Starting phenix.real_space_refine on Sun Dec 17 00:03:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h68_0147/12_2023/6h68_0147_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h68_0147/12_2023/6h68_0147.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h68_0147/12_2023/6h68_0147_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h68_0147/12_2023/6h68_0147_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h68_0147/12_2023/6h68_0147_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h68_0147/12_2023/6h68_0147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h68_0147/12_2023/6h68_0147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h68_0147/12_2023/6h68_0147_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h68_0147/12_2023/6h68_0147_updated.pdb" } resolution = 4.6 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= 0.005 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 6 6.06 5 P 68 5.49 5 S 172 5.16 5 C 23265 2.51 5 N 6431 2.21 5 O 7161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "A TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 957": "NH1" <-> "NH2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 37103 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1473, 11637 Classifications: {'peptide': 1473} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1413} Chain breaks: 5 Chain: "B" Number of atoms: 9327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9327 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1115} Chain breaks: 3 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: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} 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: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1059 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} 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: {'PCIS': 1, 'PTRANS': 2, '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: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3131 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 21, 'TRANS': 374} 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: "R" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 685 Unusual residues: {'TTD': 1} Classifications: {'DNA': 32, 'undetermined': 1} Link IDs: {'p': 1, 'rna3p': 30, None: 1} Not linked: pdbres=" DC T 17 " pdbres="TTD T 18 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "U" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 496 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 111.354 105.008 97.479 1.00 90.73 S ATOM 480 SG CYS A 65 111.455 103.287 100.662 1.00 95.85 S ATOM 535 SG CYS A 72 108.110 102.878 99.094 1.00 78.98 S ATOM 781 SG CYS A 102 73.330 140.156 92.123 1.00 57.56 S ATOM 806 SG CYS A 105 74.187 141.090 95.518 1.00 62.21 S ATOM 1589 SG CYS A 233 70.425 140.838 94.176 1.00 67.20 S ATOM 1611 SG CYS A 236 71.957 144.444 93.407 1.00 70.90 S ATOM 20266 SG CYS B1104 101.967 112.672 112.405 1.00 81.61 S ATOM 20292 SG CYS B1107 98.955 112.783 109.563 1.00 78.87 S ATOM 20439 SG CYS B1128 102.414 113.644 108.623 1.00 84.25 S ATOM 20467 SG CYS B1131 101.357 116.882 110.978 1.00 80.71 S ATOM 29180 SG CYS I 13 45.598 111.619 35.542 1.00126.06 S ATOM 29321 SG CYS I 33 45.564 114.907 34.077 1.00123.28 S ATOM 29628 SG CYS J 7 82.162 37.513 87.404 1.00 45.16 S ATOM 29651 SG CYS J 10 80.773 35.145 89.907 1.00 59.67 S ATOM 29937 SG CYS J 46 81.874 33.928 85.861 1.00 51.64 S ATOM 31023 SG CYS L 34 110.478 57.375 56.483 1.00 74.17 S ATOM 31127 SG CYS L 48 112.701 60.181 56.772 1.00106.50 S ATOM 31150 SG CYS L 51 109.182 59.905 53.482 1.00105.75 S Time building chain proxies: 19.90, per 1000 atoms: 0.54 Number of scatterers: 37103 At special positions: 0 Unit cell: (168.54, 159, 159, 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 6 29.99 S 172 16.00 P 68 15.00 O 7161 8.00 N 6431 7.00 C 23265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.27 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 65 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 62 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 72 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 105 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 102 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 236 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 233 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1131 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " Number of angles added : 15 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8478 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 161 helices and 46 sheets defined 32.4% alpha, 12.5% beta 29 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 17.43 Creating SS restraints... Processing helix chain 'A' and resid 21 through 27 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 88 through 99 removed outlier: 6.029A pdb=" N ASN A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 127 removed outlier: 4.047A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 removed outlier: 5.639A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 198 Processing helix chain 'A' and resid 210 through 228 removed outlier: 3.978A pdb=" N LEU A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 267 removed outlier: 3.612A pdb=" N LYS A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 330 Processing helix chain 'A' and resid 332 through 338 removed outlier: 4.729A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 381 through 406 Processing helix chain 'A' and resid 415 through 437 removed outlier: 4.086A pdb=" N VAL A 418 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE A 419 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 420 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN A 425 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A 430 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 551 through 557 removed outlier: 4.068A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'A' and resid 641 through 649 Processing helix chain 'A' and resid 653 through 655 No H-bonds generated for 'chain 'A' and resid 653 through 655' Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 757 through 760 No H-bonds generated for 'chain 'A' and resid 757 through 760' Processing helix chain 'A' and resid 793 through 800 Processing helix chain 'A' and resid 803 through 823 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 837 through 850 removed outlier: 4.027A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 Processing helix chain 'A' and resid 873 through 884 Processing helix chain 'A' and resid 886 through 911 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 992 through 1011 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1050 through 1052 No H-bonds generated for 'chain 'A' and resid 1050 through 1052' Processing helix chain 'A' and resid 1057 through 1059 No H-bonds generated for 'chain 'A' and resid 1057 through 1059' Processing helix chain 'A' and resid 1066 through 1071 Processing helix chain 'A' and resid 1073 through 1079 Processing helix chain 'A' and resid 1082 through 1084 No H-bonds generated for 'chain 'A' and resid 1082 through 1084' Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1094 through 1107 Processing helix chain 'A' and resid 1138 through 1150 Processing helix chain 'A' and resid 1152 through 1156 removed outlier: 3.986A pdb=" N LYS A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1152 through 1156' Processing helix chain 'A' and resid 1163 through 1176 Processing helix chain 'A' and resid 1185 through 1199 Proline residue: A1196 - end of helix removed outlier: 4.217A pdb=" N GLN A1199 " --> pdb=" O GLU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1225 removed outlier: 4.800A pdb=" N ARG A1223 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1258 Processing helix chain 'A' and resid 1264 through 1266 No H-bonds generated for 'chain 'A' and resid 1264 through 1266' Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1310 through 1319 Processing helix chain 'A' and resid 1321 through 1336 removed outlier: 4.070A pdb=" N GLN A1336 " --> pdb=" O GLU A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1451 Processing helix chain 'A' and resid 1485 through 1493 Processing helix chain 'A' and resid 1527 through 1530 No H-bonds generated for 'chain 'A' and resid 1527 through 1530' Processing helix chain 'A' and resid 1547 through 1552 Processing helix chain 'A' and resid 1556 through 1572 Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.775A pdb=" N THR A1590 " --> pdb=" O ALA A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1605 removed outlier: 3.889A pdb=" N THR A1605 " --> pdb=" O GLN A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1613 Processing helix chain 'A' and resid 1618 through 1628 Processing helix chain 'A' and resid 1637 through 1643 Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 43 through 52 removed outlier: 4.732A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 123 through 129 removed outlier: 4.023A pdb=" N ARG B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.944A pdb=" N ARG B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 300 through 316 Processing helix chain 'B' and resid 324 through 333 Processing helix chain 'B' and resid 346 through 356 Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 405 through 432 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'B' and resid 457 through 467 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.492A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 599 through 613 Processing helix chain 'B' and resid 678 through 680 No H-bonds generated for 'chain 'B' and resid 678 through 680' Processing helix chain 'B' and resid 693 through 696 Processing helix chain 'B' and resid 699 through 702 No H-bonds generated for 'chain 'B' and resid 699 through 702' Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 724 removed outlier: 4.685A pdb=" N LYS B 723 " --> pdb=" O CYS B 719 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN B 724 " --> pdb=" O GLN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 834 through 836 No H-bonds generated for 'chain 'B' and resid 834 through 836' Processing helix chain 'B' and resid 933 through 935 No H-bonds generated for 'chain 'B' and resid 933 through 935' Processing helix chain 'B' and resid 951 through 957 removed outlier: 3.618A pdb=" N PHE B 954 " --> pdb=" O PRO B 951 " (cutoff:3.500A) Proline residue: B 955 - end of helix No H-bonds generated for 'chain 'B' and resid 951 through 957' Processing helix chain 'B' and resid 961 through 974 Processing helix chain 'B' and resid 992 through 1003 Processing helix chain 'B' and resid 1040 through 1043 No H-bonds generated for 'chain 'B' and resid 1040 through 1043' Processing helix chain 'B' and resid 1073 through 1082 Processing helix chain 'B' and resid 1085 through 1092 Processing helix chain 'B' and resid 1180 through 1192 removed outlier: 3.624A pdb=" N SER B1190 " --> pdb=" O ASP B1186 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B1191 " --> pdb=" O SER B1187 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 173 through 180 removed outlier: 4.195A pdb=" N THR C 178 " --> pdb=" O GLN C 175 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE C 179 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 278 through 281 Processing helix chain 'C' and resid 310 through 330 Processing helix chain 'D' and resid 33 through 48 Processing helix chain 'D' and resid 81 through 97 removed outlier: 3.939A pdb=" N GLN D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 removed outlier: 3.935A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 removed outlier: 3.901A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 56 through 70 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 127 removed outlier: 3.884A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 17 removed outlier: 4.017A pdb=" N THR G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA G 14 " --> pdb=" O ASN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 159 through 161 No H-bonds generated for 'chain 'G' and resid 159 through 161' Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 59 through 64 Processing helix chain 'J' and resid 15 through 25 removed outlier: 4.852A pdb=" N GLU J 19 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 44 through 50 removed outlier: 3.865A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 70 through 80 Processing helix chain 'K' and resid 113 through 140 Processing helix chain 'M' and resid 117 through 131 Proline residue: M 121 - end of helix removed outlier: 3.960A pdb=" N GLU M 130 " --> pdb=" O ASN M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 146 Processing helix chain 'M' and resid 152 through 167 Processing helix chain 'M' and resid 198 through 200 No H-bonds generated for 'chain 'M' and resid 198 through 200' Processing helix chain 'M' and resid 204 through 207 No H-bonds generated for 'chain 'M' and resid 204 through 207' Processing helix chain 'M' and resid 210 through 215 removed outlier: 4.849A pdb=" N PHE M 215 " --> pdb=" O LYS M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 219 through 223 Processing helix chain 'M' and resid 227 through 232 Processing helix chain 'M' and resid 241 through 245 Processing helix chain 'M' and resid 253 through 272 removed outlier: 4.822A pdb=" N THR M 257 " --> pdb=" O SER M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 286 removed outlier: 3.989A pdb=" N ARG M 286 " --> pdb=" O LYS M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 301 Processing helix chain 'M' and resid 322 through 338 Processing helix chain 'M' and resid 347 through 353 Processing helix chain 'M' and resid 357 through 366 Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'N' and resid 150 through 153 No H-bonds generated for 'chain 'N' and resid 150 through 153' Processing sheet with id= A, first strand: chain 'A' and resid 77 through 80 Processing sheet with id= B, first strand: chain 'A' and resid 242 through 245 removed outlier: 3.766A pdb=" N LYS A 242 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 371 through 373 Processing sheet with id= D, first strand: chain 'A' and resid 479 through 482 Processing sheet with id= E, first strand: chain 'A' and resid 484 through 486 removed outlier: 6.373A pdb=" N LEU A 614 " --> pdb=" O SER A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 507 through 510 Processing sheet with id= G, first strand: chain 'A' and resid 535 through 537 Processing sheet with id= H, first strand: chain 'A' and resid 748 through 752 Processing sheet with id= I, first strand: chain 'A' and resid 1237 through 1241 removed outlier: 3.916A pdb=" N VAL A1520 " --> pdb=" O VAL A1508 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1267 through 1275 removed outlier: 6.594A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU A1274 " --> pdb=" O SER A1289 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SER A1289 " --> pdb=" O GLU A1274 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A1290 " --> pdb=" O LEU A1474 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1473 " --> pdb=" O LYS A1459 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 71 through 73 removed outlier: 6.615A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP B 143 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE B 153 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 145 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN B 151 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 194 through 196 Processing sheet with id= M, first strand: chain 'B' and resid 206 through 209 Processing sheet with id= N, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.386A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 262 " --> pdb=" O TYR B 269 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 549 through 551 Processing sheet with id= P, first strand: chain 'B' and resid 625 through 629 removed outlier: 6.231A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.140A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 769 through 775 removed outlier: 4.437A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 787 through 789 Processing sheet with id= T, first strand: chain 'B' and resid 823 through 825 removed outlier: 6.383A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE B 862 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 868 " --> pdb=" O PHE B 862 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 916 through 918 Processing sheet with id= V, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id= W, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id= X, first strand: chain 'B' and resid 1158 through 1160 Processing sheet with id= Y, first strand: chain 'C' and resid 132 through 139 removed outlier: 6.294A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 256 through 258 Processing sheet with id= AA, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.941A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 161 through 163 Processing sheet with id= AC, first strand: chain 'C' and resid 222 through 226 removed outlier: 7.126A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 229 through 235 removed outlier: 6.725A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 9.791A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 60 through 62 Processing sheet with id= AF, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.565A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AH, first strand: chain 'F' and resid 133 through 136 Processing sheet with id= AI, first strand: chain 'G' and resid 38 through 47 removed outlier: 4.356A pdb=" N TRP G 117 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 131 through 135 removed outlier: 3.692A pdb=" N ASP G 131 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP G 246 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL G 236 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER G 244 " --> pdb=" O VAL G 236 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 147 through 149 Processing sheet with id= AL, first strand: chain 'G' and resid 167 through 169 Processing sheet with id= AM, first strand: chain 'H' and resid 100 through 106 removed outlier: 6.948A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'K' and resid 47 through 50 removed outlier: 4.695A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AP, first strand: chain 'M' and resid 14 through 16 removed outlier: 4.210A pdb=" N LYS M 92 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR M 76 " --> pdb=" O ALA M 93 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.980A pdb=" N SER M 98 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 370 through 372 Processing sheet with id= AS, first strand: chain 'N' and resid 86 through 92 removed outlier: 4.131A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 110 through 112 1118 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 16.29 Time building geometry restraints manager: 16.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6094 1.31 - 1.43: 9916 1.43 - 1.56: 21537 1.56 - 1.68: 134 1.68 - 1.81: 274 Bond restraints: 37955 Sorted by residual: bond pdb=" C1R TTD T 18 " pdb=" N1T TTD T 18 " ideal model delta sigma weight residual 1.476 1.432 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C VAL M 399 " pdb=" N PRO M 400 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.42e+00 bond pdb=" C SER B 537 " pdb=" N PRO B 538 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.87e+00 bond pdb=" C ASP B 819 " pdb=" N PRO B 820 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.74e+00 bond pdb=" C ILE N 25 " pdb=" N PRO N 26 " ideal model delta sigma weight residual 1.332 1.356 -0.024 1.26e-02 6.30e+03 3.66e+00 ... (remaining 37950 not shown) Histogram of bond angle deviations from ideal: 84.59 - 94.49: 4 94.49 - 104.40: 859 104.40 - 114.30: 22795 114.30 - 124.20: 26992 124.20 - 134.11: 927 Bond angle restraints: 51577 Sorted by residual: angle pdb=" C ILE B 588 " pdb=" N ASP B 589 " pdb=" CA ASP B 589 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 angle pdb=" CA ARG M 166 " pdb=" CB ARG M 166 " pdb=" CG ARG M 166 " ideal model delta sigma weight residual 114.10 123.69 -9.59 2.00e+00 2.50e-01 2.30e+01 angle pdb=" N ASP B 819 " pdb=" CA ASP B 819 " pdb=" C ASP B 819 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 angle pdb=" CB ARG M 166 " pdb=" CG ARG M 166 " pdb=" CD ARG M 166 " ideal model delta sigma weight residual 111.30 101.34 9.96 2.30e+00 1.89e-01 1.88e+01 angle pdb=" C ASP A 409 " pdb=" N LYS A 410 " pdb=" CA LYS A 410 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 ... (remaining 51572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 22710 35.36 - 70.71: 318 70.71 - 106.07: 10 106.07 - 141.43: 0 141.43 - 176.78: 2 Dihedral angle restraints: 23040 sinusoidal: 9931 harmonic: 13109 Sorted by residual: dihedral pdb=" CA LYS A 408 " pdb=" C LYS A 408 " pdb=" N ASP A 409 " pdb=" CA ASP A 409 " ideal model delta harmonic sigma weight residual 180.00 143.01 36.99 0 5.00e+00 4.00e-02 5.47e+01 dihedral pdb=" CA ILE N 25 " pdb=" C ILE N 25 " pdb=" N PRO N 26 " pdb=" CA PRO N 26 " ideal model delta harmonic sigma weight residual -180.00 -143.73 -36.27 0 5.00e+00 4.00e-02 5.26e+01 dihedral pdb=" CA ASP B 819 " pdb=" C ASP B 819 " pdb=" N PRO B 820 " pdb=" CA PRO B 820 " ideal model delta harmonic sigma weight residual -180.00 -144.96 -35.04 0 5.00e+00 4.00e-02 4.91e+01 ... (remaining 23037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5523 0.110 - 0.220: 264 0.220 - 0.330: 3 0.330 - 0.440: 0 0.440 - 0.549: 1 Chirality restraints: 5791 Sorted by residual: chirality pdb=" C1R TTD T 18 " pdb=" C2R TTD T 18 " pdb=" N1T TTD T 18 " pdb=" O4R TTD T 18 " both_signs ideal model delta sigma weight residual False 2.48 1.93 0.55 2.00e-01 2.50e+01 7.55e+00 chirality pdb=" CB ILE B 588 " pdb=" CA ILE B 588 " pdb=" CG1 ILE B 588 " pdb=" CG2 ILE B 588 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C5T TTD T 18 " pdb=" C5 TTD T 18 " pdb=" C4T TTD T 18 " pdb=" C6T TTD T 18 " both_signs ideal model delta sigma weight residual False 2.78 2.52 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 5788 not shown) Planarity restraints: 6422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1R TTD T 18 " -0.039 2.00e-02 2.50e+03 3.39e-02 2.59e+01 pdb=" C2T TTD T 18 " 0.002 2.00e-02 2.50e+03 pdb=" C4T TTD T 18 " 0.023 2.00e-02 2.50e+03 pdb=" C5T TTD T 18 " -0.061 2.00e-02 2.50e+03 pdb=" C6T TTD T 18 " 0.064 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " 0.019 2.00e-02 2.50e+03 pdb=" N3T TTD T 18 " 0.001 2.00e-02 2.50e+03 pdb=" O2T TTD T 18 " 0.001 2.00e-02 2.50e+03 pdb=" O4T TTD T 18 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 67 " -0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO G 68 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO G 68 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 68 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U R 2 " 0.035 2.00e-02 2.50e+03 1.79e-02 7.21e+00 pdb=" N1 U R 2 " -0.037 2.00e-02 2.50e+03 pdb=" C2 U R 2 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U R 2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U R 2 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U R 2 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U R 2 " 0.011 2.00e-02 2.50e+03 pdb=" C5 U R 2 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U R 2 " -0.006 2.00e-02 2.50e+03 ... (remaining 6419 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7201 2.77 - 3.31: 33427 3.31 - 3.84: 61934 3.84 - 4.37: 70989 4.37 - 4.90: 117779 Nonbonded interactions: 291330 Sorted by model distance: nonbonded pdb=" OD1 ASP B 946 " pdb=" OG SER J 9 " model vdw 2.243 2.440 nonbonded pdb=" O VAL A 418 " pdb=" OG SER A 421 " model vdw 2.268 2.440 nonbonded pdb=" O LEU M 178 " pdb=" OG1 THR M 182 " model vdw 2.278 2.440 nonbonded pdb=" OH TYR A 791 " pdb=" O SER A1061 " model vdw 2.281 2.440 nonbonded pdb=" OG1 THR N 78 " pdb=" O ILE N 89 " model vdw 2.281 2.440 ... (remaining 291325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.470 Check model and map are aligned: 0.490 Set scattering table: 0.350 Process input model: 116.030 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 : 0.005 0.057 37955 Z= 0.309 Angle : 0.838 12.638 51577 Z= 0.458 Chirality : 0.052 0.549 5791 Planarity : 0.007 0.068 6422 Dihedral : 11.631 176.784 14562 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.05 % Allowed : 1.18 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: -3.73 (0.10), residues: 4447 helix: -2.30 (0.10), residues: 1500 sheet: -2.14 (0.18), residues: 670 loop : -2.70 (0.11), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 530 HIS 0.012 0.002 HIS A 106 PHE 0.033 0.003 PHE C 315 TYR 0.037 0.002 TYR A1595 ARG 0.010 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1367 time to evaluate : 4.799 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 outliers start: 2 outliers final: 0 residues processed: 1368 average time/residue: 0.5838 time to fit residues: 1238.9595 Evaluate side-chains 686 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 686 time to evaluate : 4.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 379 optimal weight: 8.9990 chunk 340 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 181 optimal weight: 0.0970 chunk 351 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 213 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 407 optimal weight: 0.0060 overall best weight: 4.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 213 ASN A 224 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN A 525 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS B 87 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN B 462 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN E 153 HIS F 100 GLN G 8 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN I 21 ASN I 44 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 GLN N 52 GLN N 170 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 37955 Z= 0.271 Angle : 0.689 9.723 51577 Z= 0.361 Chirality : 0.045 0.366 5791 Planarity : 0.006 0.064 6422 Dihedral : 13.138 175.625 5632 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.12), residues: 4447 helix: -0.87 (0.12), residues: 1504 sheet: -1.74 (0.19), residues: 654 loop : -2.28 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A1530 HIS 0.012 0.002 HIS A 596 PHE 0.035 0.002 PHE C 67 TYR 0.024 0.002 TYR A1595 ARG 0.013 0.001 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 803 time to evaluate : 4.143 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 outliers start: 2 outliers final: 0 residues processed: 805 average time/residue: 0.5453 time to fit residues: 709.7444 Evaluate side-chains 543 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 4.637 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 226 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 408 optimal weight: 6.9990 chunk 441 optimal weight: 0.0170 chunk 363 optimal weight: 0.2980 chunk 405 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 327 optimal weight: 0.9990 overall best weight: 1.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 221 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B1041 ASN ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN G 8 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN K 106 GLN M 18 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37955 Z= 0.179 Angle : 0.613 13.649 51577 Z= 0.316 Chirality : 0.043 0.356 5791 Planarity : 0.005 0.070 6422 Dihedral : 12.952 175.530 5632 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.12), residues: 4447 helix: -0.34 (0.13), residues: 1497 sheet: -1.55 (0.19), residues: 662 loop : -2.06 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 595 HIS 0.013 0.001 HIS B 499 PHE 0.027 0.002 PHE A1610 TYR 0.025 0.002 TYR C 82 ARG 0.011 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 745 time to evaluate : 4.528 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 outliers start: 1 outliers final: 0 residues processed: 746 average time/residue: 0.5304 time to fit residues: 649.8827 Evaluate side-chains 526 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 4.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 403 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 409 optimal weight: 0.3980 chunk 434 optimal weight: 6.9990 chunk 214 optimal weight: 0.6980 chunk 388 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS B1010 ASN ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN E 153 HIS G 8 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN J 53 HIS ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37955 Z= 0.273 Angle : 0.668 10.273 51577 Z= 0.346 Chirality : 0.044 0.357 5791 Planarity : 0.005 0.064 6422 Dihedral : 12.931 175.089 5632 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -1.89 (0.12), residues: 4447 helix: -0.16 (0.13), residues: 1499 sheet: -1.53 (0.19), residues: 658 loop : -1.94 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 530 HIS 0.009 0.002 HIS B 952 PHE 0.037 0.002 PHE B1167 TYR 0.037 0.002 TYR A1104 ARG 0.007 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 683 time to evaluate : 3.240 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 outliers start: 2 outliers final: 1 residues processed: 685 average time/residue: 0.3882 time to fit residues: 433.4534 Evaluate side-chains 483 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 482 time to evaluate : 2.833 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2703 time to fit residues: 4.8590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 361 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 6 optimal weight: 0.0470 chunk 323 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 370 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 389 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 ASN ** A1525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1581 HIS A1633 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 GLN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1157 GLN C 65 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN E 153 HIS G 20 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37955 Z= 0.321 Angle : 0.742 11.345 51577 Z= 0.386 Chirality : 0.047 0.359 5791 Planarity : 0.005 0.066 6422 Dihedral : 13.088 173.912 5632 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.12), residues: 4447 helix: -0.28 (0.13), residues: 1482 sheet: -1.59 (0.19), residues: 654 loop : -1.98 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 530 HIS 0.010 0.002 HIS B1082 PHE 0.030 0.002 PHE A 104 TYR 0.029 0.002 TYR A1595 ARG 0.007 0.001 ARG A1105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 623 time to evaluate : 4.744 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 outliers start: 3 outliers final: 2 residues processed: 625 average time/residue: 0.4561 time to fit residues: 472.9473 Evaluate side-chains 467 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 465 time to evaluate : 3.007 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2802 time to fit residues: 5.0280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 146 optimal weight: 4.9990 chunk 390 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 434 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 939 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 248 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS B1082 HIS B1094 ASN B1100 GLN B1114 GLN C 65 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN E 114 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN M 71 GLN M 274 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5563 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: