Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 17 11:53:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/08_2023/7qdr_13923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/08_2023/7qdr_13923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/08_2023/7qdr_13923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/08_2023/7qdr_13923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/08_2023/7qdr_13923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/08_2023/7qdr_13923.pdb" } resolution = 3.7 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= 0.002 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: 4 Type Number sf(0) Gaussians S 107 5.16 5 C 14440 2.51 5 N 3969 2.21 5 O 4302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 679": "OD1" <-> "OD2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ASP 691": "OD1" <-> "OD2" Residue "A TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 798": "OE1" <-> "OE2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A GLU 1006": "OE1" <-> "OE2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1041": "NH1" <-> "NH2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1136": "OE1" <-> "OE2" Residue "A PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1184": "OE1" <-> "OE2" Residue "A PHE 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 689": "OD1" <-> "OD2" Residue "B TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 781": "OD1" <-> "OD2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B TYR 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 918": "NH1" <-> "NH2" Residue "B TYR 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1076": "NH1" <-> "NH2" Residue "B TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1147": "OE1" <-> "OE2" Residue "B TYR 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1192": "OD1" <-> "OD2" Residue "B TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1250": "OD1" <-> "OD2" Residue "B ASP 1313": "OD1" <-> "OD2" Residue "B TYR 1320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1344": "OE1" <-> "OE2" Residue "B ARG 1367": "NH1" <-> "NH2" Residue "B GLU 1376": "OE1" <-> "OE2" Residue "B GLU 1388": "OE1" <-> "OE2" Residue "B ARG 1424": "NH1" <-> "NH2" Residue "B PHE 1479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1503": "NH1" <-> "NH2" Residue "B ARG 1507": "NH1" <-> "NH2" Residue "B TYR 1514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1523": "NH1" <-> "NH2" Residue "B ARG 1553": "NH1" <-> "NH2" Residue "B ARG 1560": "NH1" <-> "NH2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ASP 17": "OD1" <-> "OD2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D ASP 275": "OD1" <-> "OD2" Residue "D ASP 294": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 22818 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9065 Classifications: {'peptide': 1169} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 75, 'TRANS': 1093} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 9007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1212, 9007 Classifications: {'peptide': 1212} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 26, 'TRANS': 1185} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 298 Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "D" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Time building chain proxies: 11.52, per 1000 atoms: 0.50 Number of scatterers: 22818 At special positions: 0 Unit cell: (179.416, 133.468, 142.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 107 16.00 O 4302 8.00 N 3969 7.00 C 14440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.89 Conformation dependent library (CDL) restraints added in 3.7 seconds 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5606 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 23 sheets defined 52.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.585A pdb=" N SER A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.304A pdb=" N TRP A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.859A pdb=" N GLY A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.562A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.648A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 4.182A pdb=" N ARG A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.814A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 4.536A pdb=" N GLN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 3.740A pdb=" N SER A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.621A pdb=" N TYR A 427 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 428 " --> pdb=" O VAL A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 428' Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.163A pdb=" N TRP A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.820A pdb=" N TYR A 518 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.917A pdb=" N GLY A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 3.843A pdb=" N GLN A 582 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 583 " --> pdb=" O CYS A 579 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 609 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 618 through 631 removed outlier: 3.624A pdb=" N ARG A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.682A pdb=" N GLU A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 669 removed outlier: 4.037A pdb=" N VAL A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 703 removed outlier: 3.626A pdb=" N TYR A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.952A pdb=" N ARG A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 761 through 768 removed outlier: 4.027A pdb=" N MET A 765 " --> pdb=" O ARG A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 778 through 794 removed outlier: 4.235A pdb=" N LYS A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 831 Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.901A pdb=" N ASP A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 888 " --> pdb=" O PRO A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 888' Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 936 through 948 removed outlier: 4.261A pdb=" N LYS A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 Processing helix chain 'A' and resid 992 through 1010 Processing helix chain 'A' and resid 1011 through 1012 No H-bonds generated for 'chain 'A' and resid 1011 through 1012' Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1019 through 1044 removed outlier: 3.842A pdb=" N GLN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 Processing helix chain 'A' and resid 1075 through 1083 removed outlier: 4.147A pdb=" N ALA A1083 " --> pdb=" O ARG A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 3.994A pdb=" N THR A1102 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 4.102A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1128 through 1151 removed outlier: 3.901A pdb=" N GLU A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1163 Processing helix chain 'A' and resid 1169 through 1177 Processing helix chain 'A' and resid 1181 through 1189 removed outlier: 3.667A pdb=" N LEU A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1204 removed outlier: 3.507A pdb=" N VAL A1196 " --> pdb=" O PRO A1192 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A1197 " --> pdb=" O GLU A1193 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1218 removed outlier: 3.647A pdb=" N ARG A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A1216 " --> pdb=" O GLY A1212 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1230 removed outlier: 3.533A pdb=" N GLY A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR A1228 " --> pdb=" O ALA A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 404 through 416 removed outlier: 4.027A pdb=" N ILE B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.596A pdb=" N CYS B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.611A pdb=" N GLY B 461 " --> pdb=" O HIS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 509 through 524 removed outlier: 3.673A pdb=" N GLY B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 563 through 577 removed outlier: 3.857A pdb=" N ARG B 569 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.576A pdb=" N ALA B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 611 removed outlier: 3.530A pdb=" N TRP B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.626A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 3.995A pdb=" N VAL B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.781A pdb=" N LYS B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 686 removed outlier: 3.657A pdb=" N ASP B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 4.056A pdb=" N HIS B 709 " --> pdb=" O CYS B 705 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 726 removed outlier: 4.324A pdb=" N TRP B 717 " --> pdb=" O VAL B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 removed outlier: 3.562A pdb=" N LEU B 744 " --> pdb=" O GLY B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 773 removed outlier: 3.794A pdb=" N LEU B 772 " --> pdb=" O ARG B 768 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 796 removed outlier: 3.604A pdb=" N TRP B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 Processing helix chain 'B' and resid 824 through 836 removed outlier: 3.666A pdb=" N TRP B 828 " --> pdb=" O ASN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 857 Processing helix chain 'B' and resid 860 through 874 removed outlier: 3.773A pdb=" N TRP B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 894 through 908 removed outlier: 3.784A pdb=" N TRP B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 925 removed outlier: 3.713A pdb=" N ASN B 924 " --> pdb=" O THR B 920 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET B 925 " --> pdb=" O THR B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 943 removed outlier: 3.538A pdb=" N ASP B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 959 Processing helix chain 'B' and resid 960 through 977 Processing helix chain 'B' and resid 979 through 994 removed outlier: 3.957A pdb=" N PHE B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1010 removed outlier: 3.560A pdb=" N ALA B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.636A pdb=" N ASN B1020 " --> pdb=" O GLN B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1045 removed outlier: 3.573A pdb=" N SER B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1066 through 1080 removed outlier: 3.697A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1100 removed outlier: 3.674A pdb=" N LYS B1100 " --> pdb=" O ILE B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1116 removed outlier: 3.690A pdb=" N ALA B1107 " --> pdb=" O LYS B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'B' and resid 1139 through 1152 removed outlier: 3.837A pdb=" N HIS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1172 removed outlier: 3.747A pdb=" N GLN B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1189 Processing helix chain 'B' and resid 1192 through 1206 removed outlier: 3.832A pdb=" N TRP B1196 " --> pdb=" O ASP B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1224 Processing helix chain 'B' and resid 1228 through 1244 Processing helix chain 'B' and resid 1254 through 1266 Processing helix chain 'B' and resid 1269 through 1291 removed outlier: 4.628A pdb=" N TRP B1273 " --> pdb=" O ASP B1269 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B1274 " --> pdb=" O PRO B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1313 removed outlier: 4.077A pdb=" N ASP B1313 " --> pdb=" O ALA B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1340 Processing helix chain 'B' and resid 1341 through 1356 removed outlier: 3.560A pdb=" N SER B1355 " --> pdb=" O LYS B1351 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN B1356 " --> pdb=" O ASN B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1371 Processing helix chain 'B' and resid 1382 through 1396 removed outlier: 3.729A pdb=" N ASN B1396 " --> pdb=" O THR B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1414 removed outlier: 3.679A pdb=" N TRP B1403 " --> pdb=" O SER B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1433 Processing helix chain 'B' and resid 1436 through 1456 removed outlier: 3.987A pdb=" N ALA B1456 " --> pdb=" O LYS B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1478 Processing helix chain 'B' and resid 1480 through 1494 Processing helix chain 'B' and resid 1498 through 1511 removed outlier: 3.664A pdb=" N ARG B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1533 Processing helix chain 'B' and resid 1535 through 1548 Processing helix chain 'B' and resid 1553 through 1563 removed outlier: 3.959A pdb=" N SER B1563 " --> pdb=" O GLN B1559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.708A pdb=" N ARG A 20 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 removed outlier: 6.833A pdb=" N ILE A 285 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N SER A 479 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER A 327 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 478 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE A 329 " --> pdb=" O ILE A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 397 through 398 removed outlier: 7.985A pdb=" N MET A 398 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR A 358 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG A 355 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TRP A 419 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU A 418 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE A 451 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 420 " --> pdb=" O ILE A 451 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 383 Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 505 removed outlier: 3.656A pdb=" N LEU A 717 " --> pdb=" O TYR A 490 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 676 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 569 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA A 661 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 571 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY A 633 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 916 through 920 removed outlier: 3.641A pdb=" N ALA A 855 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 843 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL A 844 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE A 928 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 846 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 737 through 739 Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 11 removed outlier: 7.047A pdb=" N ILE C 300 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS C 10 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE C 298 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 289 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 25 removed outlier: 6.076A pdb=" N LYS C 48 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU C 56 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.614A pdb=" N ALA C 79 " --> pdb=" O TRP C 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.764A pdb=" N TYR C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY C 134 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS C 140 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.614A pdb=" N GLY C 166 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE C 154 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 164 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 174 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 196 through 198 Processing sheet with id=AB6, first strand: chain 'C' and resid 213 through 217 removed outlier: 6.079A pdb=" N ILE C 214 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR C 227 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 216 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 235 through 240 removed outlier: 3.679A pdb=" N ASN C 237 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C 268 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP C 260 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N CYS C 266 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AB9, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.620A pdb=" N TRP D 58 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS D 48 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU D 56 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.585A pdb=" N SER D 69 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 100 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AC3, first strand: chain 'D' and resid 164 through 166 removed outlier: 3.544A pdb=" N ASN D 173 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE D 174 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS D 184 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 196 through 197 Processing sheet with id=AC5, first strand: chain 'D' and resid 235 through 239 removed outlier: 6.891A pdb=" N SER D 250 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL D 238 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL D 248 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL D 256 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS D 268 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP D 260 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS D 266 " --> pdb=" O ASP D 260 " (cutoff:3.500A) 1125 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.62 Time building geometry restraints manager: 9.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7593 1.34 - 1.46: 4592 1.46 - 1.58: 10916 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 23269 Sorted by residual: bond pdb=" CB GLU C 141 " pdb=" CG GLU C 141 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.77e+00 bond pdb=" CB ILE B 968 " pdb=" CG2 ILE B 968 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.53e+00 bond pdb=" CB VAL C 290 " pdb=" CG2 VAL C 290 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.47e+00 bond pdb=" CB CYS B 724 " pdb=" SG CYS B 724 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.10e+00 bond pdb=" C VAL B1400 " pdb=" N PRO B1401 " ideal model delta sigma weight residual 1.334 1.374 -0.041 2.34e-02 1.83e+03 3.00e+00 ... (remaining 23264 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.49: 435 105.49 - 112.64: 12465 112.64 - 119.78: 7819 119.78 - 126.93: 10566 126.93 - 134.08: 313 Bond angle restraints: 31598 Sorted by residual: angle pdb=" N PRO B 417 " pdb=" CA PRO B 417 " pdb=" CB PRO B 417 " ideal model delta sigma weight residual 102.65 110.65 -8.00 6.80e-01 2.16e+00 1.38e+02 angle pdb=" N PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 103.25 111.29 -8.04 1.05e+00 9.07e-01 5.86e+01 angle pdb=" N PRO A 206 " pdb=" CA PRO A 206 " pdb=" CB PRO A 206 " ideal model delta sigma weight residual 103.25 111.23 -7.98 1.05e+00 9.07e-01 5.78e+01 angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" CB PRO B 386 " ideal model delta sigma weight residual 103.25 110.27 -7.02 1.05e+00 9.07e-01 4.47e+01 angle pdb=" C LEU B1374 " pdb=" N LEU B1375 " pdb=" CA LEU B1375 " ideal model delta sigma weight residual 121.54 130.36 -8.82 1.91e+00 2.74e-01 2.13e+01 ... (remaining 31593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 12563 17.75 - 35.49: 1242 35.49 - 53.24: 161 53.24 - 70.99: 23 70.99 - 88.73: 15 Dihedral angle restraints: 14004 sinusoidal: 5326 harmonic: 8678 Sorted by residual: dihedral pdb=" CA LEU A 586 " pdb=" C LEU A 586 " pdb=" N THR A 587 " pdb=" CA THR A 587 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP D 201 " pdb=" C ASP D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta harmonic sigma weight residual -180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA ARG B 947 " pdb=" C ARG B 947 " pdb=" N GLU B 948 " pdb=" CA GLU B 948 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 14001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2458 0.044 - 0.089: 884 0.089 - 0.133: 234 0.133 - 0.178: 36 0.178 - 0.222: 7 Chirality restraints: 3619 Sorted by residual: chirality pdb=" CA PRO B 386 " pdb=" N PRO B 386 " pdb=" C PRO B 386 " pdb=" CB PRO B 386 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA HIS B 992 " pdb=" N HIS B 992 " pdb=" C HIS B 992 " pdb=" CB HIS B 992 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO A 206 " pdb=" N PRO A 206 " pdb=" C PRO A 206 " pdb=" CB PRO A 206 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3616 not shown) Planarity restraints: 4070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 13 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 14 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 155 " 0.059 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO A 156 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 516 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C CYS B 516 " 0.056 2.00e-02 2.50e+03 pdb=" O CYS B 516 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR B 517 " -0.019 2.00e-02 2.50e+03 ... (remaining 4067 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 237 2.60 - 3.17: 20216 3.17 - 3.75: 33677 3.75 - 4.32: 44452 4.32 - 4.90: 75412 Nonbonded interactions: 173994 Sorted by model distance: nonbonded pdb=" O THR B1392 " pdb=" OG SER B1395 " model vdw 2.021 2.440 nonbonded pdb=" OH TYR A 358 " pdb=" OD2 ASP A 423 " model vdw 2.098 2.440 nonbonded pdb=" OE1 GLU A 40 " pdb=" NZ LYS B1285 " model vdw 2.122 2.520 nonbonded pdb=" OD1 ASP A1069 " pdb=" N GLU A1070 " model vdw 2.128 2.520 nonbonded pdb=" OH TYR A 554 " pdb=" OD2 ASP A 679 " model vdw 2.131 2.440 ... (remaining 173989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.190 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 58.660 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.006 0.062 23269 Z= 0.377 Angle : 0.837 14.382 31598 Z= 0.460 Chirality : 0.049 0.222 3619 Planarity : 0.006 0.101 4070 Dihedral : 14.042 88.732 8398 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.92 % Favored : 93.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2975 helix: 1.09 (0.14), residues: 1444 sheet: -1.95 (0.27), residues: 314 loop : -3.35 (0.14), residues: 1217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 3.481 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.3556 time to fit residues: 111.1573 Evaluate side-chains 154 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 232 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 269 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 GLN B 942 GLN B1253 ASN B1404 GLN D 3 ASN D 98 GLN D 221 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23269 Z= 0.226 Angle : 0.654 10.986 31598 Z= 0.338 Chirality : 0.043 0.164 3619 Planarity : 0.005 0.067 4070 Dihedral : 5.346 24.504 3199 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.55 % Favored : 89.41 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 2975 helix: 1.32 (0.14), residues: 1464 sheet: -1.76 (0.29), residues: 293 loop : -3.10 (0.15), residues: 1218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 2.839 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 179 average time/residue: 0.3436 time to fit residues: 99.2032 Evaluate side-chains 172 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 2.569 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2200 time to fit residues: 9.9695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 270 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1529 HIS B1558 ASN ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 23269 Z= 0.282 Angle : 0.636 10.066 31598 Z= 0.328 Chirality : 0.043 0.162 3619 Planarity : 0.005 0.067 4070 Dihedral : 5.212 23.471 3199 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2975 helix: 1.39 (0.14), residues: 1467 sheet: -1.63 (0.29), residues: 304 loop : -3.05 (0.15), residues: 1204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 2.723 Fit side-chains outliers start: 33 outliers final: 15 residues processed: 192 average time/residue: 0.3201 time to fit residues: 100.4495 Evaluate side-chains 169 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2004 time to fit residues: 9.1449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 140 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 287 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1253 ASN B1487 GLN D 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23269 Z= 0.192 Angle : 0.591 11.322 31598 Z= 0.302 Chirality : 0.041 0.156 3619 Planarity : 0.004 0.062 4070 Dihedral : 4.955 22.617 3199 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2975 helix: 1.57 (0.14), residues: 1470 sheet: -1.53 (0.30), residues: 302 loop : -2.94 (0.16), residues: 1203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 2.544 Fit side-chains outliers start: 46 outliers final: 19 residues processed: 211 average time/residue: 0.3206 time to fit residues: 110.6318 Evaluate side-chains 176 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 2.588 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2085 time to fit residues: 11.0512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 40.0000 chunk 244 optimal weight: 2.9990 chunk 198 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 72 optimal weight: 0.0470 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN B1205 GLN D 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23269 Z= 0.205 Angle : 0.584 10.240 31598 Z= 0.299 Chirality : 0.041 0.153 3619 Planarity : 0.004 0.058 4070 Dihedral : 4.845 22.469 3199 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2975 helix: 1.65 (0.14), residues: 1470 sheet: -1.49 (0.30), residues: 302 loop : -2.87 (0.16), residues: 1203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 2.606 Fit side-chains outliers start: 38 outliers final: 17 residues processed: 206 average time/residue: 0.3227 time to fit residues: 109.6903 Evaluate side-chains 177 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 2.666 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2079 time to fit residues: 10.4506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 168 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 287 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1413 GLN C 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23269 Z= 0.184 Angle : 0.575 12.979 31598 Z= 0.291 Chirality : 0.040 0.163 3619 Planarity : 0.004 0.056 4070 Dihedral : 4.704 22.235 3199 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2975 helix: 1.73 (0.14), residues: 1474 sheet: -1.44 (0.29), residues: 312 loop : -2.81 (0.16), residues: 1189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 2.839 Fit side-chains outliers start: 34 outliers final: 12 residues processed: 207 average time/residue: 0.3747 time to fit residues: 127.1565 Evaluate side-chains 180 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2269 time to fit residues: 8.9706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 163 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 286 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1253 ASN ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 23269 Z= 0.294 Angle : 0.626 12.527 31598 Z= 0.318 Chirality : 0.042 0.159 3619 Planarity : 0.004 0.058 4070 Dihedral : 4.855 22.785 3199 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2975 helix: 1.65 (0.14), residues: 1471 sheet: -1.49 (0.29), residues: 329 loop : -2.87 (0.16), residues: 1175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 2.721 Fit side-chains outliers start: 41 outliers final: 18 residues processed: 204 average time/residue: 0.3439 time to fit residues: 114.3109 Evaluate side-chains 183 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 2.604 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2154 time to fit residues: 10.9323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.2980 chunk 114 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23269 Z= 0.181 Angle : 0.594 11.721 31598 Z= 0.298 Chirality : 0.041 0.156 3619 Planarity : 0.004 0.060 4070 Dihedral : 4.715 23.046 3199 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2975 helix: 1.77 (0.14), residues: 1473 sheet: -1.34 (0.29), residues: 327 loop : -2.78 (0.17), residues: 1175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 2.800 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 187 average time/residue: 0.3300 time to fit residues: 100.9256 Evaluate side-chains 170 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2127 time to fit residues: 5.0169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.6980 chunk 274 optimal weight: 0.0370 chunk 250 optimal weight: 0.7980 chunk 266 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 116 optimal weight: 30.0000 chunk 209 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23269 Z= 0.185 Angle : 0.587 11.141 31598 Z= 0.295 Chirality : 0.041 0.295 3619 Planarity : 0.004 0.056 4070 Dihedral : 4.608 22.388 3199 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2975 helix: 1.81 (0.14), residues: 1475 sheet: -1.28 (0.29), residues: 325 loop : -2.72 (0.17), residues: 1175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 2.627 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 186 average time/residue: 0.3491 time to fit residues: 106.6386 Evaluate side-chains 176 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 2.513 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2591 time to fit residues: 7.2208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.9980 chunk 282 optimal weight: 0.0870 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 143 GLN A 148 ASN ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN B1228 HIS B1253 ASN D 223 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 23269 Z= 0.322 Angle : 0.648 12.202 31598 Z= 0.328 Chirality : 0.043 0.163 3619 Planarity : 0.004 0.061 4070 Dihedral : 4.803 22.868 3199 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2975 helix: 1.70 (0.14), residues: 1470 sheet: -1.40 (0.29), residues: 329 loop : -2.80 (0.17), residues: 1176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 2.672 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 170 average time/residue: 0.3551 time to fit residues: 99.1971 Evaluate side-chains 162 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 2.589 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2148 time to fit residues: 5.2621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.4980 chunk 250 optimal weight: 0.8980 chunk 72 optimal weight: 0.0470 chunk 217 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 235 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 242 optimal weight: 0.0980 chunk 29 optimal weight: 0.3980 chunk 43 optimal weight: 7.9990 overall best weight: 0.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN B1228 HIS B1558 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112410 restraints weight = 39486.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110681 restraints weight = 41325.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111931 restraints weight = 39767.309| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 23269 Z= 0.150 Angle : 0.584 10.872 31598 Z= 0.292 Chirality : 0.040 0.161 3619 Planarity : 0.004 0.058 4070 Dihedral : 4.519 21.901 3199 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2975 helix: 1.86 (0.14), residues: 1480 sheet: -1.19 (0.30), residues: 318 loop : -2.65 (0.17), residues: 1177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3581.60 seconds wall clock time: 67 minutes 13.82 seconds (4033.82 seconds total)