Starting phenix.real_space_refine on Sun Feb 18 20:12:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/02_2024/7qdr_13923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/02_2024/7qdr_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_13923/02_2024/7qdr_13923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/02_2024/7qdr_13923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/02_2024/7qdr_13923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdr_13923/02_2024/7qdr_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.73, per 1000 atoms: 0.56 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: 9.13 Conformation dependent library (CDL) restraints added in 4.8 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: 2.75 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: 8.83 Time building geometry restraints manager: 9.76 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: 2.340 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: 0.020 Extract box with map and model: 10.570 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 62.820 Find NCS groups from input model: 0.870 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.150 ------------------------------------------------------------------------------- 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 % Allowed : 0.13 % Favored : 99.87 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 49 HIS 0.010 0.001 HIS B1187 PHE 0.038 0.002 PHE C 271 TYR 0.028 0.002 TYR B1525 ARG 0.021 0.001 ARG A1001 *********************** 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 : 2.624 Fit side-chains REVERT: C 12 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7102 (mm-30) REVERT: D 50 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8080 (mmm160) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.3302 time to fit residues: 103.4719 Evaluate side-chains 154 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.816 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 221 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23269 Z= 0.228 Angle : 0.656 10.939 31598 Z= 0.339 Chirality : 0.043 0.174 3619 Planarity : 0.005 0.067 4070 Dihedral : 5.341 24.599 3199 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.42 % Favored : 89.55 % Rotamer: Outliers : 0.76 % Allowed : 9.62 % Favored : 89.62 % 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: -1.03 (0.16), residues: 2975 helix: 1.33 (0.14), residues: 1465 sheet: -1.77 (0.29), residues: 293 loop : -3.10 (0.15), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 47 HIS 0.005 0.001 HIS B1187 PHE 0.017 0.001 PHE C 271 TYR 0.021 0.001 TYR A1244 ARG 0.006 0.000 ARG A 20 *********************** 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 182 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 2.571 Fit side-chains REVERT: B 1283 ASP cc_start: 0.7687 (t0) cc_final: 0.7485 (t0) REVERT: B 1338 ASP cc_start: 0.7332 (t0) cc_final: 0.7060 (t0) REVERT: B 1455 MET cc_start: 0.7007 (mmm) cc_final: 0.6384 (mmm) REVERT: C 12 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7057 (mm-30) REVERT: D 50 ARG cc_start: 0.8467 (mmm160) cc_final: 0.8256 (mmm160) REVERT: D 71 ASP cc_start: 0.8210 (t0) cc_final: 0.7936 (t0) outliers start: 18 outliers final: 15 residues processed: 176 average time/residue: 0.3164 time to fit residues: 90.0533 Evaluate side-chains 169 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain B residue 974 GLU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 0.0980 chunk 240 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 D 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1244 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= 0.233 Angle : 0.613 9.944 31598 Z= 0.316 Chirality : 0.042 0.158 3619 Planarity : 0.004 0.065 4070 Dihedral : 5.122 23.057 3199 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 1.90 % Allowed : 12.54 % Favored : 85.56 % 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: -0.85 (0.16), residues: 2975 helix: 1.46 (0.14), residues: 1467 sheet: -1.55 (0.30), residues: 302 loop : -3.03 (0.15), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.005 0.001 HIS B 848 PHE 0.014 0.001 PHE C 271 TYR 0.022 0.001 TYR A1244 ARG 0.005 0.000 ARG A 768 *********************** 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 219 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 4.037 Fit side-chains REVERT: A 830 MET cc_start: 0.0403 (OUTLIER) cc_final: 0.0195 (pmm) REVERT: A 1180 MET cc_start: 0.7266 (ttm) cc_final: 0.6952 (ttm) REVERT: B 544 MET cc_start: 0.7951 (mmm) cc_final: 0.7614 (mmt) REVERT: B 1181 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8011 (tp40) REVERT: B 1338 ASP cc_start: 0.7260 (t0) cc_final: 0.6981 (t0) REVERT: B 1411 GLN cc_start: 0.8391 (tt0) cc_final: 0.8159 (tt0) REVERT: B 1423 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7725 (m-10) REVERT: B 1455 MET cc_start: 0.6997 (mmm) cc_final: 0.6408 (mmm) REVERT: C 141 GLU cc_start: 0.7477 (mp0) cc_final: 0.7238 (mp0) REVERT: D 52 GLU cc_start: 0.8165 (tp30) cc_final: 0.7957 (tp30) REVERT: D 71 ASP cc_start: 0.8194 (t0) cc_final: 0.7938 (t0) REVERT: D 223 ASN cc_start: 0.8645 (p0) cc_final: 0.8400 (p0) outliers start: 45 outliers final: 27 residues processed: 205 average time/residue: 0.3404 time to fit residues: 113.6236 Evaluate side-chains 189 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 974 GLU Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8400 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23269 Z= 0.224 Angle : 0.594 10.186 31598 Z= 0.304 Chirality : 0.041 0.205 3619 Planarity : 0.004 0.062 4070 Dihedral : 4.932 22.334 3199 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 2.83 % Allowed : 13.63 % Favored : 83.54 % 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: -0.70 (0.16), residues: 2975 helix: 1.58 (0.14), residues: 1469 sheet: -1.52 (0.30), residues: 302 loop : -2.94 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 49 HIS 0.004 0.001 HIS B 848 PHE 0.020 0.001 PHE B1492 TYR 0.023 0.001 TYR A1244 ARG 0.004 0.000 ARG A 20 *********************** 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 238 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 171 time to evaluate : 2.790 Fit side-chains REVERT: A 307 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.6213 (m-90) REVERT: B 544 MET cc_start: 0.7856 (mmm) cc_final: 0.7513 (mmt) REVERT: B 1181 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 1338 ASP cc_start: 0.7230 (t0) cc_final: 0.6995 (t0) REVERT: B 1423 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7749 (m-10) REVERT: B 1455 MET cc_start: 0.6933 (mmm) cc_final: 0.6372 (mmm) REVERT: D 49 TRP cc_start: 0.7579 (t-100) cc_final: 0.7325 (t-100) REVERT: D 52 GLU cc_start: 0.8284 (tp30) cc_final: 0.7792 (tp30) REVERT: D 71 ASP cc_start: 0.8234 (t0) cc_final: 0.7965 (t0) REVERT: D 223 ASN cc_start: 0.8647 (p0) cc_final: 0.8363 (p0) REVERT: D 243 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.5873 (p0) outliers start: 67 outliers final: 37 residues processed: 220 average time/residue: 0.3086 time to fit residues: 111.5363 Evaluate side-chains 198 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 256 VAL 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: 2.9990 chunk 4 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 118 optimal weight: 40.0000 chunk 244 optimal weight: 1.9990 chunk 198 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.9104 ------------------------------------------------------------------------------- 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: 0.8394 moved from start: 0.1624 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= 0.210 Angle : 0.582 9.771 31598 Z= 0.298 Chirality : 0.041 0.154 3619 Planarity : 0.004 0.059 4070 Dihedral : 4.830 22.408 3199 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.04 % Allowed : 14.52 % Favored : 82.44 % 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: -0.59 (0.16), residues: 2975 helix: 1.67 (0.14), residues: 1470 sheet: -1.51 (0.29), residues: 317 loop : -2.89 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 49 HIS 0.004 0.001 HIS C 126 PHE 0.015 0.001 PHE B1112 TYR 0.022 0.001 TYR A1244 ARG 0.003 0.000 ARG A 20 *********************** 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 242 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 170 time to evaluate : 2.519 Fit side-chains REVERT: A 307 TRP cc_start: 0.7361 (OUTLIER) cc_final: 0.6131 (m-90) REVERT: B 544 MET cc_start: 0.7826 (mmm) cc_final: 0.7495 (mmt) REVERT: B 1098 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6344 (tm-30) REVERT: B 1181 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 1338 ASP cc_start: 0.7286 (t0) cc_final: 0.7057 (t0) REVERT: B 1381 LEU cc_start: 0.8228 (mm) cc_final: 0.7524 (mt) REVERT: B 1423 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7830 (m-10) REVERT: B 1455 MET cc_start: 0.7006 (mmm) cc_final: 0.6502 (mmm) REVERT: D 49 TRP cc_start: 0.7488 (t-100) cc_final: 0.7170 (t-100) REVERT: D 52 GLU cc_start: 0.8294 (tp30) cc_final: 0.7646 (tp30) REVERT: D 223 ASN cc_start: 0.8610 (p0) cc_final: 0.8038 (p0) REVERT: D 294 ASP cc_start: 0.8530 (t70) cc_final: 0.8324 (t70) outliers start: 72 outliers final: 47 residues processed: 225 average time/residue: 0.3448 time to fit residues: 127.8470 Evaluate side-chains 211 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 161 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23269 Z= 0.210 Angle : 0.571 9.661 31598 Z= 0.292 Chirality : 0.040 0.153 3619 Planarity : 0.004 0.056 4070 Dihedral : 4.737 22.349 3199 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 3.25 % Allowed : 15.58 % Favored : 81.17 % 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: 1.73 (0.14), residues: 1470 sheet: -1.45 (0.29), residues: 327 loop : -2.84 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 49 HIS 0.004 0.001 HIS C 126 PHE 0.022 0.001 PHE B1492 TYR 0.022 0.001 TYR A1244 ARG 0.003 0.000 ARG A 20 *********************** 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 253 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 176 time to evaluate : 2.897 Fit side-chains REVERT: A 307 TRP cc_start: 0.7366 (OUTLIER) cc_final: 0.6135 (m-90) REVERT: B 544 MET cc_start: 0.7809 (mmm) cc_final: 0.7458 (mmt) REVERT: B 1098 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6368 (tm-30) REVERT: B 1181 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 1338 ASP cc_start: 0.7276 (t0) cc_final: 0.7048 (t0) REVERT: B 1423 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7853 (m-10) REVERT: B 1455 MET cc_start: 0.6889 (mmm) cc_final: 0.6350 (mmm) REVERT: C 243 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8251 (p0) REVERT: D 49 TRP cc_start: 0.7540 (t-100) cc_final: 0.7243 (t-100) REVERT: D 52 GLU cc_start: 0.8343 (tp30) cc_final: 0.7755 (tp30) REVERT: D 177 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7058 (tp) REVERT: D 223 ASN cc_start: 0.8590 (p0) cc_final: 0.8028 (p0) REVERT: D 294 ASP cc_start: 0.8512 (t70) cc_final: 0.8229 (t70) outliers start: 77 outliers final: 57 residues processed: 239 average time/residue: 0.3167 time to fit residues: 125.4297 Evaluate side-chains 229 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 167 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1411 GLN Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 163 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 241 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 286 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 C 285 ASN D 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23269 Z= 0.171 Angle : 0.566 12.833 31598 Z= 0.286 Chirality : 0.040 0.151 3619 Planarity : 0.004 0.055 4070 Dihedral : 4.633 22.303 3199 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.29 % Allowed : 16.25 % Favored : 80.46 % 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: -0.37 (0.16), residues: 2975 helix: 1.82 (0.14), residues: 1472 sheet: -1.39 (0.29), residues: 317 loop : -2.76 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 49 HIS 0.004 0.001 HIS D 246 PHE 0.015 0.001 PHE B1112 TYR 0.018 0.001 TYR A1244 ARG 0.007 0.000 ARG D 53 *********************** 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 255 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 177 time to evaluate : 2.753 Fit side-chains REVERT: A 307 TRP cc_start: 0.7293 (OUTLIER) cc_final: 0.6015 (m-90) REVERT: B 1098 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6357 (tm-30) REVERT: B 1181 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8017 (tm-30) REVERT: B 1338 ASP cc_start: 0.7229 (t0) cc_final: 0.6997 (t0) REVERT: B 1423 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: B 1455 MET cc_start: 0.6960 (mmm) cc_final: 0.6383 (mmm) REVERT: C 50 ARG cc_start: 0.7783 (tpp-160) cc_final: 0.7568 (ttm-80) REVERT: C 243 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8260 (p0) REVERT: D 49 TRP cc_start: 0.7500 (t-100) cc_final: 0.7179 (t-100) REVERT: D 52 GLU cc_start: 0.8366 (tp30) cc_final: 0.7720 (tp30) REVERT: D 53 ARG cc_start: 0.6955 (mtp-110) cc_final: 0.6391 (ptm160) REVERT: D 223 ASN cc_start: 0.8560 (p0) cc_final: 0.7957 (p0) REVERT: D 294 ASP cc_start: 0.8479 (t70) cc_final: 0.8236 (t70) outliers start: 78 outliers final: 52 residues processed: 241 average time/residue: 0.3287 time to fit residues: 130.6934 Evaluate side-chains 227 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 171 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 259 TRP Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.4980 chunk 114 optimal weight: 0.0870 chunk 170 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23269 Z= 0.166 Angle : 0.562 11.240 31598 Z= 0.284 Chirality : 0.040 0.150 3619 Planarity : 0.004 0.058 4070 Dihedral : 4.545 23.724 3199 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 3.08 % Allowed : 17.10 % Favored : 79.82 % 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: -0.27 (0.16), residues: 2975 helix: 1.88 (0.14), residues: 1478 sheet: -1.33 (0.29), residues: 317 loop : -2.68 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 49 HIS 0.008 0.001 HIS A 72 PHE 0.023 0.001 PHE B1492 TYR 0.023 0.001 TYR B1525 ARG 0.006 0.000 ARG D 53 *********************** 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 252 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 179 time to evaluate : 2.642 Fit side-chains REVERT: A 307 TRP cc_start: 0.7337 (OUTLIER) cc_final: 0.6053 (m-90) REVERT: B 1098 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: B 1181 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 1338 ASP cc_start: 0.7212 (t0) cc_final: 0.6995 (t0) REVERT: B 1411 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: B 1423 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7713 (m-10) REVERT: B 1455 MET cc_start: 0.6932 (mmm) cc_final: 0.6363 (mmm) REVERT: C 243 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8257 (p0) REVERT: D 49 TRP cc_start: 0.7479 (t-100) cc_final: 0.7208 (t-100) REVERT: D 52 GLU cc_start: 0.8380 (tp30) cc_final: 0.7752 (tp30) REVERT: D 53 ARG cc_start: 0.6999 (mtp-110) cc_final: 0.6518 (ptm160) REVERT: D 177 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6583 (tp) REVERT: D 223 ASN cc_start: 0.8513 (p0) cc_final: 0.7903 (p0) REVERT: D 294 ASP cc_start: 0.8435 (t70) cc_final: 0.8194 (t70) outliers start: 73 outliers final: 56 residues processed: 239 average time/residue: 0.3126 time to fit residues: 123.2750 Evaluate side-chains 234 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 172 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1353 LEU Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1411 GLN Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 259 TRP Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.9980 chunk 274 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 266 optimal weight: 0.0870 chunk 160 optimal weight: 0.2980 chunk 116 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 148 ASN ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN D 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23269 Z= 0.159 Angle : 0.562 10.783 31598 Z= 0.284 Chirality : 0.040 0.261 3619 Planarity : 0.004 0.057 4070 Dihedral : 4.456 22.089 3199 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 2.91 % Allowed : 17.26 % Favored : 79.82 % 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: -0.17 (0.16), residues: 2975 helix: 1.95 (0.14), residues: 1479 sheet: -1.25 (0.29), residues: 327 loop : -2.65 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1524 HIS 0.007 0.001 HIS A 72 PHE 0.013 0.001 PHE B1112 TYR 0.019 0.001 TYR B1525 ARG 0.006 0.000 ARG D 53 *********************** 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 246 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 177 time to evaluate : 2.598 Fit side-chains REVERT: A 17 LEU cc_start: 0.6928 (mp) cc_final: 0.6252 (tp) REVERT: A 307 TRP cc_start: 0.7370 (OUTLIER) cc_final: 0.6045 (m-90) REVERT: B 1098 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: B 1181 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8050 (tp40) REVERT: B 1338 ASP cc_start: 0.7183 (t0) cc_final: 0.6968 (t0) REVERT: B 1423 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7709 (m-10) REVERT: B 1455 MET cc_start: 0.6964 (mmm) cc_final: 0.6351 (mmm) REVERT: C 50 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7613 (mmp80) REVERT: C 243 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8201 (p0) REVERT: D 49 TRP cc_start: 0.7430 (t-100) cc_final: 0.7179 (t-100) REVERT: D 52 GLU cc_start: 0.8388 (tp30) cc_final: 0.7751 (tp30) REVERT: D 53 ARG cc_start: 0.7007 (mtp-110) cc_final: 0.6529 (ptm160) REVERT: D 223 ASN cc_start: 0.8457 (p0) cc_final: 0.7899 (p0) REVERT: D 294 ASP cc_start: 0.8393 (t70) cc_final: 0.8144 (t70) outliers start: 69 outliers final: 60 residues processed: 232 average time/residue: 0.3227 time to fit residues: 123.0388 Evaluate side-chains 233 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 169 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1353 LEU Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 259 TRP Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.8980 chunk 282 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 196 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 chunk 272 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** B1101 GLN B1228 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23269 Z= 0.204 Angle : 0.578 10.701 31598 Z= 0.291 Chirality : 0.040 0.149 3619 Planarity : 0.004 0.056 4070 Dihedral : 4.474 22.199 3199 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 2.91 % Allowed : 17.43 % Favored : 79.65 % 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: -0.19 (0.16), residues: 2975 helix: 1.94 (0.14), residues: 1475 sheet: -1.23 (0.29), residues: 327 loop : -2.67 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1524 HIS 0.005 0.001 HIS A 72 PHE 0.025 0.001 PHE B1492 TYR 0.019 0.001 TYR A1244 ARG 0.005 0.000 ARG D 53 ********************** 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 239 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 170 time to evaluate : 2.730 Fit side-chains REVERT: A 17 LEU cc_start: 0.7004 (mp) cc_final: 0.6283 (tp) REVERT: A 307 TRP cc_start: 0.7327 (OUTLIER) cc_final: 0.5946 (m-90) REVERT: B 1098 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: B 1181 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8033 (tm-30) REVERT: B 1338 ASP cc_start: 0.7234 (t0) cc_final: 0.7019 (t0) REVERT: B 1423 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7762 (m-10) REVERT: B 1455 MET cc_start: 0.7009 (mmm) cc_final: 0.6395 (mmm) REVERT: C 50 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7622 (mmp80) REVERT: C 243 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8207 (p0) REVERT: D 49 TRP cc_start: 0.7433 (t-100) cc_final: 0.7164 (t-100) REVERT: D 52 GLU cc_start: 0.8403 (tp30) cc_final: 0.7738 (tp30) REVERT: D 53 ARG cc_start: 0.6986 (mtp-110) cc_final: 0.6485 (ptm160) REVERT: D 223 ASN cc_start: 0.8446 (p0) cc_final: 0.7867 (p0) REVERT: D 294 ASP cc_start: 0.8407 (t70) cc_final: 0.8168 (t70) outliers start: 69 outliers final: 63 residues processed: 227 average time/residue: 0.3185 time to fit residues: 119.1965 Evaluate side-chains 232 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 165 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1353 LEU Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 259 TRP Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.0470 chunk 250 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 217 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 242 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112579 restraints weight = 39190.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110647 restraints weight = 38658.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111979 restraints weight = 37439.094| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23269 Z= 0.155 Angle : 0.566 10.422 31598 Z= 0.283 Chirality : 0.040 0.147 3619 Planarity : 0.004 0.052 4070 Dihedral : 4.393 21.919 3199 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 2.79 % Allowed : 17.73 % Favored : 79.49 % 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: -0.11 (0.16), residues: 2975 helix: 1.99 (0.14), residues: 1481 sheet: -1.22 (0.29), residues: 327 loop : -2.63 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1524 HIS 0.006 0.001 HIS A 72 PHE 0.015 0.001 PHE B1112 TYR 0.018 0.001 TYR B1525 ARG 0.005 0.000 ARG D 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3824.63 seconds wall clock time: 71 minutes 19.58 seconds (4279.58 seconds total)