: 0.8457 (mmm) REVERT: J 56 LEU cc_start: 0.9009 (tp) cc_final: 0.8532 (tt) REVERT: K 66 VAL cc_start: 0.9254 (m) cc_final: 0.9036 (t) REVERT: K 81 MET cc_start: 0.7628 (mmm) cc_final: 0.7425 (mmm) REVERT: K 125 MET cc_start: 0.6955 (mtm) cc_final: 0.6661 (mtt) REVERT: K 127 LEU cc_start: 0.8705 (tt) cc_final: 0.8474 (tt) REVERT: M 88 ILE cc_start: 0.5025 (tt) cc_final: 0.4393 (tt) REVERT: O 421 ILE cc_start: 0.7771 (mt) cc_final: 0.7450 (mt) REVERT: P 192 TYR cc_start: 0.5904 (t80) cc_final: 0.3636 (t80) REVERT: P 369 TRP cc_start: 0.5785 (m-10) cc_final: 0.5252 (m100) REVERT: P 379 LYS cc_start: 0.7418 (mmmt) cc_final: 0.7216 (tppp) REVERT: Q 214 VAL cc_start: 0.8321 (t) cc_final: 0.8118 (t) REVERT: Q 216 LEU cc_start: 0.8670 (mt) cc_final: 0.8268 (mt) REVERT: Q 238 THR cc_start: 0.8337 (p) cc_final: 0.7798 (p) outliers start: 30 outliers final: 6 residues processed: 1421 average time/residue: 0.5906 time to fit residues: 1395.8873 Evaluate side-chains 977 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 970 time to evaluate : 5.405 ------------------------------------------------------------------------------- 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: 0.0070 chunk 159 optimal weight: 8.9990 chunk 427 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 514 optimal weight: 10.0000 chunk 556 optimal weight: 20.0000 chunk 458 optimal weight: 20.0000 chunk 510 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 413 optimal weight: 30.0000 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 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 A1320 GLN ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1647 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 HIS B 547 HIS B 710 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** 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 K 118 GLN M 54 HIS ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN ** O 259 ASN ** 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 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 HIS ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN P 486 GLN ** Q 15 GLN ** 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 48460 Z= 0.350 Angle : 0.881 18.873 65937 Z= 0.458 Chirality : 0.050 0.380 7373 Planarity : 0.007 0.169 8112 Dihedral : 13.838 162.078 7276 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 1.23 % Allowed : 7.78 % Favored : 90.99 % Rotamer: Outliers : 0.22 % Allowed : 3.80 % Favored : 95.98 % 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: -1.41 (0.11), residues: 5527 helix: 0.18 (0.11), residues: 1983 sheet: -0.99 (0.17), residues: 776 loop : -1.76 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP O 324 HIS 0.017 0.002 HIS P 33 PHE 0.036 0.003 PHE P 377 TYR 0.033 0.002 TYR B1184 ARG 0.014 0.001 ARG E 192 *********************** 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 1219 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1208 time to evaluate : 5.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8025 (mttm) REVERT: A 600 MET cc_start: 0.8586 (tpp) cc_final: 0.8157 (tpp) REVERT: A 618 TYR cc_start: 0.8081 (m-80) cc_final: 0.7582 (m-80) REVERT: A 811 SER cc_start: 0.8202 (p) cc_final: 0.7895 (p) REVERT: A 907 VAL cc_start: 0.8676 (t) cc_final: 0.8187 (p) REVERT: A 947 LEU cc_start: 0.7992 (mp) cc_final: 0.7557 (mp) REVERT: A 960 MET cc_start: 0.7651 (mtm) cc_final: 0.7341 (mtp) REVERT: A 982 VAL cc_start: 0.8153 (t) cc_final: 0.7931 (t) REVERT: A 1024 THR cc_start: 0.8557 (m) cc_final: 0.8004 (t) REVERT: A 1038 ILE cc_start: 0.9055 (mm) cc_final: 0.8853 (mm) REVERT: A 1170 MET cc_start: 0.8004 (mmm) cc_final: 0.7453 (tpp) REVERT: A 1176 ARG cc_start: 0.8179 (mmp-170) cc_final: 0.7975 (mmp80) REVERT: A 1238 MET cc_start: 0.7351 (ttp) cc_final: 0.7045 (ttm) REVERT: A 1584 LEU cc_start: 0.8457 (tp) cc_final: 0.8253 (tp) REVERT: A 1608 SER cc_start: 0.9019 (t) cc_final: 0.8727 (t) REVERT: A 1613 MET cc_start: 0.7205 (ttm) cc_final: 0.6189 (ttm) REVERT: B 67 ASP cc_start: 0.6321 (t70) cc_final: 0.5968 (t70) REVERT: B 163 VAL cc_start: 0.8906 (m) cc_final: 0.8568 (t) REVERT: B 175 MET cc_start: 0.7176 (mtp) cc_final: 0.6946 (mtp) REVERT: B 178 TYR cc_start: 0.8163 (t80) cc_final: 0.7914 (t80) REVERT: B 242 ASP cc_start: 0.7943 (p0) cc_final: 0.7548 (p0) REVERT: B 277 LEU cc_start: 0.8042 (mm) cc_final: 0.7721 (mm) REVERT: B 283 THR cc_start: 0.8719 (p) cc_final: 0.8455 (p) REVERT: B 299 ASP cc_start: 0.6633 (t0) cc_final: 0.6367 (t0) REVERT: B 378 ILE cc_start: 0.8987 (mt) cc_final: 0.8766 (mm) REVERT: B 380 LYS cc_start: 0.8276 (tttt) cc_final: 0.7858 (ttmm) REVERT: B 419 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6426 (mm-30) REVERT: B 494 TYR cc_start: 0.6961 (m-10) cc_final: 0.6717 (m-80) REVERT: B 531 VAL cc_start: 0.9121 (m) cc_final: 0.8625 (p) REVERT: B 782 ASP cc_start: 0.7111 (p0) cc_final: 0.6609 (p0) REVERT: B 884 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6966 (mm-30) REVERT: B 924 LYS cc_start: 0.7818 (pttm) cc_final: 0.7448 (pttt) REVERT: B 962 MET cc_start: 0.7800 (tpp) cc_final: 0.7506 (tpp) REVERT: B 1013 MET cc_start: 0.7176 (mtp) cc_final: 0.6975 (mtp) REVERT: B 1057 MET cc_start: 0.8332 (mmp) cc_final: 0.8102 (mmm) REVERT: B 1093 LEU cc_start: 0.8284 (tp) cc_final: 0.7882 (tp) REVERT: B 1175 THR cc_start: 0.8839 (m) cc_final: 0.8485 (m) REVERT: B 1183 LYS cc_start: 0.8606 (pttt) cc_final: 0.8001 (pttt) REVERT: C 112 MET cc_start: 0.7833 (mmm) cc_final: 0.7388 (mmm) REVERT: C 191 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8699 (mp) REVERT: C 220 SER cc_start: 0.9233 (m) cc_final: 0.8817 (p) REVERT: C 287 ASP cc_start: 0.4938 (p0) cc_final: 0.4667 (p0) REVERT: D 14 THR cc_start: 0.7950 (p) cc_final: 0.7613 (p) REVERT: E 74 ASP cc_start: 0.7046 (p0) cc_final: 0.6811 (p0) REVERT: F 89 GLU cc_start: 0.7829 (pt0) cc_final: 0.7611 (pt0) REVERT: J 27 GLU cc_start: 0.7734 (pp20) cc_final: 0.7491 (pp20) REVERT: J 47 ARG cc_start: 0.8295 (mmm160) cc_final: 0.7284 (mmm-85) REVERT: J 56 LEU cc_start: 0.8959 (tp) cc_final: 0.8549 (tt) REVERT: K 66 VAL cc_start: 0.8974 (m) cc_final: 0.8763 (t) REVERT: K 81 MET cc_start: 0.7863 (mmm) cc_final: 0.7625 (mmm) REVERT: K 125 MET cc_start: 0.6973 (mtm) cc_final: 0.6396 (mtt) REVERT: K 127 LEU cc_start: 0.8792 (tt) cc_final: 0.8355 (tt) REVERT: K 130 VAL cc_start: 0.8898 (t) cc_final: 0.8499 (t) REVERT: L 49 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7866 (mmtt) REVERT: M 23 VAL cc_start: 0.7837 (p) cc_final: 0.7406 (m) REVERT: O 383 ILE cc_start: 0.5809 (mt) cc_final: 0.4701 (mt) REVERT: P 158 MET cc_start: 0.4843 (ptt) cc_final: 0.4425 (ptt) REVERT: P 192 TYR cc_start: 0.6448 (t80) cc_final: 0.6120 (t80) REVERT: P 353 VAL cc_start: 0.8424 (t) cc_final: 0.8202 (t) REVERT: P 369 TRP cc_start: 0.5653 (m-10) cc_final: 0.4895 (m100) REVERT: P 493 ILE cc_start: 0.7497 (pt) cc_final: 0.7114 (pt) REVERT: Q 21 TYR cc_start: 0.6202 (m-80) cc_final: 0.5989 (m-80) REVERT: Q 202 THR cc_start: 0.7694 (m) cc_final: 0.7271 (m) REVERT: Q 212 HIS cc_start: 0.7368 (m-70) cc_final: 0.7005 (m90) REVERT: Q 213 ILE cc_start: 0.8748 (mt) cc_final: 0.8509 (mt) REVERT: Q 216 LEU cc_start: 0.8549 (mt) cc_final: 0.8248 (mt) outliers start: 11 outliers final: 0 residues processed: 1215 average time/residue: 0.5451 time to fit residues: 1104.1247 Evaluate side-chains 891 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 890 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 508 optimal weight: 5.9990 chunk 387 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 245 optimal weight: 0.6980 chunk 345 optimal weight: 4.9990 chunk 516 optimal weight: 20.0000 chunk 547 optimal weight: 0.3980 chunk 269 optimal weight: 6.9990 chunk 489 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1320 GLN ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 462 GLN B 469 ASN B 710 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN O 259 ASN ** O 270 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 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 384 GLN ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 287 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 48460 Z= 0.261 Angle : 0.817 17.748 65937 Z= 0.423 Chirality : 0.048 0.431 7373 Planarity : 0.007 0.173 8112 Dihedral : 13.866 162.685 7276 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 1.16 % Allowed : 7.62 % Favored : 91.22 % Rotamer: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % 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: -1.14 (0.11), residues: 5527 helix: 0.45 (0.11), residues: 1987 sheet: -0.87 (0.17), residues: 804 loop : -1.66 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 530 HIS 0.014 0.001 HIS P 33 PHE 0.036 0.002 PHE A 57 TYR 0.029 0.002 TYR B1184 ARG 0.021 0.001 ARG M 31 *********************** REFINEMENT MACRO_CYCLE 4 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 1186 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1178 time to evaluate : 4.149 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: A 3 ILE cc_start: 0.8646 (pt) cc_final: 0.7998 (pt) REVERT: A 19 LEU cc_start: 0.7246 (mt) cc_final: 0.6993 (mt) REVERT: A 213 ASN cc_start: 0.7664 (t0) cc_final: 0.7442 (t0) REVERT: A 217 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8076 (mttp) REVERT: A 424 MET cc_start: 0.7011 (mmm) cc_final: 0.6735 (mmm) REVERT: A 618 TYR cc_start: 0.8418 (m-80) cc_final: 0.8058 (m-10) REVERT: A 669 LEU cc_start: 0.9113 (mp) cc_final: 0.8900 (mp) REVERT: A 699 CYS cc_start: 0.7960 (p) cc_final: 0.7694 (p) REVERT: A 780 ILE cc_start: 0.8952 (pt) cc_final: 0.8717 (pt) REVERT: A 811 SER cc_start: 0.8076 (p) cc_final: 0.7687 (p) REVERT: A 907 VAL cc_start: 0.8720 (t) cc_final: 0.8319 (p) REVERT: A 944 MET cc_start: 0.6502 (mtm) cc_final: 0.6210 (mtm) REVERT: A 947 LEU cc_start: 0.7972 (mp) cc_final: 0.7494 (mp) REVERT: A 994 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 1024 THR cc_start: 0.8378 (m) cc_final: 0.8082 (t) REVERT: A 1049 MET cc_start: 0.6945 (mtp) cc_final: 0.6550 (mmm) REVERT: A 1170 MET cc_start: 0.7868 (mmm) cc_final: 0.7365 (tpp) REVERT: A 1176 ARG cc_start: 0.8246 (mmp-170) cc_final: 0.8032 (mmp80) REVERT: A 1191 GLN cc_start: 0.7927 (mt0) cc_final: 0.7601 (mt0) REVERT: A 1238 MET cc_start: 0.7461 (ttp) cc_final: 0.6978 (ttm) REVERT: A 1589 MET cc_start: 0.8005 (mtt) cc_final: 0.7744 (mtt) REVERT: A 1613 MET cc_start: 0.7393 (ttm) cc_final: 0.6726 (ttm) REVERT: B 67 ASP cc_start: 0.6071 (t70) cc_final: 0.5742 (t70) REVERT: B 242 ASP cc_start: 0.7991 (p0) cc_final: 0.7581 (p0) REVERT: B 378 ILE cc_start: 0.9104 (mt) cc_final: 0.8806 (mm) REVERT: B 380 LYS cc_start: 0.8225 (tttt) cc_final: 0.7805 (ttmm) REVERT: B 494 TYR cc_start: 0.6434 (m-10) cc_final: 0.6122 (m-10) REVERT: B 531 VAL cc_start: 0.9126 (m) cc_final: 0.8792 (p) REVERT: B 577 PHE cc_start: 0.6958 (p90) cc_final: 0.6495 (p90) REVERT: B 782 ASP cc_start: 0.7185 (p0) cc_final: 0.6759 (p0) REVERT: B 783 MET cc_start: 0.7188 (mtm) cc_final: 0.6275 (mtm) REVERT: B 924 LYS cc_start: 0.7885 (pttm) cc_final: 0.7646 (ptpt) REVERT: B 962 MET cc_start: 0.7696 (tpp) cc_final: 0.7391 (tpp) REVERT: B 1037 ARG cc_start: 0.8454 (ptt90) cc_final: 0.8224 (ttp-170) REVERT: B 1057 MET cc_start: 0.8155 (mmp) cc_final: 0.7848 (mmm) REVERT: B 1077 ASP cc_start: 0.6465 (m-30) cc_final: 0.6192 (m-30) REVERT: B 1086 PHE cc_start: 0.7705 (m-80) cc_final: 0.7272 (m-80) REVERT: B 1094 ASN cc_start: 0.8483 (m110) cc_final: 0.8150 (m110) REVERT: B 1111 LEU cc_start: 0.7687 (tp) cc_final: 0.7456 (tp) REVERT: B 1183 LYS cc_start: 0.8477 (pttt) cc_final: 0.8221 (pttt) REVERT: C 112 MET cc_start: 0.7738 (mmm) cc_final: 0.7261 (mmm) REVERT: C 220 SER cc_start: 0.9211 (m) cc_final: 0.8925 (t) REVERT: E 2 ASP cc_start: 0.4125 (p0) cc_final: 0.3646 (p0) REVERT: E 16 PHE cc_start: 0.5605 (t80) cc_final: 0.5270 (t80) REVERT: F 102 SER cc_start: 0.8309 (p) cc_final: 0.8107 (p) REVERT: F 130 ILE cc_start: 0.7976 (mt) cc_final: 0.7648 (mt) REVERT: F 132 LEU cc_start: 0.8595 (mm) cc_final: 0.8253 (mm) REVERT: G 73 TYR cc_start: 0.6779 (t80) cc_final: 0.6503 (t80) REVERT: I 4 VAL cc_start: 0.8001 (m) cc_final: 0.7747 (m) REVERT: I 7 LEU cc_start: 0.6618 (mp) cc_final: 0.6408 (mp) REVERT: J 1 MET cc_start: 0.6347 (tpp) cc_final: 0.6125 (tpp) REVERT: K 66 VAL cc_start: 0.8953 (m) cc_final: 0.8663 (t) REVERT: K 80 ILE cc_start: 0.8718 (mt) cc_final: 0.8506 (mt) REVERT: K 125 MET cc_start: 0.6863 (mtm) cc_final: 0.6352 (mtt) REVERT: K 127 LEU cc_start: 0.8638 (tt) cc_final: 0.8346 (tt) REVERT: K 137 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6053 (mt-10) REVERT: L 49 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7872 (mmtt) REVERT: O 415 LEU cc_start: 0.6284 (tp) cc_final: 0.6018 (tp) REVERT: P 489 VAL cc_start: 0.8298 (t) cc_final: 0.7725 (t) REVERT: P 490 ASP cc_start: 0.5474 (m-30) cc_final: 0.4866 (m-30) REVERT: Q 7 THR cc_start: 0.7522 (p) cc_final: 0.7231 (p) REVERT: Q 216 LEU cc_start: 0.8575 (mt) cc_final: 0.8252 (mt) REVERT: Q 238 THR cc_start: 0.8365 (p) cc_final: 0.7932 (p) outliers start: 8 outliers final: 2 residues processed: 1182 average time/residue: 0.5502 time to fit residues: 1091.1237 Evaluate side-chains 893 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 890 time to evaluate : 5.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 455 optimal weight: 8.9990 chunk 310 optimal weight: 0.2980 chunk 7 optimal weight: 9.9990 chunk 407 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 466 optimal weight: 8.9990 chunk 378 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 279 optimal weight: 0.9980 chunk 491 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 overall best weight: 4.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 382 GLN A 383 ASN A 592 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1320 GLN ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1527 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 313 GLN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 769 GLN ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 HIS ** P 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN Q 246 GLN Q 287 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 402 ASN ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 48460 Z= 0.333 Angle : 0.820 20.828 65937 Z= 0.425 Chirality : 0.049 0.411 7373 Planarity : 0.006 0.180 8112 Dihedral : 13.915 165.083 7276 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 1.05 % Allowed : 7.96 % Favored : 90.99 % Rotamer: Outliers : 0.08 % Allowed : 2.90 % Favored : 97.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % 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: -1.05 (0.11), residues: 5527 helix: 0.57 (0.11), residues: 1986 sheet: -0.82 (0.17), residues: 788 loop : -1.64 (0.12), residues: 2753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP N 54 HIS 0.016 0.001 HIS O 479 PHE 0.031 0.002 PHE A 771 TYR 0.033 0.002 TYR B1184 ARG 0.006 0.001 ARG I 61 *********************** REFINEMENT MACRO_CYCLE 5 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 1115 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1111 time to evaluate : 5.568 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: A 19 LEU cc_start: 0.7362 (mt) cc_final: 0.7097 (mt) REVERT: A 213 ASN cc_start: 0.7873 (t0) cc_final: 0.7547 (t0) REVERT: A 217 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7867 (mttm) REVERT: A 424 MET cc_start: 0.7067 (mmm) cc_final: 0.6735 (mmm) REVERT: A 618 TYR cc_start: 0.8414 (m-80) cc_final: 0.7854 (m-80) REVERT: A 907 VAL cc_start: 0.8673 (t) cc_final: 0.8452 (p) REVERT: A 944 MET cc_start: 0.6331 (mtm) cc_final: 0.6022 (mtm) REVERT: A 947 LEU cc_start: 0.7955 (mp) cc_final: 0.7657 (mp) REVERT: A 960 MET cc_start: 0.7792 (mtm) cc_final: 0.7575 (mtp) REVERT: A 982 VAL cc_start: 0.8211 (t) cc_final: 0.8010 (t) REVERT: A 1024 THR cc_start: 0.8523 (m) cc_final: 0.8107 (t) REVERT: A 1038 ILE cc_start: 0.9037 (mm) cc_final: 0.8832 (mm) REVERT: A 1049 MET cc_start: 0.7258 (mtp) cc_final: 0.7022 (mmm) REVERT: A 1170 MET cc_start: 0.7769 (mmm) cc_final: 0.7457 (tpp) REVERT: A 1238 MET cc_start: 0.7453 (ttp) cc_final: 0.6600 (ttp) REVERT: A 1485 MET cc_start: 0.6721 (mmm) cc_final: 0.6021 (mmm) REVERT: A 1491 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6414 (mm-30) REVERT: A 1522 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 1608 SER cc_start: 0.8969 (t) cc_final: 0.8681 (t) REVERT: A 1613 MET cc_start: 0.7493 (ttm) cc_final: 0.6592 (ttm) REVERT: B 67 ASP cc_start: 0.6384 (t70) cc_final: 0.6070 (t70) REVERT: B 163 VAL cc_start: 0.8953 (m) cc_final: 0.8662 (t) REVERT: B 242 ASP cc_start: 0.8034 (p0) cc_final: 0.7598 (p0) REVERT: B 277 LEU cc_start: 0.8048 (mm) cc_final: 0.7814 (mm) REVERT: B 380 LYS cc_start: 0.8226 (tttt) cc_final: 0.7906 (ttmt) REVERT: B 412 ILE cc_start: 0.9102 (mt) cc_final: 0.8712 (mt) REVERT: B 531 VAL cc_start: 0.8894 (m) cc_final: 0.8583 (p) REVERT: B 782 ASP cc_start: 0.7493 (p0) cc_final: 0.6836 (p0) REVERT: B 918 SER cc_start: 0.8133 (t) cc_final: 0.7888 (t) REVERT: B 946 ASP cc_start: 0.8572 (m-30) cc_final: 0.8294 (m-30) REVERT: B 962 MET cc_start: 0.7693 (tpp) cc_final: 0.7202 (tpp) REVERT: B 1049 THR cc_start: 0.8291 (m) cc_final: 0.8015 (p) REVERT: B 1175 THR cc_start: 0.8806 (m) cc_final: 0.8461 (m) REVERT: B 1183 LYS cc_start: 0.8466 (pttt) cc_final: 0.8184 (pttt) REVERT: C 93 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7679 (mm-40) REVERT: C 112 MET cc_start: 0.7579 (mmm) cc_final: 0.7213 (mmm) REVERT: C 191 ILE cc_start: 0.9013 (mp) cc_final: 0.8688 (mp) REVERT: C 220 SER cc_start: 0.9301 (m) cc_final: 0.8991 (t) REVERT: C 313 ILE cc_start: 0.8891 (mt) cc_final: 0.8671 (mm) REVERT: E 2 ASP cc_start: 0.4315 (p0) cc_final: 0.3970 (p0) REVERT: E 18 THR cc_start: 0.7901 (p) cc_final: 0.7617 (t) REVERT: E 214 CYS cc_start: 0.6929 (t) cc_final: 0.6603 (t) REVERT: F 114 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7881 (tm-30) REVERT: F 130 ILE cc_start: 0.8029 (mt) cc_final: 0.6935 (mt) REVERT: I 4 VAL cc_start: 0.7997 (m) cc_final: 0.7766 (m) REVERT: J 49 MET cc_start: 0.8715 (tpp) cc_final: 0.7691 (tpp) REVERT: J 56 LEU cc_start: 0.8811 (tp) cc_final: 0.8548 (tt) REVERT: K 66 VAL cc_start: 0.9007 (m) cc_final: 0.8691 (t) REVERT: K 127 LEU cc_start: 0.8387 (tt) cc_final: 0.8025 (tt) REVERT: K 141 SER cc_start: 0.8484 (p) cc_final: 0.8173 (p) REVERT: L 49 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7938 (mmtt) REVERT: M 51 PHE cc_start: 0.6650 (m-10) cc_final: 0.6415 (m-10) REVERT: M 52 VAL cc_start: 0.8256 (t) cc_final: 0.7972 (p) REVERT: O 350 THR cc_start: 0.5590 (p) cc_final: 0.4818 (p) REVERT: P 182 ILE cc_start: 0.6534 (tt) cc_final: 0.6293 (tt) REVERT: Q 21 TYR cc_start: 0.6526 (m-80) cc_final: 0.6228 (m-10) REVERT: Q 216 LEU cc_start: 0.8596 (mt) cc_final: 0.8249 (mt) REVERT: Q 218 ASP cc_start: 0.5644 (t0) cc_final: 0.5381 (t0) REVERT: Q 238 THR cc_start: 0.8632 (p) cc_final: 0.8259 (p) outliers start: 4 outliers final: 2 residues processed: 1113 average time/residue: 0.5736 time to fit residues: 1070.9617 Evaluate side-chains 840 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 838 time to evaluate : 5.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 184 optimal weight: 4.9990 chunk 492 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 547 optimal weight: 10.0000 chunk 454 optimal weight: 8.9990 chunk 253 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 287 optimal weight: 0.0670 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 470 HIS A 592 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1191 GLN A1320 GLN ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS B 209 GLN B 462 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1163 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 23 HIS ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 106 GLN G 36 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 270 GLN O 313 GLN ** O 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 ASN ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 48460 Z= 0.220 Angle : 0.779 15.621 65937 Z= 0.402 Chirality : 0.048 0.325 7373 Planarity : 0.006 0.150 8112 Dihedral : 13.866 165.956 7276 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.15 % Favored : 91.86 % Rotamer: Outliers : 0.10 % Allowed : 2.19 % Favored : 97.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.11), residues: 5527 helix: 0.63 (0.12), residues: 1992 sheet: -0.67 (0.18), residues: 754 loop : -1.56 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP N 54 HIS 0.016 0.001 HIS O 348 PHE 0.033 0.002 PHE Q 127 TYR 0.035 0.002 TYR Q 131 ARG 0.007 0.001 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 6 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 1183 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1178 time to evaluate : 5.644 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: A 213 ASN cc_start: 0.7880 (t0) cc_final: 0.7564 (t0) REVERT: A 424 MET cc_start: 0.7167 (mmm) cc_final: 0.6852 (mmm) REVERT: A 588 LEU cc_start: 0.8964 (tt) cc_final: 0.8755 (tt) REVERT: A 659 THR cc_start: 0.9072 (t) cc_final: 0.8727 (m) REVERT: A 675 SER cc_start: 0.9172 (m) cc_final: 0.8495 (m) REVERT: A 699 CYS cc_start: 0.7814 (p) cc_final: 0.7577 (p) REVERT: A 828 CYS cc_start: 0.8161 (t) cc_final: 0.7781 (t) REVERT: A 830 MET cc_start: 0.8632 (mmm) cc_final: 0.8372 (tpp) REVERT: A 944 MET cc_start: 0.6342 (mtm) cc_final: 0.5749 (mtp) REVERT: A 947 LEU cc_start: 0.8103 (mp) cc_final: 0.7573 (mp) REVERT: A 960 MET cc_start: 0.7867 (mtm) cc_final: 0.7591 (mtp) REVERT: A 994 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 1038 ILE cc_start: 0.9059 (mm) cc_final: 0.8831 (mm) REVERT: A 1055 ILE cc_start: 0.8615 (mm) cc_final: 0.8241 (mm) REVERT: A 1170 MET cc_start: 0.7928 (mmm) cc_final: 0.7439 (tpp) REVERT: A 1238 MET cc_start: 0.7357 (ttp) cc_final: 0.6849 (ttp) REVERT: A 1491 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6571 (mm-30) REVERT: A 1543 SER cc_start: 0.8486 (t) cc_final: 0.8273 (t) REVERT: A 1608 SER cc_start: 0.9138 (t) cc_final: 0.8823 (t) REVERT: B 163 VAL cc_start: 0.8892 (m) cc_final: 0.8594 (t) REVERT: B 197 ASN cc_start: 0.8004 (m-40) cc_final: 0.7760 (m-40) REVERT: B 242 ASP cc_start: 0.8028 (p0) cc_final: 0.7104 (p0) REVERT: B 277 LEU cc_start: 0.8061 (mm) cc_final: 0.7768 (mm) REVERT: B 378 ILE cc_start: 0.9090 (mt) cc_final: 0.8765 (mm) REVERT: B 380 LYS cc_start: 0.8165 (tttt) cc_final: 0.7780 (ttmm) REVERT: B 413 LEU cc_start: 0.8896 (mm) cc_final: 0.8631 (mm) REVERT: B 414 LYS cc_start: 0.8140 (tttt) cc_final: 0.7917 (ttmm) REVERT: B 527 PHE cc_start: 0.8512 (m-80) cc_final: 0.8097 (m-10) REVERT: B 531 VAL cc_start: 0.9085 (m) cc_final: 0.8879 (p) REVERT: B 671 TYR cc_start: 0.7612 (m-80) cc_final: 0.7342 (m-80) REVERT: B 782 ASP cc_start: 0.7227 (p0) cc_final: 0.6689 (p0) REVERT: B 912 GLN cc_start: 0.7384 (mt0) cc_final: 0.7018 (mt0) REVERT: B 946 ASP cc_start: 0.8756 (m-30) cc_final: 0.8456 (m-30) REVERT: B 1057 MET cc_start: 0.8288 (mmm) cc_final: 0.7736 (mtp) REVERT: B 1086 PHE cc_start: 0.7626 (m-80) cc_final: 0.7147 (m-80) REVERT: B 1093 LEU cc_start: 0.8413 (tp) cc_final: 0.8213 (tp) REVERT: B 1094 ASN cc_start: 0.8323 (m110) cc_final: 0.8052 (m110) REVERT: B 1183 LYS cc_start: 0.8052 (pttt) cc_final: 0.7722 (pttt) REVERT: C 112 MET cc_start: 0.7474 (mmm) cc_final: 0.6953 (mmm) REVERT: C 202 ILE cc_start: 0.8281 (mt) cc_final: 0.7833 (mt) REVERT: C 220 SER cc_start: 0.9224 (m) cc_final: 0.8900 (t) REVERT: C 313 ILE cc_start: 0.8812 (mt) cc_final: 0.8483 (mm) REVERT: D 14 THR cc_start: 0.7687 (p) cc_final: 0.7371 (p) REVERT: E 2 ASP cc_start: 0.4418 (p0) cc_final: 0.4047 (p0) REVERT: E 18 THR cc_start: 0.7841 (p) cc_final: 0.7566 (t) REVERT: E 145 THR cc_start: 0.8098 (p) cc_final: 0.7472 (t) REVERT: F 130 ILE cc_start: 0.8124 (mt) cc_final: 0.7881 (mt) REVERT: F 132 LEU cc_start: 0.8457 (mm) cc_final: 0.8154 (mm) REVERT: F 134 ILE cc_start: 0.9170 (mm) cc_final: 0.8957 (mm) REVERT: G 116 THR cc_start: 0.6437 (t) cc_final: 0.6156 (t) REVERT: I 4 VAL cc_start: 0.7845 (m) cc_final: 0.7547 (m) REVERT: J 16 ASP cc_start: 0.8199 (p0) cc_final: 0.7998 (p0) REVERT: J 67 GLU cc_start: 0.7760 (tt0) cc_final: 0.7553 (tt0) REVERT: K 66 VAL cc_start: 0.8753 (m) cc_final: 0.8357 (t) REVERT: M 36 THR cc_start: 0.7202 (t) cc_final: 0.6994 (t) REVERT: O 350 THR cc_start: 0.5044 (p) cc_final: 0.4391 (p) REVERT: O 464 LEU cc_start: 0.7498 (mm) cc_final: 0.7251 (mp) REVERT: O 471 MET cc_start: 0.6137 (mmm) cc_final: 0.5600 (mmm) REVERT: P 158 MET cc_start: 0.4736 (ptm) cc_final: 0.4455 (ptm) REVERT: P 270 THR cc_start: 0.7070 (p) cc_final: 0.6857 (p) REVERT: Q 216 LEU cc_start: 0.8471 (mt) cc_final: 0.8255 (mt) REVERT: Q 238 THR cc_start: 0.8561 (p) cc_final: 0.8051 (p) REVERT: Q 293 ILE cc_start: 0.8277 (mp) cc_final: 0.8056 (mm) REVERT: Q 364 VAL cc_start: 0.8720 (m) cc_final: 0.8462 (t) outliers start: 5 outliers final: 1 residues processed: 1180 average time/residue: 0.5935 time to fit residues: 1175.4063 Evaluate side-chains 889 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 888 time to evaluate : 5.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 527 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 312 optimal weight: 20.0000 chunk 399 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 460 optimal weight: 20.0000 chunk 305 optimal weight: 20.0000 chunk 545 optimal weight: 6.9990 chunk 341 optimal weight: 40.0000 chunk 332 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1320 GLN ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1527 GLN B 235 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 979 GLN B 999 GLN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS E 106 GLN E 114 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 313 GLN ** O 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 GLN ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 HIS ** P 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 287 ASN ** Q 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 48460 Z= 0.500 Angle : 0.894 14.958 65937 Z= 0.463 Chirality : 0.051 0.468 7373 Planarity : 0.007 0.157 8112 Dihedral : 14.075 166.939 7276 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.94 % Allowed : 8.49 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % 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: -1.15 (0.11), residues: 5527 helix: 0.47 (0.11), residues: 2030 sheet: -0.89 (0.17), residues: 805 loop : -1.71 (0.12), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP A 530 HIS 0.017 0.002 HIS O 479 PHE 0.044 0.003 PHE A 771 TYR 0.042 0.003 TYR A 618 ARG 0.014 0.001 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 7 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 998 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 998 time to evaluate : 6.055 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: A 129 LEU cc_start: 0.7368 (tp) cc_final: 0.5155 (tp) REVERT: A 215 GLU cc_start: 0.6374 (tp30) cc_final: 0.5826 (tp30) REVERT: A 618 TYR cc_start: 0.8285 (m-10) cc_final: 0.8004 (m-10) REVERT: A 735 VAL cc_start: 0.9235 (m) cc_final: 0.8930 (t) REVERT: A 780 ILE cc_start: 0.8980 (pt) cc_final: 0.8765 (pt) REVERT: A 828 CYS cc_start: 0.8229 (t) cc_final: 0.8004 (t) REVERT: A 944 MET cc_start: 0.6272 (mtm) cc_final: 0.5791 (mtp) REVERT: A 947 LEU cc_start: 0.8109 (mp) cc_final: 0.7681 (mt) REVERT: A 960 MET cc_start: 0.7867 (mtm) cc_final: 0.7590 (mtp) REVERT: A 982 VAL cc_start: 0.8202 (t) cc_final: 0.7981 (t) REVERT: A 1038 ILE cc_start: 0.9026 (mm) cc_final: 0.8805 (mm) REVERT: A 1170 MET cc_start: 0.7876 (mmm) cc_final: 0.7428 (tpp) REVERT: A 1238 MET cc_start: 0.7476 (ttp) cc_final: 0.6821 (ttp) REVERT: A 1491 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6489 (mm-30) REVERT: A 1492 ILE cc_start: 0.8401 (mm) cc_final: 0.8122 (mm) REVERT: A 1584 LEU cc_start: 0.8484 (tp) cc_final: 0.8274 (tp) REVERT: B 67 ASP cc_start: 0.6421 (t70) cc_final: 0.6074 (t0) REVERT: B 242 ASP cc_start: 0.7861 (p0) cc_final: 0.6978 (p0) REVERT: B 270 LEU cc_start: 0.8532 (tp) cc_final: 0.7859 (mt) REVERT: B 414 LYS cc_start: 0.8232 (tttt) cc_final: 0.7985 (ttmm) REVERT: B 494 TYR cc_start: 0.7079 (m-10) cc_final: 0.6799 (m-80) REVERT: B 782 ASP cc_start: 0.7759 (p0) cc_final: 0.6887 (p0) REVERT: B 783 MET cc_start: 0.7719 (mtm) cc_final: 0.6767 (mtt) REVERT: B 918 SER cc_start: 0.8050 (t) cc_final: 0.7698 (t) REVERT: B 946 ASP cc_start: 0.8330 (m-30) cc_final: 0.8089 (m-30) REVERT: B 1057 MET cc_start: 0.8273 (mmm) cc_final: 0.7904 (mtp) REVERT: B 1061 LYS cc_start: 0.6444 (ptmm) cc_final: 0.6158 (pttt) REVERT: B 1094 ASN cc_start: 0.8444 (m110) cc_final: 0.7799 (m110) REVERT: B 1096 SER cc_start: 0.9110 (t) cc_final: 0.8831 (p) REVERT: C 112 MET cc_start: 0.7397 (mmm) cc_final: 0.7140 (mmm) REVERT: C 220 SER cc_start: 0.9409 (m) cc_final: 0.9175 (t) REVERT: C 313 ILE cc_start: 0.8923 (mt) cc_final: 0.8655 (mm) REVERT: E 2 ASP cc_start: 0.4324 (p0) cc_final: 0.4044 (p0) REVERT: E 18 THR cc_start: 0.7942 (p) cc_final: 0.7712 (t) REVERT: E 145 THR cc_start: 0.8274 (p) cc_final: 0.7527 (t) REVERT: F 77 ASP cc_start: 0.7391 (p0) cc_final: 0.7161 (p0) REVERT: F 114 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7791 (tm-30) REVERT: G 81 VAL cc_start: 0.7544 (t) cc_final: 0.7331 (t) REVERT: J 49 MET cc_start: 0.8613 (mmp) cc_final: 0.8196 (mmm) REVERT: K 66 VAL cc_start: 0.8998 (m) cc_final: 0.8728 (t) REVERT: K 127 LEU cc_start: 0.8343 (tt) cc_final: 0.8029 (tt) REVERT: O 350 THR cc_start: 0.5492 (p) cc_final: 0.4575 (p) REVERT: O 367 SER cc_start: 0.5112 (m) cc_final: 0.4513 (t) REVERT: O 464 LEU cc_start: 0.7547 (mm) cc_final: 0.7337 (mp) REVERT: P 1 MET cc_start: 0.5458 (tmm) cc_final: 0.4876 (mmm) REVERT: Q 216 LEU cc_start: 0.8534 (mt) cc_final: 0.8262 (mt) REVERT: Q 405 ILE cc_start: 0.7652 (tp) cc_final: 0.7196 (tp) outliers start: 0 outliers final: 0 residues processed: 998 average time/residue: 0.5753 time to fit residues: 966.2049 Evaluate side-chains 772 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 772 time to evaluate : 4.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 337 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 325 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 346 optimal weight: 30.0000 chunk 371 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 428 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN A 639 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1320 GLN ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN B 532 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 106 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 313 GLN ** O 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 701 HIS ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 48460 Z= 0.258 Angle : 0.792 17.656 65937 Z= 0.409 Chirality : 0.048 0.398 7373 Planarity : 0.006 0.154 8112 Dihedral : 13.983 166.944 7276 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.74 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.11), residues: 5527 helix: 0.66 (0.12), residues: 2000 sheet: -0.75 (0.18), residues: 770 loop : -1.61 (0.12), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 143 HIS 0.013 0.001 HIS O 348 PHE 0.032 0.002 PHE O 294 TYR 0.047 0.002 TYR Q 410 ARG 0.007 0.001 ARG I 61 *********************** REFINEMENT MACRO_CYCLE 8 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 1079 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1079 time to evaluate : 5.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.5791 (tp30) cc_final: 0.5157 (tp30) REVERT: A 601 MET cc_start: 0.7527 (mtp) cc_final: 0.7321 (mtt) REVERT: A 659 THR cc_start: 0.9092 (t) cc_final: 0.8654 (m) REVERT: A 699 CYS cc_start: 0.7974 (p) cc_final: 0.7760 (p) REVERT: A 811 SER cc_start: 0.8570 (p) cc_final: 0.7976 (p) REVERT: A 830 MET cc_start: 0.8413 (mmm) cc_final: 0.8117 (tpp) REVERT: A 947 LEU cc_start: 0.7995 (mp) cc_final: 0.7694 (mp) REVERT: A 994 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 1055 ILE cc_start: 0.8674 (mm) cc_final: 0.8447 (mm) REVERT: A 1170 MET cc_start: 0.7847 (mmm) cc_final: 0.7405 (tpp) REVERT: A 1238 MET cc_start: 0.7196 (ttp) cc_final: 0.6948 (ttm) REVERT: A 1646 LEU cc_start: 0.8770 (tp) cc_final: 0.8568 (tp) REVERT: B 163 VAL cc_start: 0.8880 (m) cc_final: 0.8610 (t) REVERT: B 242 ASP cc_start: 0.8017 (p0) cc_final: 0.7146 (p0) REVERT: B 270 LEU cc_start: 0.8474 (tp) cc_final: 0.7998 (mt) REVERT: B 380 LYS cc_start: 0.8177 (tttt) cc_final: 0.7815 (ttmm) REVERT: B 467 THR cc_start: 0.8029 (p) cc_final: 0.7826 (p) REVERT: B 492 ASN cc_start: 0.8851 (t0) cc_final: 0.8175 (t0) REVERT: B 494 TYR cc_start: 0.6684 (m-10) cc_final: 0.6462 (m-80) REVERT: B 561 ILE cc_start: 0.8875 (mm) cc_final: 0.8621 (mm) REVERT: B 782 ASP cc_start: 0.7317 (p0) cc_final: 0.6493 (p0) REVERT: B 912 GLN cc_start: 0.7442 (mt0) cc_final: 0.7178 (mt0) REVERT: B 962 MET cc_start: 0.7750 (tpp) cc_final: 0.7399 (tpp) REVERT: B 1057 MET cc_start: 0.8283 (mmm) cc_final: 0.7976 (mtp) REVERT: B 1086 PHE cc_start: 0.7553 (m-80) cc_final: 0.7127 (m-80) REVERT: B 1093 LEU cc_start: 0.8285 (tp) cc_final: 0.8010 (tp) REVERT: B 1094 ASN cc_start: 0.8385 (m110) cc_final: 0.7800 (m110) REVERT: B 1175 THR cc_start: 0.8683 (m) cc_final: 0.8456 (m) REVERT: C 72 ILE cc_start: 0.8917 (mm) cc_final: 0.8690 (mm) REVERT: C 112 MET cc_start: 0.7261 (mmm) cc_final: 0.6831 (mmm) REVERT: C 191 ILE cc_start: 0.9203 (mp) cc_final: 0.8971 (mp) REVERT: C 220 SER cc_start: 0.9290 (m) cc_final: 0.9058 (t) REVERT: E 2 ASP cc_start: 0.4352 (p0) cc_final: 0.4076 (p0) REVERT: E 18 THR cc_start: 0.7879 (p) cc_final: 0.7611 (t) REVERT: E 145 THR cc_start: 0.8159 (p) cc_final: 0.7428 (t) REVERT: G 81 VAL cc_start: 0.7507 (t) cc_final: 0.7156 (t) REVERT: G 116 THR cc_start: 0.6779 (t) cc_final: 0.6550 (t) REVERT: I 4 VAL cc_start: 0.7890 (m) cc_final: 0.7640 (m) REVERT: I 21 ASN cc_start: 0.6301 (t0) cc_final: 0.6027 (t0) REVERT: J 56 LEU cc_start: 0.8728 (tp) cc_final: 0.8511 (tp) REVERT: K 66 VAL cc_start: 0.8957 (m) cc_final: 0.8613 (t) REVERT: M 26 PHE cc_start: 0.6948 (m-10) cc_final: 0.6619 (m-10) REVERT: O 350 THR cc_start: 0.5385 (p) cc_final: 0.4575 (p) REVERT: O 415 LEU cc_start: 0.7676 (tp) cc_final: 0.7432 (tp) REVERT: O 471 MET cc_start: 0.6456 (mmm) cc_final: 0.5918 (mmm) REVERT: Q 216 LEU cc_start: 0.8546 (mt) cc_final: 0.8286 (mt) REVERT: Q 257 ILE cc_start: 0.9054 (mm) cc_final: 0.8737 (tp) REVERT: Q 364 VAL cc_start: 0.8752 (m) cc_final: 0.8493 (t) REVERT: Q 405 ILE cc_start: 0.7646 (tp) cc_final: 0.7221 (tp) outliers start: 0 outliers final: 0 residues processed: 1079 average time/residue: 0.5959 time to fit residues: 1078.9461 Evaluate side-chains 839 residues out of total 5033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 839 time to evaluate : 5.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-dev-5513/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-5513/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-dev-5513/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-5513/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-dev-5513/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-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-dev-5513/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-5513/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-5513/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: 63.9925 > 50: distance: 69 - 75: 5.916 distance: 75 - 76: 12.235 distance: 76 - 77: 26.362 distance: 76 - 79: 20.729 distance: 77 - 78: 30.807 distance: 77 - 87: 36.405 distance: 79 - 80: 18.388 distance: 80 - 81: 9.177 distance: 80 - 82: 14.243 distance: 81 - 83: 13.086 distance: 82 - 84: 9.527 distance: 83 - 85: 9.295 distance: 84 - 85: 8.031 distance: 85 - 86: 5.164 distance: 87 - 88: 12.842 distance: 88 - 89: 18.694 distance: 88 - 91: 16.230 distance: 89 - 90: 17.799 distance: 89 - 99: 34.419 distance: 90 - 112: 21.757 distance: 91 - 92: 12.204 distance: 92 - 93: 7.146 distance: 92 - 94: 18.241 distance: 93 - 95: 5.274 distance: 94 - 96: 10.412 distance: 95 - 97: 18.298 distance: 96 - 97: 11.494 distance: 97 - 98: 12.096 distance: 99 - 100: 7.797 distance: 100 - 101: 32.406 distance: 100 - 103: 14.402 distance: 101 - 102: 19.507 distance: 101 - 106: 6.705 distance: 102 - 120: 9.506 distance: 103 - 104: 28.278 distance: 103 - 105: 11.230 distance: 106 - 107: 15.436 distance: 107 - 108: 28.474 distance: 107 - 110: 24.124 distance: 108 - 109: 14.593 distance: 108 - 112: 20.434 distance: 110 - 111: 30.018 distance: 112 - 113: 30.602 distance: 113 - 114: 10.710 distance: 113 - 116: 24.650 distance: 114 - 115: 4.027 distance: 114 - 120: 11.675 distance: 116 - 117: 16.938 distance: 116 - 118: 19.751 distance: 117 - 119: 28.166 distance: 120 - 121: 20.410 distance: 121 - 122: 6.761 distance: 121 - 124: 7.865 distance: 122 - 123: 26.182 distance: 122 - 128: 6.786 distance: 124 - 125: 33.758 distance: 125 - 126: 18.296 distance: 125 - 127: 13.202 distance: 128 - 129: 12.959 distance: 129 - 130: 26.734 distance: 129 - 132: 17.014 distance: 130 - 131: 38.525 distance: 130 - 137: 33.914 distance: 133 - 134: 11.210 distance: 134 - 135: 36.850 distance: 134 - 136: 37.042 distance: 137 - 138: 31.247 distance: 138 - 139: 24.823 distance: 139 - 140: 30.845 distance: 139 - 141: 16.984 distance: 141 - 142: 9.116 distance: 142 - 143: 6.876 distance: 142 - 145: 20.881 distance: 143 - 144: 33.565 distance: 143 - 147: 16.849 distance: 145 - 146: 11.075 distance: 147 - 148: 10.856 distance: 148 - 149: 4.032 distance: 148 - 151: 15.448 distance: 149 - 150: 14.683 distance: 149 - 155: 26.284 distance: 151 - 152: 3.645 distance: 151 - 153: 11.259 distance: 152 - 154: 22.611