Starting phenix.real_space_refine on Sat Jun 28 03:26:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zu3_60479/06_2025/8zu3_60479_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zu3_60479/06_2025/8zu3_60479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zu3_60479/06_2025/8zu3_60479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zu3_60479/06_2025/8zu3_60479.map" model { file = "/net/cci-nas-00/data/ceres_data/8zu3_60479/06_2025/8zu3_60479_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zu3_60479/06_2025/8zu3_60479_neut.cif" } resolution = 3.1 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= 0.007 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 207 5.16 5 C 21327 2.51 5 N 5295 2.21 5 O 5340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32172 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 10463 Classifications: {'peptide': 1280} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 1238} Chain breaks: 15 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 150 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'D12': 2, 'L9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'D12': 2, 'L9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'D12': 2, 'L9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, D, E, F Time building chain proxies: 41.56, per 1000 atoms: 1.29 Number of scatterers: 32172 At special positions: 0 Unit cell: (219.45, 217.74, 149.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 207 16.00 P 3 15.00 O 5340 8.00 N 5295 7.00 C 21327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2411 " - pdb=" SG CYS A2415 " distance=2.04 Simple disulfide: pdb=" CA CYS B 584 " - pdb=" SG CYS B 584 " distance=2.80 Simple disulfide: pdb=" SG CYS B2411 " - pdb=" SG CYS B2415 " distance=2.04 Simple disulfide: pdb=" SG CYS D2411 " - pdb=" SG CYS D2415 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.60 Conformation dependent library (CDL) restraints added in 4.1 seconds 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7452 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 9 sheets defined 69.4% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 570 through 579 removed outlier: 4.161A pdb=" N GLY A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 592 Processing helix chain 'A' and resid 598 through 604 removed outlier: 3.503A pdb=" N ILE A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 618 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.877A pdb=" N VAL A 633 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 634 " --> pdb=" O TRP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 700 Proline residue: A 687 - end of helix removed outlier: 3.516A pdb=" N PHE A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 810 through 815 removed outlier: 4.071A pdb=" N LEU A 813 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 828 through 849 removed outlier: 4.248A pdb=" N LEU A 849 " --> pdb=" O VAL A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 931 through 955 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 989 through 1009 removed outlier: 4.061A pdb=" N LYS A 993 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU A 996 " --> pdb=" O TYR A 992 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLU A 997 " --> pdb=" O LYS A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1027 removed outlier: 4.018A pdb=" N LEU A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS A1018 " --> pdb=" O LEU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1036 removed outlier: 3.568A pdb=" N ARG A1036 " --> pdb=" O GLN A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1057 Processing helix chain 'A' and resid 1097 through 1117 removed outlier: 3.937A pdb=" N SER A1117 " --> pdb=" O TRP A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1163 Processing helix chain 'A' and resid 1165 through 1181 removed outlier: 3.503A pdb=" N GLY A1178 " --> pdb=" O VAL A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1199 removed outlier: 3.708A pdb=" N LEU A1187 " --> pdb=" O SER A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1206 removed outlier: 3.847A pdb=" N GLN A1205 " --> pdb=" O THR A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1231 removed outlier: 3.594A pdb=" N MET A1231 " --> pdb=" O ILE A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1302 Processing helix chain 'A' and resid 1305 through 1320 removed outlier: 3.727A pdb=" N VAL A1310 " --> pdb=" O TYR A1306 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1370 removed outlier: 3.740A pdb=" N ARG A1365 " --> pdb=" O GLN A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1414 Processing helix chain 'A' and resid 1417 through 1422 Processing helix chain 'A' and resid 1514 through 1540 removed outlier: 5.316A pdb=" N HIS A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS A1536 " --> pdb=" O PHE A1532 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1660 No H-bonds generated for 'chain 'A' and resid 1658 through 1660' Processing helix chain 'A' and resid 1661 through 1669 removed outlier: 4.535A pdb=" N PHE A1665 " --> pdb=" O GLU A1661 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1666 " --> pdb=" O ALA A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1686 Processing helix chain 'A' and resid 1686 through 1702 Processing helix chain 'A' and resid 1709 through 1717 Processing helix chain 'A' and resid 1727 through 1746 Processing helix chain 'A' and resid 1785 through 1803 Processing helix chain 'A' and resid 1941 through 1952 Processing helix chain 'A' and resid 1960 through 1978 Processing helix chain 'A' and resid 2000 through 2024 Processing helix chain 'A' and resid 2026 through 2044 Processing helix chain 'A' and resid 2061 through 2084 Processing helix chain 'A' and resid 2092 through 2096 removed outlier: 3.576A pdb=" N LYS A2096 " --> pdb=" O PHE A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2100 through 2112 Processing helix chain 'A' and resid 2114 through 2127 Processing helix chain 'A' and resid 2132 through 2159 Processing helix chain 'A' and resid 2168 through 2200 removed outlier: 4.498A pdb=" N PHE A2189 " --> pdb=" O ALA A2185 " (cutoff:3.500A) Proline residue: A2190 - end of helix removed outlier: 3.944A pdb=" N VAL A2200 " --> pdb=" O LEU A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2236 through 2247 Processing helix chain 'A' and resid 2250 through 2260 Processing helix chain 'A' and resid 2281 through 2294 Processing helix chain 'A' and resid 2332 through 2344 Processing helix chain 'A' and resid 2438 through 2457 Processing helix chain 'A' and resid 2461 through 2465 removed outlier: 3.718A pdb=" N SER A2465 " --> pdb=" O ILE A2462 " (cutoff:3.500A) Processing helix chain 'A' and resid 2474 through 2490 Processing helix chain 'A' and resid 2492 through 2507 removed outlier: 3.714A pdb=" N GLU A2496 " --> pdb=" O GLU A2492 " (cutoff:3.500A) Processing helix chain 'A' and resid 2509 through 2517 Processing helix chain 'B' and resid 571 through 579 Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 598 through 604 removed outlier: 3.503A pdb=" N ILE B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 618 Processing helix chain 'B' and resid 626 through 643 removed outlier: 3.877A pdb=" N VAL B 633 " --> pdb=" O PHE B 629 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 634 " --> pdb=" O TRP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 700 Proline residue: B 687 - end of helix removed outlier: 3.516A pdb=" N PHE B 690 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA B 693 " --> pdb=" O PHE B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 792 through 802 Processing helix chain 'B' and resid 810 through 815 removed outlier: 4.072A pdb=" N LEU B 813 " --> pdb=" O VAL B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 823 Processing helix chain 'B' and resid 825 through 827 No H-bonds generated for 'chain 'B' and resid 825 through 827' Processing helix chain 'B' and resid 828 through 849 removed outlier: 4.248A pdb=" N LEU B 849 " --> pdb=" O VAL B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 930 Processing helix chain 'B' and resid 931 through 955 Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 989 through 1009 removed outlier: 4.061A pdb=" N LYS B 993 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B 996 " --> pdb=" O TYR B 992 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLU B 997 " --> pdb=" O LYS B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1027 removed outlier: 4.018A pdb=" N LEU B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1036 removed outlier: 3.568A pdb=" N ARG B1036 " --> pdb=" O GLN B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1057 Processing helix chain 'B' and resid 1097 through 1117 removed outlier: 3.936A pdb=" N SER B1117 " --> pdb=" O TRP B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1163 Processing helix chain 'B' and resid 1165 through 1181 removed outlier: 3.503A pdb=" N GLY B1178 " --> pdb=" O VAL B1174 " (cutoff:3.500A) Processing helix chain 'B' and resid 1183 through 1199 removed outlier: 3.708A pdb=" N LEU B1187 " --> pdb=" O SER B1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 1201 through 1206 removed outlier: 3.847A pdb=" N GLN B1205 " --> pdb=" O THR B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1212 through 1231 removed outlier: 3.595A pdb=" N MET B1231 " --> pdb=" O ILE B1227 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1302 Processing helix chain 'B' and resid 1305 through 1320 removed outlier: 3.727A pdb=" N VAL B1310 " --> pdb=" O TYR B1306 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B1318 " --> pdb=" O LEU B1314 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B1319 " --> pdb=" O GLN B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1320 through 1370 removed outlier: 3.740A pdb=" N ARG B1365 " --> pdb=" O GLN B1361 " (cutoff:3.500A) Processing helix chain 'B' and resid 1409 through 1414 Processing helix chain 'B' and resid 1417 through 1422 Processing helix chain 'B' and resid 1514 through 1540 removed outlier: 5.317A pdb=" N HIS B1535 " --> pdb=" O GLU B1531 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS B1536 " --> pdb=" O PHE B1532 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1660 No H-bonds generated for 'chain 'B' and resid 1658 through 1660' Processing helix chain 'B' and resid 1661 through 1669 removed outlier: 4.536A pdb=" N PHE B1665 " --> pdb=" O GLU B1661 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B1666 " --> pdb=" O ALA B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1672 through 1686 Processing helix chain 'B' and resid 1686 through 1702 Processing helix chain 'B' and resid 1709 through 1717 Processing helix chain 'B' and resid 1727 through 1746 Processing helix chain 'B' and resid 1785 through 1803 Processing helix chain 'B' and resid 1941 through 1952 Processing helix chain 'B' and resid 1960 through 1978 Processing helix chain 'B' and resid 2000 through 2024 Processing helix chain 'B' and resid 2026 through 2044 Processing helix chain 'B' and resid 2061 through 2084 Processing helix chain 'B' and resid 2092 through 2096 removed outlier: 3.576A pdb=" N LYS B2096 " --> pdb=" O PHE B2093 " (cutoff:3.500A) Processing helix chain 'B' and resid 2100 through 2112 Processing helix chain 'B' and resid 2114 through 2127 Processing helix chain 'B' and resid 2132 through 2159 Processing helix chain 'B' and resid 2168 through 2200 removed outlier: 4.498A pdb=" N PHE B2189 " --> pdb=" O ALA B2185 " (cutoff:3.500A) Proline residue: B2190 - end of helix removed outlier: 3.944A pdb=" N VAL B2200 " --> pdb=" O LEU B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2236 through 2247 Processing helix chain 'B' and resid 2250 through 2260 Processing helix chain 'B' and resid 2281 through 2294 Processing helix chain 'B' and resid 2332 through 2344 Processing helix chain 'B' and resid 2438 through 2457 Processing helix chain 'B' and resid 2461 through 2465 removed outlier: 3.717A pdb=" N SER B2465 " --> pdb=" O ILE B2462 " (cutoff:3.500A) Processing helix chain 'B' and resid 2474 through 2490 Processing helix chain 'B' and resid 2492 through 2507 removed outlier: 3.714A pdb=" N GLU B2496 " --> pdb=" O GLU B2492 " (cutoff:3.500A) Processing helix chain 'B' and resid 2509 through 2517 Processing helix chain 'D' and resid 571 through 579 Processing helix chain 'D' and resid 580 through 592 Processing helix chain 'D' and resid 598 through 604 removed outlier: 3.503A pdb=" N ILE D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 618 Processing helix chain 'D' and resid 626 through 643 removed outlier: 3.877A pdb=" N VAL D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 634 " --> pdb=" O TRP D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 700 Proline residue: D 687 - end of helix removed outlier: 3.516A pdb=" N PHE D 690 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA D 693 " --> pdb=" O PHE D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 707 Processing helix chain 'D' and resid 768 through 786 Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 792 through 802 Processing helix chain 'D' and resid 810 through 815 removed outlier: 4.071A pdb=" N LEU D 813 " --> pdb=" O VAL D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 823 Processing helix chain 'D' and resid 825 through 827 No H-bonds generated for 'chain 'D' and resid 825 through 827' Processing helix chain 'D' and resid 828 through 849 removed outlier: 4.247A pdb=" N LEU D 849 " --> pdb=" O VAL D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 930 Processing helix chain 'D' and resid 931 through 955 Processing helix chain 'D' and resid 978 through 989 Processing helix chain 'D' and resid 989 through 1009 removed outlier: 4.062A pdb=" N LYS D 993 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU D 996 " --> pdb=" O TYR D 992 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLU D 997 " --> pdb=" O LYS D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1027 removed outlier: 4.018A pdb=" N LEU D1017 " --> pdb=" O PHE D1013 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS D1018 " --> pdb=" O LEU D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1036 removed outlier: 3.568A pdb=" N ARG D1036 " --> pdb=" O GLN D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1057 Processing helix chain 'D' and resid 1097 through 1117 removed outlier: 3.937A pdb=" N SER D1117 " --> pdb=" O TRP D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1155 through 1163 Processing helix chain 'D' and resid 1165 through 1181 removed outlier: 3.503A pdb=" N GLY D1178 " --> pdb=" O VAL D1174 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1199 removed outlier: 3.708A pdb=" N LEU D1187 " --> pdb=" O SER D1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 1201 through 1206 removed outlier: 3.846A pdb=" N GLN D1205 " --> pdb=" O THR D1201 " (cutoff:3.500A) Processing helix chain 'D' and resid 1212 through 1231 removed outlier: 3.595A pdb=" N MET D1231 " --> pdb=" O ILE D1227 " (cutoff:3.500A) Processing helix chain 'D' and resid 1285 through 1302 Processing helix chain 'D' and resid 1305 through 1320 removed outlier: 3.727A pdb=" N VAL D1310 " --> pdb=" O TYR D1306 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D1318 " --> pdb=" O LEU D1314 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D1319 " --> pdb=" O GLN D1315 " (cutoff:3.500A) Processing helix chain 'D' and resid 1320 through 1370 removed outlier: 3.741A pdb=" N ARG D1365 " --> pdb=" O GLN D1361 " (cutoff:3.500A) Processing helix chain 'D' and resid 1409 through 1414 Processing helix chain 'D' and resid 1417 through 1422 Processing helix chain 'D' and resid 1514 through 1540 removed outlier: 5.316A pdb=" N HIS D1535 " --> pdb=" O GLU D1531 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS D1536 " --> pdb=" O PHE D1532 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1660 No H-bonds generated for 'chain 'D' and resid 1658 through 1660' Processing helix chain 'D' and resid 1661 through 1669 removed outlier: 4.535A pdb=" N PHE D1665 " --> pdb=" O GLU D1661 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D1666 " --> pdb=" O ALA D1662 " (cutoff:3.500A) Processing helix chain 'D' and resid 1672 through 1686 Processing helix chain 'D' and resid 1686 through 1702 Processing helix chain 'D' and resid 1709 through 1717 Processing helix chain 'D' and resid 1727 through 1746 Processing helix chain 'D' and resid 1785 through 1803 Processing helix chain 'D' and resid 1941 through 1952 Processing helix chain 'D' and resid 1960 through 1978 Processing helix chain 'D' and resid 2000 through 2024 Processing helix chain 'D' and resid 2026 through 2044 Processing helix chain 'D' and resid 2061 through 2084 Processing helix chain 'D' and resid 2092 through 2096 removed outlier: 3.576A pdb=" N LYS D2096 " --> pdb=" O PHE D2093 " (cutoff:3.500A) Processing helix chain 'D' and resid 2100 through 2112 Processing helix chain 'D' and resid 2114 through 2127 Processing helix chain 'D' and resid 2132 through 2159 Processing helix chain 'D' and resid 2168 through 2200 removed outlier: 4.498A pdb=" N PHE D2189 " --> pdb=" O ALA D2185 " (cutoff:3.500A) Proline residue: D2190 - end of helix removed outlier: 3.944A pdb=" N VAL D2200 " --> pdb=" O LEU D2196 " (cutoff:3.500A) Processing helix chain 'D' and resid 2236 through 2247 Processing helix chain 'D' and resid 2250 through 2260 Processing helix chain 'D' and resid 2281 through 2294 Processing helix chain 'D' and resid 2332 through 2344 Processing helix chain 'D' and resid 2438 through 2457 Processing helix chain 'D' and resid 2461 through 2465 removed outlier: 3.718A pdb=" N SER D2465 " --> pdb=" O ILE D2462 " (cutoff:3.500A) Processing helix chain 'D' and resid 2474 through 2490 Processing helix chain 'D' and resid 2492 through 2507 removed outlier: 3.714A pdb=" N GLU D2496 " --> pdb=" O GLU D2492 " (cutoff:3.500A) Processing helix chain 'D' and resid 2509 through 2517 Processing helix chain 'C' and resid 229 through 245 Processing helix chain 'E' and resid 229 through 245 Processing helix chain 'F' and resid 229 through 245 Processing sheet with id=AA1, first strand: chain 'A' and resid 2211 through 2215 Processing sheet with id=AA2, first strand: chain 'A' and resid 2233 through 2234 Processing sheet with id=AA3, first strand: chain 'A' and resid 2350 through 2352 removed outlier: 3.542A pdb=" N VAL A2385 " --> pdb=" O ILE A2352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2211 through 2215 Processing sheet with id=AA5, first strand: chain 'B' and resid 2233 through 2234 Processing sheet with id=AA6, first strand: chain 'B' and resid 2350 through 2352 removed outlier: 3.542A pdb=" N VAL B2385 " --> pdb=" O ILE B2352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 2211 through 2215 Processing sheet with id=AA8, first strand: chain 'D' and resid 2233 through 2234 Processing sheet with id=AA9, first strand: chain 'D' and resid 2350 through 2352 removed outlier: 3.542A pdb=" N VAL D2385 " --> pdb=" O ILE D2352 " (cutoff:3.500A) 1968 hydrogen bonds defined for protein. 5796 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: 12.07 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4830 1.32 - 1.44: 9279 1.44 - 1.57: 18489 1.57 - 1.69: 12 1.69 - 1.81: 315 Bond restraints: 32925 Sorted by residual: bond pdb=" C39 L9Q D2601 " pdb=" C40 L9Q D2601 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" C39 L9Q B2601 " pdb=" C40 L9Q B2601 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.95e+01 bond pdb=" C39 L9Q A2603 " pdb=" C40 L9Q A2603 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C11 L9Q A2603 " pdb=" O3 L9Q A2603 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C11 L9Q B2601 " pdb=" O3 L9Q B2601 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.93e+01 ... (remaining 32920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 43038 3.36 - 6.72: 1231 6.72 - 10.07: 191 10.07 - 13.43: 33 13.43 - 16.79: 6 Bond angle restraints: 44499 Sorted by residual: angle pdb=" N GLN B 930 " pdb=" CA GLN B 930 " pdb=" C GLN B 930 " ideal model delta sigma weight residual 113.19 126.52 -13.33 1.19e+00 7.06e-01 1.26e+02 angle pdb=" N GLN D 930 " pdb=" CA GLN D 930 " pdb=" C GLN D 930 " ideal model delta sigma weight residual 113.19 126.51 -13.32 1.19e+00 7.06e-01 1.25e+02 angle pdb=" N GLN A 930 " pdb=" CA GLN A 930 " pdb=" C GLN A 930 " ideal model delta sigma weight residual 113.19 126.51 -13.32 1.19e+00 7.06e-01 1.25e+02 angle pdb=" N LEU D2374 " pdb=" CA LEU D2374 " pdb=" C LEU D2374 " ideal model delta sigma weight residual 111.07 100.31 10.76 1.07e+00 8.73e-01 1.01e+02 angle pdb=" N LEU B2374 " pdb=" CA LEU B2374 " pdb=" C LEU B2374 " ideal model delta sigma weight residual 111.07 100.33 10.74 1.07e+00 8.73e-01 1.01e+02 ... (remaining 44494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 15395 23.51 - 47.02: 2654 47.02 - 70.54: 1316 70.54 - 94.05: 78 94.05 - 117.56: 6 Dihedral angle restraints: 19449 sinusoidal: 7980 harmonic: 11469 Sorted by residual: dihedral pdb=" CB CYS B 584 " pdb=" CA CYS B 584 " pdb=" SG CYS B 584 " pdb=" CB CYS B 584 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS B2411 " pdb=" SG CYS B2411 " pdb=" SG CYS B2415 " pdb=" CB CYS B2415 " ideal model delta sinusoidal sigma weight residual -86.00 -145.54 59.54 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CB CYS D2411 " pdb=" SG CYS D2411 " pdb=" SG CYS D2415 " pdb=" CB CYS D2415 " ideal model delta sinusoidal sigma weight residual -86.00 -145.53 59.53 1 1.00e+01 1.00e-02 4.73e+01 ... (remaining 19446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4510 0.144 - 0.288: 453 0.288 - 0.432: 67 0.432 - 0.576: 13 0.576 - 0.720: 3 Chirality restraints: 5046 Sorted by residual: chirality pdb=" CG LEU D1155 " pdb=" CB LEU D1155 " pdb=" CD1 LEU D1155 " pdb=" CD2 LEU D1155 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CG LEU A1155 " pdb=" CB LEU A1155 " pdb=" CD1 LEU A1155 " pdb=" CD2 LEU A1155 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CG LEU B1155 " pdb=" CB LEU B1155 " pdb=" CD1 LEU B1155 " pdb=" CD2 LEU B1155 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 5043 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q A2603 " 0.136 2.00e-02 2.50e+03 1.36e-01 1.86e+02 pdb=" C39 L9Q A2603 " -0.136 2.00e-02 2.50e+03 pdb=" C40 L9Q A2603 " -0.137 2.00e-02 2.50e+03 pdb=" C41 L9Q A2603 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q D2601 " 0.136 2.00e-02 2.50e+03 1.36e-01 1.86e+02 pdb=" C39 L9Q D2601 " -0.136 2.00e-02 2.50e+03 pdb=" C40 L9Q D2601 " -0.137 2.00e-02 2.50e+03 pdb=" C41 L9Q D2601 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B2601 " 0.136 2.00e-02 2.50e+03 1.36e-01 1.86e+02 pdb=" C39 L9Q B2601 " -0.135 2.00e-02 2.50e+03 pdb=" C40 L9Q B2601 " -0.137 2.00e-02 2.50e+03 pdb=" C41 L9Q B2601 " 0.136 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 3 1.87 - 2.63: 667 2.63 - 3.38: 43514 3.38 - 4.14: 90163 4.14 - 4.90: 150467 Nonbonded interactions: 284814 Sorted by model distance: nonbonded pdb=" O LEU B1650 " pdb=" CD1 LEU B1650 " model vdw 1.111 3.460 nonbonded pdb=" O LEU A1650 " pdb=" CD1 LEU A1650 " model vdw 1.111 3.460 nonbonded pdb=" O LEU D1650 " pdb=" CD1 LEU D1650 " model vdw 1.111 3.460 nonbonded pdb=" CB LYS B2323 " pdb=" NZ LYS B2323 " model vdw 2.007 3.520 nonbonded pdb=" CB LYS D2323 " pdb=" NZ LYS D2323 " model vdw 2.007 3.520 ... (remaining 284809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 570 through 2521 or resid 2602)) selection = (chain 'B' and (resid 570 through 2521 or resid 2602)) selection = (chain 'D' and (resid 570 through 2521 or resid 2602)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } 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 individual isotropic 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: 285.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.820 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 94.430 Find NCS groups from input model: 2.090 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 387.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.774 32929 Z= 0.603 Angle : 1.439 74.518 44507 Z= 0.932 Chirality : 0.094 0.720 5046 Planarity : 0.008 0.170 5424 Dihedral : 26.455 117.560 11985 Min Nonbonded Distance : 1.111 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 2.68 % Allowed : 11.60 % Favored : 85.71 % Rotamer: Outliers : 42.24 % Allowed : 14.72 % Favored : 43.03 % Cbeta Deviations : 0.56 % 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: -4.08 (0.11), residues: 3801 helix: -1.72 (0.09), residues: 2529 sheet: -5.11 (0.27), residues: 114 loop : -4.50 (0.14), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1168 HIS 0.007 0.001 HIS B 951 PHE 0.031 0.002 PHE B 615 TYR 0.018 0.002 TYR B1165 ARG 0.007 0.001 ARG A1547 Details of bonding type rmsd hydrogen bonds : bond 0.16954 ( 1968) hydrogen bonds : angle 7.60778 ( 5796) SS BOND : bond 0.38680 ( 4) SS BOND : angle 35.73121 ( 8) covalent geometry : bond 0.00784 (32925) covalent geometry : angle 1.35698 (44499) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2268 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1446 poor density : 822 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 TRP cc_start: 0.2821 (OUTLIER) cc_final: 0.1994 (t-100) REVERT: A 691 LEU cc_start: 0.3345 (OUTLIER) cc_final: 0.2589 (tp) REVERT: A 975 LEU cc_start: 0.4892 (OUTLIER) cc_final: 0.4384 (tt) REVERT: A 1230 ASN cc_start: 0.7445 (t0) cc_final: 0.7097 (t0) REVERT: A 1233 SER cc_start: 0.0356 (OUTLIER) cc_final: 0.0058 (t) REVERT: A 1303 LEU cc_start: 0.4773 (OUTLIER) cc_final: 0.4484 (mp) REVERT: A 2000 VAL cc_start: 0.3955 (OUTLIER) cc_final: 0.3566 (t) REVERT: A 2153 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.5334 (mmp-170) REVERT: A 2321 ASN cc_start: 0.1404 (OUTLIER) cc_final: 0.1044 (p0) REVERT: A 2364 ASN cc_start: 0.1986 (OUTLIER) cc_final: 0.0300 (p0) REVERT: A 2406 ILE cc_start: 0.2205 (OUTLIER) cc_final: 0.0690 (mt) REVERT: A 2511 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 580 TRP cc_start: 0.2942 (OUTLIER) cc_final: 0.2054 (t-100) REVERT: B 691 LEU cc_start: 0.3455 (OUTLIER) cc_final: 0.2730 (tp) REVERT: B 975 LEU cc_start: 0.4824 (OUTLIER) cc_final: 0.4516 (tt) REVERT: B 978 ASP cc_start: 0.3250 (OUTLIER) cc_final: 0.2944 (t70) REVERT: B 1233 SER cc_start: 0.0263 (OUTLIER) cc_final: -0.0023 (t) REVERT: B 1303 LEU cc_start: 0.4832 (OUTLIER) cc_final: 0.4358 (mp) REVERT: B 2000 VAL cc_start: 0.4226 (OUTLIER) cc_final: 0.3789 (t) REVERT: B 2153 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.5154 (mmp-170) REVERT: B 2321 ASN cc_start: 0.1443 (OUTLIER) cc_final: 0.1134 (p0) REVERT: B 2364 ASN cc_start: 0.2018 (OUTLIER) cc_final: 0.0369 (p0) REVERT: B 2406 ILE cc_start: 0.2222 (OUTLIER) cc_final: 0.0605 (mt) REVERT: B 2465 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8338 (p) REVERT: B 2511 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.6744 (mm-30) REVERT: D 580 TRP cc_start: 0.2838 (OUTLIER) cc_final: 0.1995 (t-100) REVERT: D 691 LEU cc_start: 0.3333 (OUTLIER) cc_final: 0.2540 (tp) REVERT: D 975 LEU cc_start: 0.4837 (OUTLIER) cc_final: 0.4445 (tt) REVERT: D 1216 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: D 1233 SER cc_start: 0.0433 (OUTLIER) cc_final: 0.0125 (t) REVERT: D 1303 LEU cc_start: 0.4797 (OUTLIER) cc_final: 0.4323 (mp) REVERT: D 2000 VAL cc_start: 0.3856 (OUTLIER) cc_final: 0.3439 (t) REVERT: D 2153 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.5245 (mmp-170) REVERT: D 2321 ASN cc_start: 0.1543 (OUTLIER) cc_final: 0.0809 (p0) REVERT: D 2364 ASN cc_start: 0.2064 (OUTLIER) cc_final: 0.0409 (p0) REVERT: D 2406 ILE cc_start: 0.2103 (OUTLIER) cc_final: 0.0544 (mt) REVERT: D 2465 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8300 (p) outliers start: 1446 outliers final: 233 residues processed: 1885 average time/residue: 0.6174 time to fit residues: 1801.3618 Evaluate side-chains 717 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 448 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 687 PRO Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1533 THR Chi-restraints excluded: chain A residue 1556 GLN Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1655 ARG Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1675 LEU Chi-restraints excluded: chain A residue 1677 ARG Chi-restraints excluded: chain A residue 1707 SER Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1958 THR Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2083 CYS Chi-restraints excluded: chain A residue 2089 ILE Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2116 VAL Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2271 GLU Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2292 LEU Chi-restraints excluded: chain A residue 2309 ARG Chi-restraints excluded: chain A residue 2318 GLU Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2321 ASN Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2346 SER Chi-restraints excluded: chain A residue 2356 PHE Chi-restraints excluded: chain A residue 2364 ASN Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2406 ILE Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2413 THR Chi-restraints excluded: chain A residue 2414 ASP Chi-restraints excluded: chain A residue 2426 LYS Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2465 SER Chi-restraints excluded: chain A residue 2473 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2512 THR Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 687 PRO Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 848 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1104 LEU Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1208 THR Chi-restraints excluded: chain B residue 1219 ILE Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1233 SER Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1304 SER Chi-restraints excluded: chain B residue 1308 LEU Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1423 SER Chi-restraints excluded: chain B residue 1533 THR Chi-restraints excluded: chain B residue 1556 GLN Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1649 LEU Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1675 LEU Chi-restraints excluded: chain B residue 1677 ARG Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1786 ASP Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1958 THR Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2000 VAL Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2083 CYS Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2116 VAL Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2210 VAL Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2270 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2292 LEU Chi-restraints excluded: chain B residue 2309 ARG Chi-restraints excluded: chain B residue 2318 GLU Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2321 ASN Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2346 SER Chi-restraints excluded: chain B residue 2356 PHE Chi-restraints excluded: chain B residue 2364 ASN Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2406 ILE Chi-restraints excluded: chain B residue 2412 ARG Chi-restraints excluded: chain B residue 2413 THR Chi-restraints excluded: chain B residue 2414 ASP Chi-restraints excluded: chain B residue 2426 LYS Chi-restraints excluded: chain B residue 2443 LEU Chi-restraints excluded: chain B residue 2465 SER Chi-restraints excluded: chain B residue 2473 CYS Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2512 THR Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 687 PRO Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 828 PHE Chi-restraints excluded: chain D residue 836 SER Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1104 LEU Chi-restraints excluded: chain D residue 1187 LEU Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1216 ASP Chi-restraints excluded: chain D residue 1219 ILE Chi-restraints excluded: chain D residue 1227 ILE Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1233 SER Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1304 SER Chi-restraints excluded: chain D residue 1308 LEU Chi-restraints excluded: chain D residue 1336 ILE Chi-restraints excluded: chain D residue 1533 THR Chi-restraints excluded: chain D residue 1556 GLN Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1649 LEU Chi-restraints excluded: chain D residue 1656 ILE Chi-restraints excluded: chain D residue 1675 LEU Chi-restraints excluded: chain D residue 1677 ARG Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1731 MET Chi-restraints excluded: chain D residue 1786 ASP Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1958 THR Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2000 VAL Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2008 LEU Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2083 CYS Chi-restraints excluded: chain D residue 2116 VAL Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2210 VAL Chi-restraints excluded: chain D residue 2222 LEU Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2271 GLU Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2292 LEU Chi-restraints excluded: chain D residue 2309 ARG Chi-restraints excluded: chain D residue 2318 GLU Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2321 ASN Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2346 SER Chi-restraints excluded: chain D residue 2356 PHE Chi-restraints excluded: chain D residue 2358 LYS Chi-restraints excluded: chain D residue 2364 ASN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2406 ILE Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2413 THR Chi-restraints excluded: chain D residue 2414 ASP Chi-restraints excluded: chain D residue 2426 LYS Chi-restraints excluded: chain D residue 2443 LEU Chi-restraints excluded: chain D residue 2465 SER Chi-restraints excluded: chain D residue 2473 CYS Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2511 GLU Chi-restraints excluded: chain D residue 2512 THR Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain F residue 243 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 0.9990 chunk 295 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 305 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 185 optimal weight: 0.5980 chunk 227 optimal weight: 10.0000 chunk 354 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A 781 GLN A 930 GLN A 934 GLN A 949 GLN A1009 GLN A1012 ASN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN A1409 HIS A1535 HIS A1951 HIS A2011 GLN ** A2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2324 HIS A2375 GLN A2416 ASN B 781 GLN B 930 GLN B 934 GLN B 949 GLN B1009 GLN B1012 ASN B1114 GLN B1222 ASN B1409 HIS B1535 HIS B1951 HIS B2011 GLN ** B2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2206 GLN B2269 GLN ** B2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2324 HIS B2416 ASN D 697 GLN D 930 GLN D 934 GLN D 949 GLN D1009 GLN D1012 ASN D1114 GLN D1222 ASN D1409 HIS D1535 HIS D1951 HIS D2011 GLN ** D2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2102 ASN D2206 GLN D2269 GLN ** D2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2324 HIS D2375 GLN D2416 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.183561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.121395 restraints weight = 62690.819| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.91 r_work: 0.3520 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32929 Z= 0.182 Angle : 0.904 56.085 44507 Z= 0.454 Chirality : 0.045 0.212 5046 Planarity : 0.006 0.098 5424 Dihedral : 14.909 110.094 5064 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.87 % Favored : 91.40 % Rotamer: Outliers : 10.98 % Allowed : 26.41 % Favored : 62.61 % 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: -1.73 (0.14), residues: 3801 helix: 0.18 (0.10), residues: 2580 sheet: -5.05 (0.30), residues: 141 loop : -3.87 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D1021 HIS 0.008 0.001 HIS B 932 PHE 0.032 0.002 PHE D 615 TYR 0.020 0.002 TYR A 992 ARG 0.008 0.001 ARG B1547 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 1968) hydrogen bonds : angle 5.18044 ( 5796) SS BOND : bond 0.02143 ( 4) SS BOND : angle 25.16581 ( 8) covalent geometry : bond 0.00403 (32925) covalent geometry : angle 0.83907 (44499) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 376 poor density : 480 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 HIS cc_start: 0.2335 (OUTLIER) cc_final: 0.1418 (t-90) REVERT: A 703 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6381 (mmt180) REVERT: A 711 MET cc_start: 0.2500 (mmm) cc_final: 0.1208 (mtp) REVERT: A 776 VAL cc_start: 0.8341 (t) cc_final: 0.7991 (m) REVERT: A 798 LEU cc_start: 0.5804 (mt) cc_final: 0.5550 (mt) REVERT: A 813 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7114 (tp) REVERT: A 946 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6377 (m-80) REVERT: A 1198 LEU cc_start: 0.8503 (tp) cc_final: 0.8206 (tp) REVERT: A 1231 MET cc_start: 0.7093 (mtm) cc_final: 0.6886 (mtm) REVERT: A 1355 GLU cc_start: 0.8853 (pt0) cc_final: 0.8550 (pp20) REVERT: A 1532 PHE cc_start: 0.8903 (m-80) cc_final: 0.8536 (m-10) REVERT: A 1552 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8401 (pm20) REVERT: A 1553 GLU cc_start: 0.8420 (pm20) cc_final: 0.8217 (mp0) REVERT: A 1943 ARG cc_start: 0.7897 (ttm110) cc_final: 0.7448 (ttt-90) REVERT: A 2093 PHE cc_start: 0.3944 (m-80) cc_final: 0.3034 (t80) REVERT: A 2137 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8359 (mtm) REVERT: A 2140 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: A 2156 GLU cc_start: 0.8347 (tp30) cc_final: 0.8121 (mt-10) REVERT: A 2158 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8553 (ttmt) REVERT: A 2305 TRP cc_start: 0.7416 (m100) cc_final: 0.7180 (m100) REVERT: A 2416 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7357 (t0) REVERT: A 2506 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 2511 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: B 702 HIS cc_start: 0.2367 (OUTLIER) cc_final: 0.2163 (t-90) REVERT: B 711 MET cc_start: 0.2565 (mmm) cc_final: 0.1889 (ttm) REVERT: B 776 VAL cc_start: 0.8283 (t) cc_final: 0.7956 (m) REVERT: B 794 LYS cc_start: 0.5941 (tppt) cc_final: 0.5725 (tppt) REVERT: B 803 VAL cc_start: 0.6926 (t) cc_final: 0.6674 (p) REVERT: B 828 PHE cc_start: 0.5100 (OUTLIER) cc_final: 0.4638 (p90) REVERT: B 919 VAL cc_start: 0.5597 (OUTLIER) cc_final: 0.5135 (p) REVERT: B 1198 LEU cc_start: 0.8470 (tp) cc_final: 0.8227 (tp) REVERT: B 1303 LEU cc_start: 0.3260 (OUTLIER) cc_final: 0.2883 (mp) REVERT: B 1355 GLU cc_start: 0.8851 (pt0) cc_final: 0.8542 (pp20) REVERT: B 1515 TRP cc_start: 0.5426 (t60) cc_final: 0.5144 (t60) REVERT: B 1552 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: B 1553 GLU cc_start: 0.8480 (pm20) cc_final: 0.8092 (mp0) REVERT: B 1943 ARG cc_start: 0.8047 (ttm110) cc_final: 0.7625 (ttt-90) REVERT: B 2093 PHE cc_start: 0.3960 (m-80) cc_final: 0.2880 (t80) REVERT: B 2096 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8111 (mtmm) REVERT: B 2137 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8322 (mtm) REVERT: B 2140 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: B 2158 LYS cc_start: 0.8958 (ttmm) cc_final: 0.8511 (ttpp) REVERT: B 2269 GLN cc_start: 0.5640 (tp-100) cc_final: 0.5426 (tp-100) REVERT: B 2305 TRP cc_start: 0.7457 (m100) cc_final: 0.6925 (m100) REVERT: B 2506 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8665 (tp) REVERT: D 587 MET cc_start: 0.5487 (mmp) cc_final: 0.5219 (mmt) REVERT: D 621 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.1964 (tp) REVERT: D 711 MET cc_start: 0.2643 (mmm) cc_final: 0.1247 (mtp) REVERT: D 776 VAL cc_start: 0.8303 (t) cc_final: 0.7944 (m) REVERT: D 798 LEU cc_start: 0.5853 (mt) cc_final: 0.5589 (mt) REVERT: D 803 VAL cc_start: 0.6909 (t) cc_final: 0.6634 (p) REVERT: D 813 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7213 (tp) REVERT: D 828 PHE cc_start: 0.5099 (OUTLIER) cc_final: 0.4734 (p90) REVERT: D 920 ARG cc_start: 0.1752 (OUTLIER) cc_final: 0.1485 (tpm170) REVERT: D 1303 LEU cc_start: 0.3159 (OUTLIER) cc_final: 0.2749 (mp) REVERT: D 1329 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7911 (t0) REVERT: D 1355 GLU cc_start: 0.8854 (pt0) cc_final: 0.8543 (pp20) REVERT: D 1360 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7645 (ttmt) REVERT: D 1515 TRP cc_start: 0.5488 (t60) cc_final: 0.5188 (t60) REVERT: D 1552 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: D 1554 LEU cc_start: 0.8684 (tp) cc_final: 0.8470 (tt) REVERT: D 1943 ARG cc_start: 0.7930 (ttm110) cc_final: 0.7450 (ttt-90) REVERT: D 2093 PHE cc_start: 0.3993 (m-80) cc_final: 0.3094 (t80) REVERT: D 2100 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6930 (t70) REVERT: D 2140 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: D 2156 GLU cc_start: 0.8420 (tp30) cc_final: 0.8148 (mt-10) REVERT: D 2305 TRP cc_start: 0.7419 (m100) cc_final: 0.7197 (m100) REVERT: D 2313 LYS cc_start: 0.3598 (OUTLIER) cc_final: 0.2599 (pttp) REVERT: D 2386 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6990 (mtp85) REVERT: D 2416 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7327 (t0) REVERT: D 2506 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8357 (tp) REVERT: C 235 GLU cc_start: 0.7715 (tp30) cc_final: 0.7152 (tp30) REVERT: C 238 MET cc_start: 0.7548 (tpt) cc_final: 0.7225 (tpt) REVERT: C 243 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5972 (mm) REVERT: F 243 ILE cc_start: 0.6318 (OUTLIER) cc_final: 0.5984 (mm) outliers start: 376 outliers final: 170 residues processed: 791 average time/residue: 0.4479 time to fit residues: 563.8637 Evaluate side-chains 594 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 389 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 833 SER Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1707 SER Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2236 THR Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2281 SER Chi-restraints excluded: chain A residue 2294 ASN Chi-restraints excluded: chain A residue 2313 LYS Chi-restraints excluded: chain A residue 2318 GLU Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2346 SER Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2364 ASN Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2413 THR Chi-restraints excluded: chain A residue 2414 ASP Chi-restraints excluded: chain A residue 2416 ASN Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2459 PHE Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 799 TYR Chi-restraints excluded: chain B residue 828 PHE Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1097 THR Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1104 LEU Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1182 ILE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1228 SER Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1552 GLN Chi-restraints excluded: chain B residue 1677 ARG Chi-restraints excluded: chain B residue 1701 VAL Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1783 ILE Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1966 LEU Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2048 ILE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2096 LYS Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2196 LEU Chi-restraints excluded: chain B residue 2236 THR Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2292 LEU Chi-restraints excluded: chain B residue 2294 ASN Chi-restraints excluded: chain B residue 2313 LYS Chi-restraints excluded: chain B residue 2318 GLU Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2346 SER Chi-restraints excluded: chain B residue 2364 ASN Chi-restraints excluded: chain B residue 2375 GLN Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2413 THR Chi-restraints excluded: chain B residue 2414 ASP Chi-restraints excluded: chain B residue 2447 ILE Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 799 TYR Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 828 PHE Chi-restraints excluded: chain D residue 833 SER Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1097 THR Chi-restraints excluded: chain D residue 1104 LEU Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1177 THR Chi-restraints excluded: chain D residue 1182 ILE Chi-restraints excluded: chain D residue 1187 LEU Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1329 ASN Chi-restraints excluded: chain D residue 1360 LYS Chi-restraints excluded: chain D residue 1424 ASP Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1552 GLN Chi-restraints excluded: chain D residue 1701 VAL Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1731 MET Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1783 ILE Chi-restraints excluded: chain D residue 1786 ASP Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1966 LEU Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2000 VAL Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2048 ILE Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2100 HIS Chi-restraints excluded: chain D residue 2117 GLU Chi-restraints excluded: chain D residue 2140 GLU Chi-restraints excluded: chain D residue 2193 PHE Chi-restraints excluded: chain D residue 2236 THR Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2313 LYS Chi-restraints excluded: chain D residue 2318 GLU Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2346 SER Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2364 ASN Chi-restraints excluded: chain D residue 2375 GLN Chi-restraints excluded: chain D residue 2386 ARG Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2413 THR Chi-restraints excluded: chain D residue 2414 ASP Chi-restraints excluded: chain D residue 2416 ASN Chi-restraints excluded: chain D residue 2447 ILE Chi-restraints excluded: chain D residue 2504 ILE Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain F residue 243 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 306 optimal weight: 0.7980 chunk 369 optimal weight: 40.0000 chunk 379 optimal weight: 0.0040 chunk 45 optimal weight: 0.7980 chunk 224 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A 930 GLN A1012 ASN A1114 GLN ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2102 ASN A2107 GLN ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN B1012 ASN ** B2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2354 ASN B2377 ASN B2416 ASN ** D 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 930 GLN D1230 ASN D2042 HIS ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2306 ASN D2354 ASN D2377 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.182497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119737 restraints weight = 62911.267| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.91 r_work: 0.3499 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32929 Z= 0.151 Angle : 0.810 56.033 44507 Z= 0.401 Chirality : 0.042 0.234 5046 Planarity : 0.005 0.087 5424 Dihedral : 11.361 76.674 4733 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.60 % Favored : 90.84 % Rotamer: Outliers : 7.62 % Allowed : 27.58 % Favored : 64.80 % 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: -0.89 (0.14), residues: 3801 helix: 0.83 (0.10), residues: 2586 sheet: -4.57 (0.33), residues: 168 loop : -3.60 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 622 HIS 0.008 0.001 HIS D1699 PHE 0.030 0.002 PHE A 615 TYR 0.026 0.001 TYR A2293 ARG 0.007 0.001 ARG A2386 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 1968) hydrogen bonds : angle 4.65128 ( 5796) SS BOND : bond 0.02376 ( 4) SS BOND : angle 25.12164 ( 8) covalent geometry : bond 0.00340 (32925) covalent geometry : angle 0.73710 (44499) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 436 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 LEU cc_start: 0.5540 (tp) cc_final: 0.4822 (tp) REVERT: A 679 GLU cc_start: -0.2151 (OUTLIER) cc_final: -0.3612 (mt-10) REVERT: A 703 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6461 (mmt180) REVERT: A 711 MET cc_start: 0.2728 (mmm) cc_final: 0.1415 (mtp) REVERT: A 785 ARG cc_start: 0.8306 (mmm-85) cc_final: 0.8100 (mmm-85) REVERT: A 794 LYS cc_start: 0.5875 (tppt) cc_final: 0.5651 (tppt) REVERT: A 813 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7046 (tp) REVERT: A 1198 LEU cc_start: 0.8604 (tp) cc_final: 0.8285 (tp) REVERT: A 1231 MET cc_start: 0.6917 (mtm) cc_final: 0.6633 (mtm) REVERT: A 1355 GLU cc_start: 0.8849 (pt0) cc_final: 0.8514 (pp20) REVERT: A 1515 TRP cc_start: 0.5606 (t60) cc_final: 0.5133 (t60) REVERT: A 1552 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: A 1553 GLU cc_start: 0.8481 (pm20) cc_final: 0.8262 (mp0) REVERT: A 1943 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7504 (ttt-90) REVERT: A 2034 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.6967 (tp40) REVERT: A 2082 ARG cc_start: 0.8543 (ptt180) cc_final: 0.8310 (ttp80) REVERT: A 2093 PHE cc_start: 0.4459 (m-80) cc_final: 0.2757 (t80) REVERT: A 2137 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8283 (mtm) REVERT: A 2140 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: A 2153 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7498 (mmt180) REVERT: A 2156 GLU cc_start: 0.8354 (tp30) cc_final: 0.8031 (mt-10) REVERT: A 2158 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8282 (tmmt) REVERT: A 2205 ASN cc_start: 0.4055 (t0) cc_final: 0.3430 (t0) REVERT: A 2438 TYR cc_start: 0.5502 (m-80) cc_final: 0.5238 (m-10) REVERT: A 2511 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8627 (mm-30) REVERT: B 679 GLU cc_start: -0.2275 (OUTLIER) cc_final: -0.3718 (mt-10) REVERT: B 711 MET cc_start: 0.2871 (mmm) cc_final: 0.1364 (mtp) REVERT: B 794 LYS cc_start: 0.5953 (tppt) cc_final: 0.5547 (tppt) REVERT: B 795 LEU cc_start: 0.7705 (tt) cc_final: 0.7501 (tp) REVERT: B 798 LEU cc_start: 0.5453 (mt) cc_final: 0.5205 (mt) REVERT: B 803 VAL cc_start: 0.6798 (t) cc_final: 0.6538 (p) REVERT: B 828 PHE cc_start: 0.5406 (OUTLIER) cc_final: 0.4431 (p90) REVERT: B 946 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: B 1020 CYS cc_start: 0.8014 (p) cc_final: 0.7492 (t) REVERT: B 1198 LEU cc_start: 0.8617 (tp) cc_final: 0.8283 (tp) REVERT: B 1209 ARG cc_start: 0.6972 (tpt170) cc_final: 0.6537 (tmt-80) REVERT: B 1303 LEU cc_start: 0.3577 (OUTLIER) cc_final: 0.3136 (mp) REVERT: B 1355 GLU cc_start: 0.8832 (pt0) cc_final: 0.8537 (pp20) REVERT: B 1515 TRP cc_start: 0.5560 (t60) cc_final: 0.5218 (t60) REVERT: B 1552 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: B 1553 GLU cc_start: 0.8573 (pm20) cc_final: 0.8154 (mp0) REVERT: B 1676 LEU cc_start: 0.7941 (mp) cc_final: 0.7511 (mt) REVERT: B 1943 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7570 (ttt-90) REVERT: B 2034 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7557 (tp40) REVERT: B 2082 ARG cc_start: 0.8494 (ptt180) cc_final: 0.8198 (ttp80) REVERT: B 2093 PHE cc_start: 0.4447 (m-80) cc_final: 0.2695 (t80) REVERT: B 2096 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8285 (mtmm) REVERT: B 2137 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8302 (mtm) REVERT: B 2140 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: B 2153 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7521 (mmt180) REVERT: B 2156 GLU cc_start: 0.8368 (tp30) cc_final: 0.8007 (mt-10) REVERT: B 2158 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8475 (ttpp) REVERT: B 2438 TYR cc_start: 0.5491 (m-80) cc_final: 0.5260 (m-10) REVERT: B 2486 LEU cc_start: 0.8291 (tp) cc_final: 0.8059 (tp) REVERT: B 2498 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: D 587 MET cc_start: 0.5543 (mmp) cc_final: 0.5324 (mmt) REVERT: D 621 LEU cc_start: 0.2499 (OUTLIER) cc_final: 0.1818 (tp) REVERT: D 679 GLU cc_start: -0.2153 (OUTLIER) cc_final: -0.3583 (mt-10) REVERT: D 711 MET cc_start: 0.2878 (mmm) cc_final: 0.1323 (mtp) REVERT: D 813 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7074 (tp) REVERT: D 1209 ARG cc_start: 0.7025 (tpt170) cc_final: 0.6596 (tmt-80) REVERT: D 1303 LEU cc_start: 0.3462 (OUTLIER) cc_final: 0.2981 (mp) REVERT: D 1355 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8538 (pp20) REVERT: D 1515 TRP cc_start: 0.5562 (t60) cc_final: 0.5207 (t60) REVERT: D 1552 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8350 (pm20) REVERT: D 1943 ARG cc_start: 0.7952 (ttm110) cc_final: 0.7441 (ttt-90) REVERT: D 2034 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.6914 (tp40) REVERT: D 2093 PHE cc_start: 0.4412 (m-80) cc_final: 0.2801 (t80) REVERT: D 2140 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: D 2153 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7647 (mmt180) REVERT: D 2156 GLU cc_start: 0.8426 (tp30) cc_final: 0.8076 (mt-10) REVERT: D 2158 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8292 (ttpt) REVERT: D 2438 TYR cc_start: 0.5501 (m-80) cc_final: 0.5220 (m-10) REVERT: C 235 GLU cc_start: 0.7772 (tp30) cc_final: 0.7073 (tt0) REVERT: C 243 ILE cc_start: 0.6005 (OUTLIER) cc_final: 0.5791 (mm) REVERT: E 235 GLU cc_start: 0.7948 (tt0) cc_final: 0.7449 (tt0) REVERT: E 238 MET cc_start: 0.7140 (tpt) cc_final: 0.6823 (tpp) outliers start: 261 outliers final: 147 residues processed: 645 average time/residue: 0.4523 time to fit residues: 462.9323 Evaluate side-chains 542 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 365 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1345 LYS Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2236 THR Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2318 GLU Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2364 ASN Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2413 THR Chi-restraints excluded: chain A residue 2459 PHE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 799 TYR Chi-restraints excluded: chain B residue 828 PHE Chi-restraints excluded: chain B residue 848 MET Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1228 SER Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1552 GLN Chi-restraints excluded: chain B residue 1701 VAL Chi-restraints excluded: chain B residue 1783 ILE Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1966 LEU Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2048 ILE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2096 LYS Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2196 LEU Chi-restraints excluded: chain B residue 2236 THR Chi-restraints excluded: chain B residue 2270 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2318 GLU Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2364 ASN Chi-restraints excluded: chain B residue 2375 GLN Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2413 THR Chi-restraints excluded: chain B residue 2498 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 573 LYS Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 679 GLU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 799 TYR Chi-restraints excluded: chain D residue 809 SER Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain D residue 1103 PHE Chi-restraints excluded: chain D residue 1228 SER Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1355 GLU Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1552 GLN Chi-restraints excluded: chain D residue 1555 LEU Chi-restraints excluded: chain D residue 1701 VAL Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1783 ILE Chi-restraints excluded: chain D residue 1798 SER Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1964 MET Chi-restraints excluded: chain D residue 1966 LEU Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2034 GLN Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2048 ILE Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2117 GLU Chi-restraints excluded: chain D residue 2140 GLU Chi-restraints excluded: chain D residue 2152 SER Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2193 PHE Chi-restraints excluded: chain D residue 2196 LEU Chi-restraints excluded: chain D residue 2236 THR Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2318 GLU Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2364 ASN Chi-restraints excluded: chain D residue 2385 VAL Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2413 THR Chi-restraints excluded: chain D residue 2462 ILE Chi-restraints excluded: chain D residue 2504 ILE Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain F residue 235 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 223 optimal weight: 5.9990 chunk 364 optimal weight: 0.0170 chunk 6 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 301 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 336 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 HIS A1018 HIS ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 GLN A2042 HIS ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2354 ASN A2377 ASN B1012 ASN B1018 HIS ** B1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2042 HIS ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2102 ASN ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2416 ASN D 702 HIS D1018 HIS D1567 GLN ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.175923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.115651 restraints weight = 62298.109| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 4.13 r_work: 0.3304 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 32929 Z= 0.246 Angle : 0.858 56.062 44507 Z= 0.425 Chirality : 0.046 0.276 5046 Planarity : 0.005 0.085 5424 Dihedral : 10.664 72.909 4662 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.34 % Favored : 91.11 % Rotamer: Outliers : 8.12 % Allowed : 26.82 % Favored : 65.06 % 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: -0.97 (0.14), residues: 3801 helix: 0.78 (0.10), residues: 2553 sheet: -4.31 (0.35), residues: 168 loop : -3.55 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 622 HIS 0.009 0.002 HIS D2464 PHE 0.033 0.002 PHE A 615 TYR 0.021 0.002 TYR D1961 ARG 0.009 0.001 ARG D 920 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 1968) hydrogen bonds : angle 4.66015 ( 5796) SS BOND : bond 0.02359 ( 4) SS BOND : angle 25.12860 ( 8) covalent geometry : bond 0.00591 (32925) covalent geometry : angle 0.78894 (44499) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 416 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 703 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6455 (mmt180) REVERT: A 794 LYS cc_start: 0.6249 (tppt) cc_final: 0.6005 (tppt) REVERT: A 802 TRP cc_start: 0.5402 (m-90) cc_final: 0.5125 (m-90) REVERT: A 813 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7272 (tp) REVERT: A 1116 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6628 (t80) REVERT: A 1231 MET cc_start: 0.7159 (mtm) cc_final: 0.6821 (mtm) REVERT: A 1355 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8633 (pp20) REVERT: A 1412 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8271 (p) REVERT: A 1515 TRP cc_start: 0.5656 (t60) cc_final: 0.5135 (t60) REVERT: A 1552 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8233 (pm20) REVERT: A 1553 GLU cc_start: 0.8616 (pm20) cc_final: 0.8175 (mp0) REVERT: A 1653 ARG cc_start: 0.6553 (mmt180) cc_final: 0.5799 (mmp80) REVERT: A 1727 LYS cc_start: 0.5202 (tptt) cc_final: 0.4887 (tptt) REVERT: A 1943 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7684 (ttt-90) REVERT: A 2034 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7132 (tp40) REVERT: A 2082 ARG cc_start: 0.8714 (ptt180) cc_final: 0.8451 (ttp80) REVERT: A 2093 PHE cc_start: 0.5834 (m-80) cc_final: 0.4919 (m-10) REVERT: A 2137 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8402 (mtm) REVERT: A 2140 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: A 2153 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7676 (mmt180) REVERT: A 2156 GLU cc_start: 0.8598 (tp30) cc_final: 0.8155 (mt-10) REVERT: A 2158 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8132 (tmmt) REVERT: A 2288 MET cc_start: 0.4415 (ptt) cc_final: 0.3796 (ptt) REVERT: A 2375 GLN cc_start: 0.3189 (OUTLIER) cc_final: 0.2457 (pm20) REVERT: A 2498 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: A 2511 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8609 (mm-30) REVERT: B 711 MET cc_start: 0.3390 (mmm) cc_final: 0.2957 (mtp) REVERT: B 785 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.8291 (mmm-85) REVERT: B 802 TRP cc_start: 0.5571 (m-10) cc_final: 0.5276 (m-90) REVERT: B 946 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: B 1209 ARG cc_start: 0.7125 (tpt170) cc_final: 0.6766 (tmt-80) REVERT: B 1231 MET cc_start: 0.7074 (mtm) cc_final: 0.6872 (mtm) REVERT: B 1328 TYR cc_start: 0.8260 (t80) cc_final: 0.8008 (t80) REVERT: B 1329 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7884 (t0) REVERT: B 1355 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8594 (pp20) REVERT: B 1412 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 1515 TRP cc_start: 0.5621 (t60) cc_final: 0.5262 (t60) REVERT: B 1552 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: B 1553 GLU cc_start: 0.8627 (pm20) cc_final: 0.8176 (mp0) REVERT: B 1653 ARG cc_start: 0.6710 (mmt180) cc_final: 0.5954 (mmp80) REVERT: B 1727 LYS cc_start: 0.5256 (tptt) cc_final: 0.4956 (tptt) REVERT: B 1943 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7788 (ttt-90) REVERT: B 2034 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7691 (tp40) REVERT: B 2082 ARG cc_start: 0.8678 (ptt180) cc_final: 0.8256 (ttp80) REVERT: B 2093 PHE cc_start: 0.5652 (m-80) cc_final: 0.4521 (m-10) REVERT: B 2096 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8630 (mtmm) REVERT: B 2137 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8462 (mtm) REVERT: B 2140 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: B 2153 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7638 (mmt180) REVERT: B 2156 GLU cc_start: 0.8606 (tp30) cc_final: 0.8185 (mt-10) REVERT: B 2158 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8353 (ttpp) REVERT: B 2270 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.6228 (tp) REVERT: B 2288 MET cc_start: 0.4245 (ptt) cc_final: 0.3622 (ptt) REVERT: B 2342 LEU cc_start: 0.3086 (OUTLIER) cc_final: 0.2836 (tt) REVERT: B 2498 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: B 2511 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8669 (mm-30) REVERT: D 621 LEU cc_start: 0.2697 (OUTLIER) cc_final: 0.2108 (tp) REVERT: D 711 MET cc_start: 0.3233 (mmm) cc_final: 0.1482 (mtp) REVERT: D 802 TRP cc_start: 0.5680 (m-90) cc_final: 0.5180 (m-90) REVERT: D 813 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7262 (tp) REVERT: D 828 PHE cc_start: 0.6088 (OUTLIER) cc_final: 0.4948 (p90) REVERT: D 1011 MET cc_start: 0.8417 (mmt) cc_final: 0.8146 (mmt) REVERT: D 1116 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6644 (t80) REVERT: D 1209 ARG cc_start: 0.7074 (tpt170) cc_final: 0.6781 (tmt-80) REVERT: D 1355 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8646 (pp20) REVERT: D 1515 TRP cc_start: 0.5611 (t60) cc_final: 0.5241 (t60) REVERT: D 1552 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: D 1653 ARG cc_start: 0.6395 (mmt180) cc_final: 0.5615 (mmp80) REVERT: D 1738 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8478 (mt-10) REVERT: D 1943 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7595 (ttt-90) REVERT: D 2034 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7067 (tp40) REVERT: D 2093 PHE cc_start: 0.5695 (m-80) cc_final: 0.4072 (m-80) REVERT: D 2140 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: D 2153 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7778 (mmt180) REVERT: D 2156 GLU cc_start: 0.8631 (tp30) cc_final: 0.8184 (mt-10) REVERT: D 2288 MET cc_start: 0.4364 (ptm) cc_final: 0.4080 (ptt) REVERT: D 2375 GLN cc_start: 0.2939 (OUTLIER) cc_final: 0.2256 (pm20) REVERT: D 2498 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: D 2511 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8669 (mm-30) REVERT: C 235 GLU cc_start: 0.7833 (tp30) cc_final: 0.7321 (tt0) outliers start: 278 outliers final: 170 residues processed: 637 average time/residue: 0.4949 time to fit residues: 511.3786 Evaluate side-chains 577 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 368 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1345 LYS Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1707 SER Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1966 LEU Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2236 THR Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2364 ASN Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2413 THR Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2459 PHE Chi-restraints excluded: chain A residue 2498 GLU Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 848 MET Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1097 THR Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1180 THR Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1228 SER Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1329 ASN Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1335 SER Chi-restraints excluded: chain B residue 1345 LYS Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1413 ILE Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1552 GLN Chi-restraints excluded: chain B residue 1701 VAL Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1741 VAL Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1783 ILE Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1966 LEU Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2010 ILE Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2048 ILE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2065 LEU Chi-restraints excluded: chain B residue 2096 LYS Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2196 LEU Chi-restraints excluded: chain B residue 2210 VAL Chi-restraints excluded: chain B residue 2236 THR Chi-restraints excluded: chain B residue 2270 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2342 LEU Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2364 ASN Chi-restraints excluded: chain B residue 2375 GLN Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2413 THR Chi-restraints excluded: chain B residue 2447 ILE Chi-restraints excluded: chain B residue 2498 GLU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 573 LYS Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 828 PHE Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain D residue 1097 THR Chi-restraints excluded: chain D residue 1116 PHE Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1225 VAL Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1332 ASN Chi-restraints excluded: chain D residue 1355 GLU Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1552 GLN Chi-restraints excluded: chain D residue 1701 VAL Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1741 VAL Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1783 ILE Chi-restraints excluded: chain D residue 1798 SER Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1954 TYR Chi-restraints excluded: chain D residue 1964 MET Chi-restraints excluded: chain D residue 1966 LEU Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2034 GLN Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2048 ILE Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2065 LEU Chi-restraints excluded: chain D residue 2116 VAL Chi-restraints excluded: chain D residue 2117 GLU Chi-restraints excluded: chain D residue 2140 GLU Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2183 LEU Chi-restraints excluded: chain D residue 2193 PHE Chi-restraints excluded: chain D residue 2196 LEU Chi-restraints excluded: chain D residue 2236 THR Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2364 ASN Chi-restraints excluded: chain D residue 2375 GLN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2413 THR Chi-restraints excluded: chain D residue 2447 ILE Chi-restraints excluded: chain D residue 2498 GLU Chi-restraints excluded: chain D residue 2504 ILE Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2511 GLU Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain E residue 243 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 172 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 198 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 329 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 HIS A 956 HIS ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2416 ASN ** D 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1012 ASN ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.178732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.114314 restraints weight = 62181.206| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.82 r_work: 0.3409 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.7701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32929 Z= 0.142 Angle : 0.777 56.068 44507 Z= 0.380 Chirality : 0.042 0.383 5046 Planarity : 0.005 0.075 5424 Dihedral : 10.116 65.883 4640 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.81 % Favored : 91.66 % Rotamer: Outliers : 6.54 % Allowed : 28.48 % Favored : 64.97 % 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: -0.45 (0.14), residues: 3801 helix: 1.17 (0.10), residues: 2550 sheet: -3.94 (0.38), residues: 168 loop : -3.37 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 622 HIS 0.007 0.001 HIS B 951 PHE 0.028 0.001 PHE A 615 TYR 0.015 0.001 TYR A1165 ARG 0.011 0.000 ARG B 947 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 1968) hydrogen bonds : angle 4.38032 ( 5796) SS BOND : bond 0.02358 ( 4) SS BOND : angle 25.11575 ( 8) covalent geometry : bond 0.00323 (32925) covalent geometry : angle 0.70035 (44499) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 418 time to evaluate : 3.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 703 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6492 (mmt180) REVERT: A 813 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7216 (tp) REVERT: A 1191 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 1355 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8513 (pp20) REVERT: A 1412 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 1515 TRP cc_start: 0.5656 (t60) cc_final: 0.5279 (t60) REVERT: A 1550 LEU cc_start: 0.6705 (tp) cc_final: 0.6415 (tp) REVERT: A 1552 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: A 1553 GLU cc_start: 0.8556 (pm20) cc_final: 0.8161 (mp0) REVERT: A 1653 ARG cc_start: 0.6792 (mmt180) cc_final: 0.6128 (mmp80) REVERT: A 1738 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8434 (mt-10) REVERT: A 1943 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7680 (ttt-90) REVERT: A 2034 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.6879 (tp40) REVERT: A 2093 PHE cc_start: 0.5716 (m-80) cc_final: 0.4579 (m-10) REVERT: A 2137 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8403 (mtm) REVERT: A 2140 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: A 2153 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7570 (mmt180) REVERT: A 2156 GLU cc_start: 0.8369 (tp30) cc_final: 0.8002 (mt-10) REVERT: A 2288 MET cc_start: 0.4138 (ptt) cc_final: 0.3464 (ptt) REVERT: A 2375 GLN cc_start: 0.2859 (OUTLIER) cc_final: 0.2244 (pm20) REVERT: A 2498 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: A 2511 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8678 (mm-30) REVERT: B 785 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8246 (mmm-85) REVERT: B 795 LEU cc_start: 0.7749 (tt) cc_final: 0.7507 (tp) REVERT: B 802 TRP cc_start: 0.5493 (m-10) cc_final: 0.5232 (m-90) REVERT: B 835 LEU cc_start: 0.5776 (mt) cc_final: 0.5515 (mp) REVERT: B 946 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: B 1112 GLN cc_start: 0.6804 (tp40) cc_final: 0.6260 (tp40) REVERT: B 1209 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6792 (tmt-80) REVERT: B 1231 MET cc_start: 0.6815 (mtm) cc_final: 0.6606 (mtm) REVERT: B 1355 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8560 (pp20) REVERT: B 1412 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8348 (p) REVERT: B 1515 TRP cc_start: 0.5685 (t60) cc_final: 0.5291 (t60) REVERT: B 1552 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: B 1553 GLU cc_start: 0.8598 (pm20) cc_final: 0.8033 (mp0) REVERT: B 1653 ARG cc_start: 0.6917 (mmt180) cc_final: 0.6218 (mmp80) REVERT: B 1943 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7804 (ttt-90) REVERT: B 2034 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7521 (tp40) REVERT: B 2093 PHE cc_start: 0.5532 (m-80) cc_final: 0.4176 (m-10) REVERT: B 2096 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8624 (mtmm) REVERT: B 2137 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8354 (mtm) REVERT: B 2140 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: B 2153 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7609 (mmt180) REVERT: B 2156 GLU cc_start: 0.8404 (tp30) cc_final: 0.8037 (mt-10) REVERT: B 2158 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8345 (ttpp) REVERT: B 2288 MET cc_start: 0.4266 (ptt) cc_final: 0.3680 (ptt) REVERT: B 2498 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: D 621 LEU cc_start: 0.2829 (OUTLIER) cc_final: 0.2328 (tp) REVERT: D 711 MET cc_start: 0.3243 (mmm) cc_final: 0.1479 (mtp) REVERT: D 794 LYS cc_start: 0.5959 (tppt) cc_final: 0.5690 (tppt) REVERT: D 802 TRP cc_start: 0.5555 (m-10) cc_final: 0.5143 (m-90) REVERT: D 813 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7154 (tp) REVERT: D 1011 MET cc_start: 0.8431 (mmt) cc_final: 0.8148 (mmt) REVERT: D 1209 ARG cc_start: 0.7052 (tpt170) cc_final: 0.6790 (tmt-80) REVERT: D 1328 TYR cc_start: 0.7956 (t80) cc_final: 0.7154 (t80) REVERT: D 1355 GLU cc_start: 0.8804 (pt0) cc_final: 0.8499 (pp20) REVERT: D 1515 TRP cc_start: 0.5710 (t60) cc_final: 0.5316 (t60) REVERT: D 1550 LEU cc_start: 0.6674 (tp) cc_final: 0.6451 (tp) REVERT: D 1552 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: D 1653 ARG cc_start: 0.6596 (mmt180) cc_final: 0.5861 (mmp80) REVERT: D 1943 ARG cc_start: 0.8084 (ttm110) cc_final: 0.7815 (mmp-170) REVERT: D 2034 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.6831 (tp40) REVERT: D 2093 PHE cc_start: 0.5565 (m-80) cc_final: 0.4503 (m-10) REVERT: D 2140 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: D 2153 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7847 (mmt-90) REVERT: D 2156 GLU cc_start: 0.8402 (tp30) cc_final: 0.8005 (mt-10) REVERT: D 2288 MET cc_start: 0.4543 (ptm) cc_final: 0.4306 (ptt) REVERT: D 2375 GLN cc_start: 0.2602 (OUTLIER) cc_final: 0.2326 (pm20) REVERT: D 2498 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: C 235 GLU cc_start: 0.7857 (tp30) cc_final: 0.7487 (tt0) REVERT: C 243 ILE cc_start: 0.6118 (OUTLIER) cc_final: 0.5677 (mm) outliers start: 224 outliers final: 150 residues processed: 586 average time/residue: 0.4439 time to fit residues: 424.0949 Evaluate side-chains 559 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 377 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1707 SER Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1741 VAL Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2236 THR Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2364 ASN Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2413 THR Chi-restraints excluded: chain A residue 2459 PHE Chi-restraints excluded: chain A residue 2498 GLU Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 848 MET Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1345 LYS Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1521 LEU Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1552 GLN Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1783 ILE Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2048 ILE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2065 LEU Chi-restraints excluded: chain B residue 2096 LYS Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2196 LEU Chi-restraints excluded: chain B residue 2236 THR Chi-restraints excluded: chain B residue 2270 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2364 ASN Chi-restraints excluded: chain B residue 2375 GLN Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2413 THR Chi-restraints excluded: chain B residue 2498 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 982 CYS Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain D residue 1116 PHE Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1335 SER Chi-restraints excluded: chain D residue 1521 LEU Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1552 GLN Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1783 ILE Chi-restraints excluded: chain D residue 1798 SER Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2008 LEU Chi-restraints excluded: chain D residue 2034 GLN Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2048 ILE Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2065 LEU Chi-restraints excluded: chain D residue 2117 GLU Chi-restraints excluded: chain D residue 2140 GLU Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2183 LEU Chi-restraints excluded: chain D residue 2193 PHE Chi-restraints excluded: chain D residue 2196 LEU Chi-restraints excluded: chain D residue 2236 THR Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2364 ASN Chi-restraints excluded: chain D residue 2375 GLN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2413 THR Chi-restraints excluded: chain D residue 2418 LEU Chi-restraints excluded: chain D residue 2498 GLU Chi-restraints excluded: chain D residue 2504 ILE Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 11 optimal weight: 20.0000 chunk 168 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 276 optimal weight: 0.3980 chunk 117 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 317 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 GLN ** B1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1012 ASN ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.178111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.113176 restraints weight = 62238.995| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.86 r_work: 0.3394 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.7999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32929 Z= 0.150 Angle : 0.780 56.052 44507 Z= 0.377 Chirality : 0.042 0.200 5046 Planarity : 0.005 0.071 5424 Dihedral : 9.912 61.856 4636 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.50 % Favored : 91.98 % Rotamer: Outliers : 6.60 % Allowed : 29.07 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3801 helix: 1.24 (0.10), residues: 2580 sheet: -3.69 (0.40), residues: 168 loop : -3.20 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 802 HIS 0.005 0.001 HIS B2464 PHE 0.029 0.002 PHE D 606 TYR 0.015 0.001 TYR A1307 ARG 0.010 0.001 ARG B 947 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1968) hydrogen bonds : angle 4.28602 ( 5796) SS BOND : bond 0.02352 ( 4) SS BOND : angle 25.12529 ( 8) covalent geometry : bond 0.00346 (32925) covalent geometry : angle 0.70317 (44499) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 404 time to evaluate : 5.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 LYS cc_start: 0.5840 (tppt) cc_final: 0.5563 (tppt) REVERT: A 802 TRP cc_start: 0.5305 (m-90) cc_final: 0.4803 (m-90) REVERT: A 813 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7282 (tp) REVERT: A 1328 TYR cc_start: 0.7880 (t80) cc_final: 0.7142 (t80) REVERT: A 1355 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8518 (pp20) REVERT: A 1412 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8312 (p) REVERT: A 1515 TRP cc_start: 0.5666 (t60) cc_final: 0.5326 (t60) REVERT: A 1550 LEU cc_start: 0.6670 (tp) cc_final: 0.6360 (tp) REVERT: A 1552 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: A 1553 GLU cc_start: 0.8579 (pm20) cc_final: 0.7985 (mp0) REVERT: A 1653 ARG cc_start: 0.6884 (mmt180) cc_final: 0.6310 (mmp80) REVERT: A 1943 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7688 (ttt-90) REVERT: A 2005 LEU cc_start: 0.7978 (mt) cc_final: 0.7646 (tp) REVERT: A 2034 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.6842 (tp40) REVERT: A 2093 PHE cc_start: 0.5747 (m-80) cc_final: 0.4575 (m-10) REVERT: A 2137 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: A 2140 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 2153 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7715 (mmt180) REVERT: A 2156 GLU cc_start: 0.8356 (tp30) cc_final: 0.7971 (mt-10) REVERT: A 2288 MET cc_start: 0.4154 (ptt) cc_final: 0.3508 (ptt) REVERT: A 2375 GLN cc_start: 0.3187 (OUTLIER) cc_final: 0.2791 (pm20) REVERT: A 2498 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: A 2511 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8651 (mm-30) REVERT: B 591 VAL cc_start: 0.4094 (OUTLIER) cc_final: 0.3830 (t) REVERT: B 835 LEU cc_start: 0.5773 (mt) cc_final: 0.5515 (mp) REVERT: B 946 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: B 1050 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6372 (tt) REVERT: B 1112 GLN cc_start: 0.6849 (tp40) cc_final: 0.6357 (tp40) REVERT: B 1209 ARG cc_start: 0.7051 (tpt170) cc_final: 0.6787 (tmt-80) REVERT: B 1328 TYR cc_start: 0.7838 (t80) cc_final: 0.7148 (t80) REVERT: B 1355 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8501 (pp20) REVERT: B 1412 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8332 (p) REVERT: B 1515 TRP cc_start: 0.5734 (t60) cc_final: 0.5331 (t60) REVERT: B 1552 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: B 1553 GLU cc_start: 0.8615 (pm20) cc_final: 0.8037 (mp0) REVERT: B 1653 ARG cc_start: 0.7039 (mmt180) cc_final: 0.6463 (mmp80) REVERT: B 1943 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7831 (ttt-90) REVERT: B 2093 PHE cc_start: 0.5625 (m-80) cc_final: 0.4252 (m-10) REVERT: B 2096 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8643 (mtmm) REVERT: B 2137 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8295 (mtm) REVERT: B 2140 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: B 2153 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7640 (mmt180) REVERT: B 2156 GLU cc_start: 0.8382 (tp30) cc_final: 0.7971 (mt-10) REVERT: B 2158 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8258 (ttpp) REVERT: B 2288 MET cc_start: 0.4331 (ptt) cc_final: 0.3731 (ptt) REVERT: B 2498 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: B 2511 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8628 (mm-30) REVERT: D 591 VAL cc_start: 0.3955 (OUTLIER) cc_final: 0.3753 (t) REVERT: D 621 LEU cc_start: 0.2930 (OUTLIER) cc_final: 0.2506 (tp) REVERT: D 802 TRP cc_start: 0.5544 (m-10) cc_final: 0.5126 (m-90) REVERT: D 813 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7222 (tp) REVERT: D 920 ARG cc_start: 0.6286 (tmt170) cc_final: 0.6002 (ttp80) REVERT: D 946 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: D 1011 MET cc_start: 0.8378 (mmt) cc_final: 0.8078 (mmt) REVERT: D 1050 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6245 (tt) REVERT: D 1191 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8118 (mp) REVERT: D 1209 ARG cc_start: 0.7003 (tpt170) cc_final: 0.6740 (tmt-80) REVERT: D 1328 TYR cc_start: 0.7954 (t80) cc_final: 0.7181 (t80) REVERT: D 1355 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8511 (pp20) REVERT: D 1515 TRP cc_start: 0.5788 (t60) cc_final: 0.5537 (t60) REVERT: D 1541 ASP cc_start: 0.8031 (t70) cc_final: 0.7695 (t70) REVERT: D 1550 LEU cc_start: 0.6650 (tp) cc_final: 0.6411 (tp) REVERT: D 1552 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: D 1554 LEU cc_start: 0.9036 (tp) cc_final: 0.8765 (tt) REVERT: D 1653 ARG cc_start: 0.6699 (mmt180) cc_final: 0.6254 (mmp80) REVERT: D 1669 GLN cc_start: 0.7525 (tp-100) cc_final: 0.7284 (tp-100) REVERT: D 1943 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7671 (ttt-90) REVERT: D 2034 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.6779 (tp40) REVERT: D 2093 PHE cc_start: 0.5682 (m-80) cc_final: 0.4590 (m-10) REVERT: D 2140 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: D 2153 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7840 (mmt-90) REVERT: D 2156 GLU cc_start: 0.8361 (tp30) cc_final: 0.7894 (mt-10) REVERT: D 2288 MET cc_start: 0.4677 (ptm) cc_final: 0.4442 (ptt) REVERT: D 2375 GLN cc_start: 0.2931 (OUTLIER) cc_final: 0.2465 (pm20) REVERT: C 235 GLU cc_start: 0.7860 (tp30) cc_final: 0.7400 (tt0) REVERT: C 243 ILE cc_start: 0.6101 (OUTLIER) cc_final: 0.5665 (mm) outliers start: 226 outliers final: 156 residues processed: 575 average time/residue: 0.4728 time to fit residues: 438.2228 Evaluate side-chains 571 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 379 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1707 SER Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1741 VAL Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2236 THR Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2364 ASN Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2414 ASP Chi-restraints excluded: chain A residue 2418 LEU Chi-restraints excluded: chain A residue 2459 PHE Chi-restraints excluded: chain A residue 2498 GLU Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 848 MET Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1413 ILE Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1521 LEU Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1552 GLN Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1783 ILE Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2048 ILE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2065 LEU Chi-restraints excluded: chain B residue 2096 LYS Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2196 LEU Chi-restraints excluded: chain B residue 2236 THR Chi-restraints excluded: chain B residue 2270 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2364 ASN Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2447 ILE Chi-restraints excluded: chain B residue 2498 GLU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 982 CYS Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain D residue 1097 THR Chi-restraints excluded: chain D residue 1116 PHE Chi-restraints excluded: chain D residue 1191 LEU Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1335 SER Chi-restraints excluded: chain D residue 1355 GLU Chi-restraints excluded: chain D residue 1521 LEU Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1552 GLN Chi-restraints excluded: chain D residue 1676 LEU Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1783 ILE Chi-restraints excluded: chain D residue 1798 SER Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1954 TYR Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2008 LEU Chi-restraints excluded: chain D residue 2034 GLN Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2048 ILE Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2065 LEU Chi-restraints excluded: chain D residue 2117 GLU Chi-restraints excluded: chain D residue 2140 GLU Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2183 LEU Chi-restraints excluded: chain D residue 2184 ILE Chi-restraints excluded: chain D residue 2191 LEU Chi-restraints excluded: chain D residue 2193 PHE Chi-restraints excluded: chain D residue 2196 LEU Chi-restraints excluded: chain D residue 2236 THR Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2364 ASN Chi-restraints excluded: chain D residue 2375 GLN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2418 LEU Chi-restraints excluded: chain D residue 2447 ILE Chi-restraints excluded: chain D residue 2467 MET Chi-restraints excluded: chain D residue 2504 ILE Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 250 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 HIS A1012 ASN A1567 GLN ** A1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2100 HIS ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.175737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.117301 restraints weight = 61958.950| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.87 r_work: 0.3332 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.8339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 32929 Z= 0.218 Angle : 0.816 56.055 44507 Z= 0.401 Chirality : 0.044 0.301 5046 Planarity : 0.005 0.072 5424 Dihedral : 10.006 59.995 4629 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.87 % Favored : 91.63 % Rotamer: Outliers : 7.01 % Allowed : 29.36 % Favored : 63.63 % 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: -0.46 (0.14), residues: 3801 helix: 1.02 (0.10), residues: 2595 sheet: -3.69 (0.39), residues: 168 loop : -3.20 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 622 HIS 0.008 0.002 HIS A1305 PHE 0.035 0.002 PHE D 606 TYR 0.020 0.002 TYR A1189 ARG 0.009 0.001 ARG B 947 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 1968) hydrogen bonds : angle 4.45777 ( 5796) SS BOND : bond 0.02394 ( 4) SS BOND : angle 25.10228 ( 8) covalent geometry : bond 0.00517 (32925) covalent geometry : angle 0.74326 (44499) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 393 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 TRP cc_start: -0.1835 (OUTLIER) cc_final: -0.2659 (t-100) REVERT: A 794 LYS cc_start: 0.6203 (tppt) cc_final: 0.5918 (tppt) REVERT: A 802 TRP cc_start: 0.5805 (m-90) cc_final: 0.5188 (m-90) REVERT: A 813 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7692 (tp) REVERT: A 1050 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6534 (tt) REVERT: A 1116 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6948 (t80) REVERT: A 1191 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8561 (mp) REVERT: A 1328 TYR cc_start: 0.8149 (t80) cc_final: 0.7408 (t80) REVERT: A 1355 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8693 (pp20) REVERT: A 1412 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8707 (p) REVERT: A 1515 TRP cc_start: 0.5764 (t60) cc_final: 0.5438 (t60) REVERT: A 1550 LEU cc_start: 0.6675 (tp) cc_final: 0.6364 (tp) REVERT: A 1552 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: A 1553 GLU cc_start: 0.8544 (pm20) cc_final: 0.8108 (pm20) REVERT: A 1653 ARG cc_start: 0.6996 (mmt180) cc_final: 0.6302 (mmp80) REVERT: A 1943 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7866 (ttt-90) REVERT: A 2034 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7227 (tp40) REVERT: A 2137 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8537 (mtm) REVERT: A 2140 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: A 2153 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7969 (mmt180) REVERT: A 2156 GLU cc_start: 0.8619 (tp30) cc_final: 0.8323 (mt-10) REVERT: A 2158 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8666 (ttmm) REVERT: A 2288 MET cc_start: 0.4121 (ptt) cc_final: 0.3286 (ptt) REVERT: A 2375 GLN cc_start: 0.3288 (OUTLIER) cc_final: 0.2793 (pm20) REVERT: A 2498 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: A 2511 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8535 (mm-30) REVERT: B 580 TRP cc_start: -0.1622 (OUTLIER) cc_final: -0.2576 (t-100) REVERT: B 802 TRP cc_start: 0.5994 (m-90) cc_final: 0.5382 (m-90) REVERT: B 835 LEU cc_start: 0.6173 (mt) cc_final: 0.5890 (mp) REVERT: B 946 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: B 1050 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6620 (tt) REVERT: B 1328 TYR cc_start: 0.8039 (t80) cc_final: 0.7439 (t80) REVERT: B 1355 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8671 (pp20) REVERT: B 1412 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8619 (p) REVERT: B 1515 TRP cc_start: 0.5864 (t60) cc_final: 0.5449 (t60) REVERT: B 1552 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: B 1653 ARG cc_start: 0.7159 (mmt180) cc_final: 0.6497 (mmp80) REVERT: B 1669 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7753 (tp-100) REVERT: B 1943 ARG cc_start: 0.8312 (ttm110) cc_final: 0.8017 (mmp-170) REVERT: B 2005 LEU cc_start: 0.8314 (mt) cc_final: 0.7992 (tp) REVERT: B 2034 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7843 (tp40) REVERT: B 2096 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8766 (mtmm) REVERT: B 2137 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8493 (mtm) REVERT: B 2140 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: B 2153 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7956 (mmt180) REVERT: B 2156 GLU cc_start: 0.8660 (tp30) cc_final: 0.8352 (mt-10) REVERT: B 2158 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8490 (ttpp) REVERT: B 2288 MET cc_start: 0.4331 (ptt) cc_final: 0.3732 (ptt) REVERT: B 2498 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: B 2511 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8504 (mm-30) REVERT: D 580 TRP cc_start: -0.1852 (OUTLIER) cc_final: -0.2599 (t-100) REVERT: D 605 MET cc_start: 0.4836 (mmm) cc_final: 0.4468 (mpp) REVERT: D 794 LYS cc_start: 0.6338 (tppt) cc_final: 0.6081 (tppt) REVERT: D 813 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7562 (tp) REVERT: D 1050 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6570 (tt) REVERT: D 1116 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6895 (t80) REVERT: D 1191 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 1209 ARG cc_start: 0.7089 (tpt170) cc_final: 0.6839 (tmt-80) REVERT: D 1328 TYR cc_start: 0.8195 (t80) cc_final: 0.7429 (t80) REVERT: D 1355 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8670 (pp20) REVERT: D 1515 TRP cc_start: 0.5908 (t60) cc_final: 0.5635 (t60) REVERT: D 1541 ASP cc_start: 0.8059 (t70) cc_final: 0.7640 (t70) REVERT: D 1550 LEU cc_start: 0.6824 (tp) cc_final: 0.6574 (tp) REVERT: D 1552 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: D 1653 ARG cc_start: 0.6930 (mmt180) cc_final: 0.6466 (mmp80) REVERT: D 1669 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7551 (tp-100) REVERT: D 1943 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7809 (ttt-90) REVERT: D 2005 LEU cc_start: 0.8351 (mt) cc_final: 0.8008 (tp) REVERT: D 2034 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7159 (tp40) REVERT: D 2140 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: D 2153 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7619 (mmt180) REVERT: D 2156 GLU cc_start: 0.8634 (tp30) cc_final: 0.8277 (mt-10) REVERT: D 2288 MET cc_start: 0.4655 (ptm) cc_final: 0.4426 (ptt) REVERT: D 2375 GLN cc_start: 0.3062 (OUTLIER) cc_final: 0.2491 (pm20) REVERT: D 2511 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: C 235 GLU cc_start: 0.8173 (tp30) cc_final: 0.7788 (tt0) outliers start: 240 outliers final: 163 residues processed: 576 average time/residue: 0.4259 time to fit residues: 400.8331 Evaluate side-chains 575 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 372 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1707 SER Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1791 MET Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2013 SER Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2236 THR Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2418 LEU Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2459 PHE Chi-restraints excluded: chain A residue 2498 GLU Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1165 TYR Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1228 SER Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1413 ILE Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1521 LEU Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1552 GLN Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1783 ILE Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2010 ILE Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2048 ILE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2065 LEU Chi-restraints excluded: chain B residue 2096 LYS Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2196 LEU Chi-restraints excluded: chain B residue 2236 THR Chi-restraints excluded: chain B residue 2270 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2375 GLN Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2447 ILE Chi-restraints excluded: chain B residue 2498 GLU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 982 CYS Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain D residue 1097 THR Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1116 PHE Chi-restraints excluded: chain D residue 1180 THR Chi-restraints excluded: chain D residue 1191 LEU Chi-restraints excluded: chain D residue 1203 LEU Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1335 SER Chi-restraints excluded: chain D residue 1355 GLU Chi-restraints excluded: chain D residue 1413 ILE Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1552 GLN Chi-restraints excluded: chain D residue 1676 LEU Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1783 ILE Chi-restraints excluded: chain D residue 1798 SER Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1954 TYR Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2008 LEU Chi-restraints excluded: chain D residue 2034 GLN Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2048 ILE Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2065 LEU Chi-restraints excluded: chain D residue 2117 GLU Chi-restraints excluded: chain D residue 2140 GLU Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2183 LEU Chi-restraints excluded: chain D residue 2184 ILE Chi-restraints excluded: chain D residue 2193 PHE Chi-restraints excluded: chain D residue 2196 LEU Chi-restraints excluded: chain D residue 2236 THR Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2375 GLN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2418 LEU Chi-restraints excluded: chain D residue 2447 ILE Chi-restraints excluded: chain D residue 2504 ILE Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2511 GLU Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 342 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 318 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2100 HIS A2205 ASN ** A2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2107 GLN ** D2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.178510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.119220 restraints weight = 61731.591| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.57 r_work: 0.3389 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.8518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32929 Z= 0.141 Angle : 0.784 56.067 44507 Z= 0.379 Chirality : 0.042 0.262 5046 Planarity : 0.005 0.065 5424 Dihedral : 9.555 59.861 4615 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.29 % Favored : 92.24 % Rotamer: Outliers : 6.02 % Allowed : 30.47 % Favored : 63.51 % 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: -0.13 (0.14), residues: 3801 helix: 1.25 (0.10), residues: 2595 sheet: -3.48 (0.39), residues: 168 loop : -3.01 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 802 HIS 0.004 0.001 HIS B2464 PHE 0.030 0.001 PHE B 615 TYR 0.016 0.001 TYR A 946 ARG 0.008 0.000 ARG B1368 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 1968) hydrogen bonds : angle 4.29491 ( 5796) SS BOND : bond 0.02371 ( 4) SS BOND : angle 25.10143 ( 8) covalent geometry : bond 0.00319 (32925) covalent geometry : angle 0.70810 (44499) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 385 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 TRP cc_start: -0.1885 (OUTLIER) cc_final: -0.2690 (t-100) REVERT: A 587 MET cc_start: 0.4177 (ttp) cc_final: 0.3937 (ttp) REVERT: A 605 MET cc_start: 0.3458 (mmm) cc_final: 0.2705 (mpp) REVERT: A 802 TRP cc_start: 0.5722 (m-90) cc_final: 0.5046 (m-90) REVERT: A 813 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7612 (tp) REVERT: A 1050 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6492 (tt) REVERT: A 1116 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6621 (t80) REVERT: A 1191 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 1328 TYR cc_start: 0.8101 (t80) cc_final: 0.7413 (t80) REVERT: A 1355 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8662 (pp20) REVERT: A 1412 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8688 (p) REVERT: A 1515 TRP cc_start: 0.5822 (t60) cc_final: 0.5436 (t60) REVERT: A 1550 LEU cc_start: 0.6632 (tp) cc_final: 0.6304 (tp) REVERT: A 1552 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: A 1553 GLU cc_start: 0.8556 (pm20) cc_final: 0.8144 (pm20) REVERT: A 1653 ARG cc_start: 0.7066 (mmt180) cc_final: 0.6647 (mmp80) REVERT: A 1669 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7835 (tp-100) REVERT: A 1943 ARG cc_start: 0.8209 (ttm110) cc_final: 0.7810 (ttt-90) REVERT: A 2005 LEU cc_start: 0.8208 (mt) cc_final: 0.7925 (tp) REVERT: A 2034 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.6993 (tp40) REVERT: A 2065 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 2137 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8588 (mtm) REVERT: A 2140 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: A 2153 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7899 (mmt180) REVERT: A 2156 GLU cc_start: 0.8460 (tp30) cc_final: 0.8161 (mt-10) REVERT: A 2205 ASN cc_start: 0.4687 (t0) cc_final: 0.3294 (p0) REVERT: A 2288 MET cc_start: 0.4104 (ptt) cc_final: 0.3216 (ptt) REVERT: A 2375 GLN cc_start: 0.2896 (OUTLIER) cc_final: 0.2680 (pm20) REVERT: A 2498 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: A 2511 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8487 (mm-30) REVERT: B 580 TRP cc_start: -0.1658 (OUTLIER) cc_final: -0.2595 (t-100) REVERT: B 605 MET cc_start: 0.3912 (mmm) cc_final: 0.3391 (mpp) REVERT: B 802 TRP cc_start: 0.5963 (m-90) cc_final: 0.5431 (m-90) REVERT: B 835 LEU cc_start: 0.6099 (mt) cc_final: 0.5815 (mp) REVERT: B 946 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: B 1011 MET cc_start: 0.8583 (mmt) cc_final: 0.7960 (mmt) REVERT: B 1050 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6563 (tt) REVERT: B 1116 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7836 (t80) REVERT: B 1328 TYR cc_start: 0.7986 (t80) cc_final: 0.7427 (t80) REVERT: B 1355 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8626 (pp20) REVERT: B 1412 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8675 (p) REVERT: B 1515 TRP cc_start: 0.5901 (t60) cc_final: 0.5501 (t60) REVERT: B 1541 ASP cc_start: 0.7956 (t70) cc_final: 0.7577 (t70) REVERT: B 1552 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: B 1653 ARG cc_start: 0.7135 (mmt180) cc_final: 0.6544 (mmp80) REVERT: B 1943 ARG cc_start: 0.8243 (ttm110) cc_final: 0.7932 (ttt-90) REVERT: B 2005 LEU cc_start: 0.8235 (mt) cc_final: 0.7859 (tp) REVERT: B 2093 PHE cc_start: 0.6044 (m-80) cc_final: 0.4730 (m-10) REVERT: B 2096 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8784 (mtmm) REVERT: B 2137 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8540 (mtm) REVERT: B 2140 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: B 2153 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7809 (mmt180) REVERT: B 2156 GLU cc_start: 0.8465 (tp30) cc_final: 0.8136 (mt-10) REVERT: B 2158 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8396 (ttpp) REVERT: B 2205 ASN cc_start: 0.5223 (t0) cc_final: 0.3740 (p0) REVERT: B 2288 MET cc_start: 0.4405 (ptt) cc_final: 0.3840 (ptt) REVERT: B 2511 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8454 (mm-30) REVERT: D 580 TRP cc_start: -0.1878 (OUTLIER) cc_final: -0.2627 (t-100) REVERT: D 794 LYS cc_start: 0.6263 (tppt) cc_final: 0.6001 (tppt) REVERT: D 802 TRP cc_start: 0.5908 (m-90) cc_final: 0.5203 (m-90) REVERT: D 813 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7562 (tp) REVERT: D 1050 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6487 (tt) REVERT: D 1116 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6535 (t80) REVERT: D 1191 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8501 (mp) REVERT: D 1209 ARG cc_start: 0.7106 (tpt170) cc_final: 0.6873 (tmt-80) REVERT: D 1328 TYR cc_start: 0.8142 (t80) cc_final: 0.7419 (t80) REVERT: D 1355 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8627 (pp20) REVERT: D 1515 TRP cc_start: 0.5885 (t60) cc_final: 0.5628 (t60) REVERT: D 1541 ASP cc_start: 0.7983 (t70) cc_final: 0.7435 (t70) REVERT: D 1550 LEU cc_start: 0.6735 (tp) cc_final: 0.6435 (tp) REVERT: D 1552 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: D 1554 LEU cc_start: 0.9115 (tp) cc_final: 0.8888 (tt) REVERT: D 1652 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.5481 (mmm160) REVERT: D 1943 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7785 (ttt-90) REVERT: D 2005 LEU cc_start: 0.8270 (mt) cc_final: 0.7849 (tp) REVERT: D 2034 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.6960 (tp40) REVERT: D 2140 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: D 2153 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8124 (mmt-90) REVERT: D 2156 GLU cc_start: 0.8475 (tp30) cc_final: 0.8118 (mt-10) REVERT: D 2158 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8455 (ttpp) REVERT: D 2375 GLN cc_start: 0.2651 (OUTLIER) cc_final: 0.2334 (pm20) REVERT: D 2511 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8463 (mm-30) REVERT: C 235 GLU cc_start: 0.8074 (tp30) cc_final: 0.7732 (tt0) outliers start: 206 outliers final: 140 residues processed: 542 average time/residue: 0.4469 time to fit residues: 392.6355 Evaluate side-chains 553 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 372 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1707 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2236 THR Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2459 PHE Chi-restraints excluded: chain A residue 2498 GLU Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1165 TYR Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1228 SER Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1335 SER Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1413 ILE Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1521 LEU Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1552 GLN Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1783 ILE Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1966 LEU Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2048 ILE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2065 LEU Chi-restraints excluded: chain B residue 2096 LYS Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2196 LEU Chi-restraints excluded: chain B residue 2236 THR Chi-restraints excluded: chain B residue 2270 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 982 CYS Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain D residue 1097 THR Chi-restraints excluded: chain D residue 1116 PHE Chi-restraints excluded: chain D residue 1191 LEU Chi-restraints excluded: chain D residue 1203 LEU Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1335 SER Chi-restraints excluded: chain D residue 1355 GLU Chi-restraints excluded: chain D residue 1413 ILE Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1552 GLN Chi-restraints excluded: chain D residue 1652 ARG Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1798 SER Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1966 LEU Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2008 LEU Chi-restraints excluded: chain D residue 2034 GLN Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2048 ILE Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2065 LEU Chi-restraints excluded: chain D residue 2117 GLU Chi-restraints excluded: chain D residue 2140 GLU Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2183 LEU Chi-restraints excluded: chain D residue 2184 ILE Chi-restraints excluded: chain D residue 2193 PHE Chi-restraints excluded: chain D residue 2196 LEU Chi-restraints excluded: chain D residue 2236 THR Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2375 GLN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2504 ILE Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2511 GLU Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain F residue 235 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 91 optimal weight: 0.5980 chunk 270 optimal weight: 6.9990 chunk 325 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 286 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1012 ASN A1111 GLN ** A1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1698 ASN ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1305 HIS ** D2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.179135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120535 restraints weight = 61800.640| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.87 r_work: 0.3400 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.8679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32929 Z= 0.136 Angle : 0.777 56.071 44507 Z= 0.375 Chirality : 0.041 0.261 5046 Planarity : 0.005 0.062 5424 Dihedral : 9.312 59.607 4613 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.87 % Favored : 92.66 % Rotamer: Outliers : 5.58 % Allowed : 30.82 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3801 helix: 1.29 (0.10), residues: 2613 sheet: -3.42 (0.40), residues: 168 loop : -2.91 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B2404 HIS 0.005 0.001 HIS D1699 PHE 0.030 0.001 PHE D 615 TYR 0.016 0.001 TYR A1307 ARG 0.007 0.000 ARG B1368 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 1968) hydrogen bonds : angle 4.24142 ( 5796) SS BOND : bond 0.02370 ( 4) SS BOND : angle 25.10679 ( 8) covalent geometry : bond 0.00307 (32925) covalent geometry : angle 0.70066 (44499) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 393 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 TRP cc_start: -0.1884 (OUTLIER) cc_final: -0.2684 (t-100) REVERT: A 802 TRP cc_start: 0.5668 (m-90) cc_final: 0.5005 (m-90) REVERT: A 813 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7535 (tp) REVERT: A 1050 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6461 (tt) REVERT: A 1191 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 1328 TYR cc_start: 0.8101 (t80) cc_final: 0.7421 (t80) REVERT: A 1355 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8653 (pp20) REVERT: A 1412 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8662 (p) REVERT: A 1515 TRP cc_start: 0.5845 (t60) cc_final: 0.5457 (t60) REVERT: A 1550 LEU cc_start: 0.6638 (tp) cc_final: 0.6298 (tp) REVERT: A 1552 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: A 1553 GLU cc_start: 0.8528 (pm20) cc_final: 0.8051 (pm20) REVERT: A 1653 ARG cc_start: 0.7037 (mmt180) cc_final: 0.6624 (mmp80) REVERT: A 1669 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7848 (tp-100) REVERT: A 1943 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7756 (ttt-90) REVERT: A 2005 LEU cc_start: 0.8173 (mt) cc_final: 0.7860 (tp) REVERT: A 2034 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.6909 (tp40) REVERT: A 2065 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8046 (mp) REVERT: A 2093 PHE cc_start: 0.6131 (m-80) cc_final: 0.4771 (m-10) REVERT: A 2137 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8547 (mtm) REVERT: A 2140 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: A 2153 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7863 (mmt180) REVERT: A 2156 GLU cc_start: 0.8427 (tp30) cc_final: 0.8091 (mt-10) REVERT: A 2205 ASN cc_start: 0.4797 (t0) cc_final: 0.3316 (p0) REVERT: A 2288 MET cc_start: 0.4097 (ptt) cc_final: 0.3390 (ptt) REVERT: A 2375 GLN cc_start: 0.3105 (OUTLIER) cc_final: 0.2881 (pm20) REVERT: A 2404 TRP cc_start: 0.4785 (OUTLIER) cc_final: 0.4536 (m-10) REVERT: A 2498 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: A 2511 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8514 (mm-30) REVERT: B 580 TRP cc_start: -0.1670 (OUTLIER) cc_final: -0.2595 (t-100) REVERT: B 802 TRP cc_start: 0.5805 (m-90) cc_final: 0.5301 (m-90) REVERT: B 835 LEU cc_start: 0.6029 (mt) cc_final: 0.5742 (mp) REVERT: B 946 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: B 1002 MET cc_start: 0.7465 (tpp) cc_final: 0.7060 (mmp) REVERT: B 1011 MET cc_start: 0.8578 (mmt) cc_final: 0.7984 (mmt) REVERT: B 1050 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6535 (tt) REVERT: B 1116 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7650 (t80) REVERT: B 1328 TYR cc_start: 0.7979 (t80) cc_final: 0.7427 (t80) REVERT: B 1355 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8614 (pp20) REVERT: B 1412 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 1515 TRP cc_start: 0.5886 (t60) cc_final: 0.5510 (t60) REVERT: B 1552 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: B 1553 GLU cc_start: 0.8150 (mp0) cc_final: 0.7947 (mp0) REVERT: B 1653 ARG cc_start: 0.7147 (mmt180) cc_final: 0.6558 (mmp80) REVERT: B 1943 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7942 (ttt-90) REVERT: B 2005 LEU cc_start: 0.8235 (mt) cc_final: 0.7856 (tp) REVERT: B 2093 PHE cc_start: 0.6036 (m-80) cc_final: 0.4688 (m-10) REVERT: B 2096 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8802 (mtmm) REVERT: B 2137 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8488 (mtm) REVERT: B 2140 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 2153 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7756 (mmt180) REVERT: B 2156 GLU cc_start: 0.8468 (tp30) cc_final: 0.8124 (mt-10) REVERT: B 2158 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8361 (ttpp) REVERT: B 2205 ASN cc_start: 0.5386 (t0) cc_final: 0.3788 (p0) REVERT: B 2288 MET cc_start: 0.4410 (ptt) cc_final: 0.3790 (ptt) REVERT: B 2404 TRP cc_start: 0.4667 (OUTLIER) cc_final: 0.4373 (m-10) REVERT: B 2511 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8492 (mm-30) REVERT: D 580 TRP cc_start: -0.1935 (OUTLIER) cc_final: -0.2656 (t-100) REVERT: D 711 MET cc_start: 0.2230 (ptp) cc_final: 0.1131 (mpp) REVERT: D 794 LYS cc_start: 0.6248 (tppt) cc_final: 0.5984 (tppt) REVERT: D 802 TRP cc_start: 0.5836 (m-90) cc_final: 0.5157 (m-90) REVERT: D 813 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7566 (tp) REVERT: D 1050 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6471 (tt) REVERT: D 1191 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8485 (mp) REVERT: D 1209 ARG cc_start: 0.7047 (tpt170) cc_final: 0.6813 (tmt-80) REVERT: D 1328 TYR cc_start: 0.8125 (t80) cc_final: 0.7408 (t80) REVERT: D 1355 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8616 (pp20) REVERT: D 1515 TRP cc_start: 0.5890 (t60) cc_final: 0.5631 (t60) REVERT: D 1541 ASP cc_start: 0.7972 (t70) cc_final: 0.7428 (t70) REVERT: D 1550 LEU cc_start: 0.6781 (tp) cc_final: 0.6478 (tp) REVERT: D 1552 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: D 1554 LEU cc_start: 0.9146 (tp) cc_final: 0.8915 (tt) REVERT: D 1652 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.5422 (mmm160) REVERT: D 1943 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7750 (ttt-90) REVERT: D 2005 LEU cc_start: 0.8282 (mt) cc_final: 0.7842 (tp) REVERT: D 2034 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.6872 (tp40) REVERT: D 2140 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: D 2153 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7968 (mmt180) REVERT: D 2156 GLU cc_start: 0.8444 (tp30) cc_final: 0.8074 (mt-10) REVERT: D 2158 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8418 (ttpp) REVERT: D 2375 GLN cc_start: 0.3055 (OUTLIER) cc_final: 0.2665 (pm20) REVERT: D 2511 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8495 (mm-30) REVERT: C 235 GLU cc_start: 0.8099 (tp30) cc_final: 0.7726 (tt0) outliers start: 191 outliers final: 135 residues processed: 537 average time/residue: 0.4364 time to fit residues: 380.6238 Evaluate side-chains 551 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 375 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2236 THR Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2418 LEU Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2459 PHE Chi-restraints excluded: chain A residue 2498 GLU Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1165 TYR Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1228 SER Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1335 SER Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1413 ILE Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1552 GLN Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2048 ILE Chi-restraints excluded: chain B residue 2065 LEU Chi-restraints excluded: chain B residue 2096 LYS Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2196 LEU Chi-restraints excluded: chain B residue 2236 THR Chi-restraints excluded: chain B residue 2270 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 982 CYS Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain D residue 1097 THR Chi-restraints excluded: chain D residue 1191 LEU Chi-restraints excluded: chain D residue 1203 LEU Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1335 SER Chi-restraints excluded: chain D residue 1355 GLU Chi-restraints excluded: chain D residue 1413 ILE Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1552 GLN Chi-restraints excluded: chain D residue 1652 ARG Chi-restraints excluded: chain D residue 1676 LEU Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1798 SER Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1966 LEU Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2008 LEU Chi-restraints excluded: chain D residue 2034 GLN Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2048 ILE Chi-restraints excluded: chain D residue 2065 LEU Chi-restraints excluded: chain D residue 2117 GLU Chi-restraints excluded: chain D residue 2140 GLU Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2183 LEU Chi-restraints excluded: chain D residue 2184 ILE Chi-restraints excluded: chain D residue 2193 PHE Chi-restraints excluded: chain D residue 2196 LEU Chi-restraints excluded: chain D residue 2236 THR Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2375 GLN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2504 ILE Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2511 GLU Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain F residue 235 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 153 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 335 optimal weight: 0.9990 chunk 264 optimal weight: 20.0000 chunk 254 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 208 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 371 optimal weight: 9.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1567 GLN ** D2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.177971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.119675 restraints weight = 61380.271| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 4.09 r_work: 0.3369 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.8825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32929 Z= 0.158 Angle : 0.793 56.071 44507 Z= 0.382 Chirality : 0.042 0.265 5046 Planarity : 0.005 0.061 5424 Dihedral : 9.126 59.652 4601 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.97 % Favored : 92.55 % Rotamer: Outliers : 5.61 % Allowed : 30.73 % Favored : 63.66 % 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: 0.01 (0.14), residues: 3801 helix: 1.27 (0.10), residues: 2613 sheet: -3.28 (0.40), residues: 165 loop : -2.82 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B2404 HIS 0.005 0.001 HIS D1699 PHE 0.029 0.002 PHE B 615 TYR 0.017 0.001 TYR B1307 ARG 0.007 0.000 ARG D1352 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1968) hydrogen bonds : angle 4.23180 ( 5796) SS BOND : bond 0.02343 ( 4) SS BOND : angle 25.09123 ( 8) covalent geometry : bond 0.00365 (32925) covalent geometry : angle 0.71849 (44499) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 371 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 TRP cc_start: -0.1827 (OUTLIER) cc_final: -0.2676 (t-100) REVERT: A 813 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7616 (tp) REVERT: A 1050 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6460 (tt) REVERT: A 1116 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6576 (t80) REVERT: A 1191 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8528 (mp) REVERT: A 1328 TYR cc_start: 0.8127 (t80) cc_final: 0.7460 (t80) REVERT: A 1355 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8660 (pp20) REVERT: A 1412 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8663 (p) REVERT: A 1515 TRP cc_start: 0.5807 (t60) cc_final: 0.5424 (t60) REVERT: A 1550 LEU cc_start: 0.6685 (tp) cc_final: 0.6338 (tp) REVERT: A 1552 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: A 1553 GLU cc_start: 0.8541 (pm20) cc_final: 0.7996 (pm20) REVERT: A 1653 ARG cc_start: 0.7058 (mmt180) cc_final: 0.6439 (mmp80) REVERT: A 1669 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7830 (tp-100) REVERT: A 1943 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7756 (ttt-90) REVERT: A 2005 LEU cc_start: 0.8241 (mt) cc_final: 0.7921 (tp) REVERT: A 2034 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7001 (tp40) REVERT: A 2065 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 2137 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: A 2140 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: A 2153 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7939 (mmt180) REVERT: A 2156 GLU cc_start: 0.8452 (tp30) cc_final: 0.8120 (mt-10) REVERT: A 2205 ASN cc_start: 0.4936 (t0) cc_final: 0.3400 (p0) REVERT: A 2288 MET cc_start: 0.4007 (ptt) cc_final: 0.3313 (ptt) REVERT: A 2498 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: A 2511 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8547 (mm-30) REVERT: B 580 TRP cc_start: -0.1575 (OUTLIER) cc_final: -0.2512 (t-100) REVERT: B 587 MET cc_start: 0.4211 (ttt) cc_final: 0.3977 (ttt) REVERT: B 802 TRP cc_start: 0.5770 (m-90) cc_final: 0.5042 (m-90) REVERT: B 835 LEU cc_start: 0.6053 (mt) cc_final: 0.5769 (mp) REVERT: B 946 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: B 1002 MET cc_start: 0.7540 (tpp) cc_final: 0.7117 (mmp) REVERT: B 1050 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6568 (tt) REVERT: B 1328 TYR cc_start: 0.7988 (t80) cc_final: 0.7442 (t80) REVERT: B 1355 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8617 (pp20) REVERT: B 1412 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 1515 TRP cc_start: 0.5909 (t60) cc_final: 0.5520 (t60) REVERT: B 1552 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: B 1553 GLU cc_start: 0.8192 (mp0) cc_final: 0.7965 (mp0) REVERT: B 1653 ARG cc_start: 0.7145 (mmt180) cc_final: 0.6520 (mmp80) REVERT: B 1943 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7950 (ttt-90) REVERT: B 2005 LEU cc_start: 0.8313 (mt) cc_final: 0.7934 (tp) REVERT: B 2034 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7771 (tp40) REVERT: B 2093 PHE cc_start: 0.6061 (m-80) cc_final: 0.4745 (m-10) REVERT: B 2096 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8800 (mtmm) REVERT: B 2137 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8474 (mtm) REVERT: B 2140 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: B 2153 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7843 (mmt180) REVERT: B 2156 GLU cc_start: 0.8508 (tp30) cc_final: 0.8158 (mt-10) REVERT: B 2158 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8356 (ttpp) REVERT: B 2288 MET cc_start: 0.4411 (ptt) cc_final: 0.3793 (ptt) REVERT: B 2511 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8518 (mm-30) REVERT: D 580 TRP cc_start: -0.1933 (OUTLIER) cc_final: -0.2657 (t-100) REVERT: D 794 LYS cc_start: 0.6300 (tppt) cc_final: 0.6051 (tppt) REVERT: D 802 TRP cc_start: 0.5821 (m-90) cc_final: 0.5121 (m-90) REVERT: D 813 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7665 (tp) REVERT: D 1050 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6487 (tt) REVERT: D 1191 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8527 (mp) REVERT: D 1328 TYR cc_start: 0.8165 (t80) cc_final: 0.7449 (t80) REVERT: D 1355 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8619 (pp20) REVERT: D 1515 TRP cc_start: 0.5880 (t60) cc_final: 0.5604 (t60) REVERT: D 1541 ASP cc_start: 0.7988 (t70) cc_final: 0.7451 (t70) REVERT: D 1550 LEU cc_start: 0.6832 (tp) cc_final: 0.6526 (tp) REVERT: D 1552 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8261 (pm20) REVERT: D 1652 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.5357 (mmm160) REVERT: D 1943 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7710 (ttt-90) REVERT: D 2034 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.6927 (tp40) REVERT: D 2140 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: D 2153 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7892 (mmt180) REVERT: D 2156 GLU cc_start: 0.8473 (tp30) cc_final: 0.8100 (mt-10) REVERT: D 2158 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8423 (ttpp) REVERT: D 2375 GLN cc_start: 0.2992 (OUTLIER) cc_final: 0.2629 (pm20) REVERT: D 2511 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8511 (mm-30) REVERT: D 2516 TRP cc_start: 0.9377 (OUTLIER) cc_final: 0.8414 (t60) REVERT: C 235 GLU cc_start: 0.8144 (tp30) cc_final: 0.7758 (tt0) outliers start: 192 outliers final: 138 residues processed: 514 average time/residue: 0.4666 time to fit residues: 392.2318 Evaluate side-chains 545 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 367 time to evaluate : 3.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 TRP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1335 SER Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2236 THR Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2319 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2418 LEU Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2459 PHE Chi-restraints excluded: chain A residue 2498 GLU Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1165 TYR Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1228 SER Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1301 VAL Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1335 SER Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1413 ILE Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1552 GLN Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2048 ILE Chi-restraints excluded: chain B residue 2065 LEU Chi-restraints excluded: chain B residue 2096 LYS Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2196 LEU Chi-restraints excluded: chain B residue 2236 THR Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2319 TYR Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2447 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 580 TRP Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 982 CYS Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1096 SER Chi-restraints excluded: chain D residue 1097 THR Chi-restraints excluded: chain D residue 1191 LEU Chi-restraints excluded: chain D residue 1203 LEU Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1335 SER Chi-restraints excluded: chain D residue 1355 GLU Chi-restraints excluded: chain D residue 1413 ILE Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1552 GLN Chi-restraints excluded: chain D residue 1652 ARG Chi-restraints excluded: chain D residue 1676 LEU Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1798 SER Chi-restraints excluded: chain D residue 1802 CYS Chi-restraints excluded: chain D residue 1966 LEU Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2008 LEU Chi-restraints excluded: chain D residue 2034 GLN Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2048 ILE Chi-restraints excluded: chain D residue 2065 LEU Chi-restraints excluded: chain D residue 2117 GLU Chi-restraints excluded: chain D residue 2140 GLU Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2183 LEU Chi-restraints excluded: chain D residue 2184 ILE Chi-restraints excluded: chain D residue 2193 PHE Chi-restraints excluded: chain D residue 2196 LEU Chi-restraints excluded: chain D residue 2236 THR Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2319 TYR Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2375 GLN Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2504 ILE Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2511 GLU Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain F residue 235 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 99 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 375 optimal weight: 7.9990 chunk 331 optimal weight: 0.9980 chunk 212 optimal weight: 0.5980 chunk 361 optimal weight: 9.9990 chunk 293 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1305 HIS ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 GLN D1012 ASN ** D2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.179309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124104 restraints weight = 61686.453| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.97 r_work: 0.3413 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.8968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32929 Z= 0.134 Angle : 0.784 56.051 44507 Z= 0.376 Chirality : 0.042 0.280 5046 Planarity : 0.005 0.058 5424 Dihedral : 8.877 59.309 4597 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.84 % Favored : 92.69 % Rotamer: Outliers : 5.14 % Allowed : 31.03 % Favored : 63.83 % 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: 0.20 (0.14), residues: 3801 helix: 1.38 (0.10), residues: 2613 sheet: -3.14 (0.34), residues: 213 loop : -2.60 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B2278 HIS 0.004 0.001 HIS B1414 PHE 0.029 0.001 PHE B 615 TYR 0.017 0.001 TYR B1307 ARG 0.009 0.000 ARG D 920 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 1968) hydrogen bonds : angle 4.15109 ( 5796) SS BOND : bond 0.02352 ( 4) SS BOND : angle 25.10631 ( 8) covalent geometry : bond 0.00303 (32925) covalent geometry : angle 0.70769 (44499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33062.48 seconds wall clock time: 574 minutes 15.35 seconds (34455.35 seconds total)