Starting phenix.real_space_refine on Tue Aug 26 04:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vmx_65195/08_2025/9vmx_65195_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vmx_65195/08_2025/9vmx_65195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vmx_65195/08_2025/9vmx_65195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vmx_65195/08_2025/9vmx_65195.map" model { file = "/net/cci-nas-00/data/ceres_data/9vmx_65195/08_2025/9vmx_65195_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vmx_65195/08_2025/9vmx_65195_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.010 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 10.65, per 1000 atoms: 0.33 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: 2.44 Conformation dependent library (CDL) restraints added in 917.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.91 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: 5.61 Time building geometry restraints manager: 3.06 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: 0.04 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: 44.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.250 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.550 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5060 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG A1547 TYR 0.018 0.002 TYR B1165 PHE 0.031 0.002 PHE B 615 TRP 0.022 0.002 TRP A1168 HIS 0.007 0.001 HIS B 951 Details of bonding type rmsd covalent geometry : bond 0.00784 (32925) covalent geometry : angle 1.35698 (44499) SS BOND : bond 0.38680 ( 4) SS BOND : angle 35.73121 ( 8) hydrogen bonds : bond 0.16954 ( 1968) hydrogen bonds : angle 7.60778 ( 5796) *********************** 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 2095 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1446 poor density : 649 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 VAL cc_start: 0.0004 (OUTLIER) cc_final: -0.0819 (t) REVERT: A 695 ILE cc_start: 0.1065 (OUTLIER) cc_final: -0.0617 (tt) REVERT: A 768 GLU cc_start: 0.3833 (OUTLIER) cc_final: 0.3452 (pt0) REVERT: A 917 PHE cc_start: 0.1884 (OUTLIER) cc_final: 0.1157 (m-80) REVERT: A 920 ARG cc_start: 0.3521 (OUTLIER) cc_final: 0.1035 (mmm160) REVERT: A 984 LYS cc_start: 0.1992 (OUTLIER) cc_final: 0.0946 (ttmt) REVERT: A 1048 PHE cc_start: 0.2805 (OUTLIER) cc_final: 0.2502 (t80) REVERT: A 1103 PHE cc_start: 0.4971 (OUTLIER) cc_final: 0.4346 (t80) REVERT: A 1205 GLN cc_start: 0.1925 (OUTLIER) cc_final: 0.1184 (pt0) REVERT: A 1286 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.6133 (tp) REVERT: A 1546 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.2233 (mp0) REVERT: A 1565 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4538 (mt) REVERT: A 1681 GLN cc_start: 0.4524 (OUTLIER) cc_final: 0.3716 (mm-40) REVERT: A 1787 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6497 (tp) REVERT: A 1793 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6313 (mt) REVERT: A 1801 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6504 (mt) REVERT: A 2023 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7802 (tp) REVERT: A 2153 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.4953 (mtp-110) REVERT: A 2154 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: A 2375 GLN cc_start: 0.3382 (OUTLIER) cc_final: 0.3079 (mp10) REVERT: B 581 ILE cc_start: 0.1510 (OUTLIER) cc_final: 0.1270 (pt) REVERT: B 695 ILE cc_start: 0.1056 (OUTLIER) cc_final: -0.0559 (tt) REVERT: B 768 GLU cc_start: 0.3891 (OUTLIER) cc_final: 0.3320 (pt0) REVERT: B 917 PHE cc_start: 0.1824 (OUTLIER) cc_final: 0.1065 (m-80) REVERT: B 920 ARG cc_start: 0.3582 (OUTLIER) cc_final: 0.1354 (mmm160) REVERT: B 975 LEU cc_start: 0.4069 (OUTLIER) cc_final: 0.2235 (tt) REVERT: B 1103 PHE cc_start: 0.4975 (OUTLIER) cc_final: 0.4365 (t80) REVERT: B 1116 PHE cc_start: 0.5006 (OUTLIER) cc_final: 0.4712 (t80) REVERT: B 1205 GLN cc_start: 0.1881 (OUTLIER) cc_final: 0.1199 (pt0) REVERT: B 1286 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.6126 (tp) REVERT: B 1546 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.2297 (mp0) REVERT: B 1565 LEU cc_start: 0.4980 (OUTLIER) cc_final: 0.4379 (mt) REVERT: B 1681 GLN cc_start: 0.4465 (OUTLIER) cc_final: 0.3605 (mm-40) REVERT: B 1787 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6463 (tp) REVERT: B 1793 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6290 (mt) REVERT: B 1801 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6538 (mt) REVERT: B 1975 ILE cc_start: 0.6081 (mm) cc_final: 0.5875 (mm) REVERT: B 2023 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7786 (tp) REVERT: B 2065 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7024 (tp) REVERT: B 2140 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: B 2153 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.4860 (mtp-110) REVERT: B 2154 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6785 (tp30) REVERT: B 2456 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6843 (tpp-160) REVERT: D 581 ILE cc_start: 0.1611 (OUTLIER) cc_final: 0.1321 (pt) REVERT: D 695 ILE cc_start: 0.1295 (OUTLIER) cc_final: -0.0419 (tt) REVERT: D 768 GLU cc_start: 0.3742 (OUTLIER) cc_final: 0.3408 (pt0) REVERT: D 917 PHE cc_start: 0.1837 (OUTLIER) cc_final: 0.1097 (m-80) REVERT: D 920 ARG cc_start: 0.3614 (OUTLIER) cc_final: 0.1073 (mmm160) REVERT: D 1048 PHE cc_start: 0.2780 (OUTLIER) cc_final: 0.2335 (t80) REVERT: D 1205 GLN cc_start: 0.1889 (OUTLIER) cc_final: 0.1670 (pt0) REVERT: D 1286 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.6177 (tp) REVERT: D 1546 GLU cc_start: 0.5776 (OUTLIER) cc_final: 0.2208 (mp0) REVERT: D 1565 LEU cc_start: 0.4970 (OUTLIER) cc_final: 0.4450 (mt) REVERT: D 1681 GLN cc_start: 0.4493 (OUTLIER) cc_final: 0.3635 (mm-40) REVERT: D 1787 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6484 (tp) REVERT: D 1793 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6373 (mt) REVERT: D 1801 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6610 (mt) REVERT: D 1975 ILE cc_start: 0.6085 (mm) cc_final: 0.5885 (mm) REVERT: D 2023 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7843 (tp) REVERT: D 2140 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: D 2152 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7902 (m) REVERT: D 2153 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.4541 (ptm-80) REVERT: D 2154 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: D 2456 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6769 (tpp-160) outliers start: 1446 outliers final: 253 residues processed: 1782 average time/residue: 0.2040 time to fit residues: 563.7113 Evaluate side-chains 684 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 315 poor density : 369 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 687 PRO Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 917 PHE Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1030 HIS 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 1116 PHE Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1544 ARG Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1556 GLN Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1647 GLU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1667 GLU Chi-restraints excluded: chain A residue 1669 GLN Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1699 HIS Chi-restraints excluded: chain A residue 1707 SER Chi-restraints excluded: chain A residue 1783 ILE Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1803 TYR Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1999 GLN Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2077 SER Chi-restraints excluded: chain A residue 2080 GLN Chi-restraints excluded: chain A residue 2083 CYS Chi-restraints excluded: chain A residue 2094 LEU Chi-restraints excluded: chain A residue 2135 SER Chi-restraints excluded: chain A residue 2140 GLU Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2250 GLN Chi-restraints excluded: chain A residue 2265 ILE Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2340 SER Chi-restraints excluded: chain A residue 2354 ASN Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2374 LEU Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2405 VAL Chi-restraints excluded: chain A residue 2406 ILE Chi-restraints excluded: chain A residue 2414 ASP Chi-restraints excluded: chain A residue 2420 MET Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2465 SER Chi-restraints excluded: chain A residue 2470 GLU Chi-restraints excluded: chain A residue 2480 LEU Chi-restraints excluded: chain A residue 2487 VAL Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2509 SER Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2512 THR Chi-restraints excluded: chain A residue 2513 MET Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 687 PRO Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 848 MET Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 917 PHE Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1198 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1208 THR Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1286 ILE Chi-restraints excluded: chain B residue 1304 SER Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1544 ARG Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1549 LEU Chi-restraints excluded: chain B residue 1556 GLN Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1647 GLU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1665 PHE Chi-restraints excluded: chain B residue 1667 GLU Chi-restraints excluded: chain B residue 1681 GLN Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1697 LEU Chi-restraints excluded: chain B residue 1699 HIS Chi-restraints excluded: chain B residue 1707 SER Chi-restraints excluded: chain B residue 1783 ILE Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1793 LEU Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1803 TYR Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 1999 GLN Chi-restraints excluded: chain B residue 2006 VAL Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2065 LEU Chi-restraints excluded: chain B residue 2077 SER Chi-restraints excluded: chain B residue 2080 GLN Chi-restraints excluded: chain B residue 2083 CYS Chi-restraints excluded: chain B residue 2094 LEU Chi-restraints excluded: chain B residue 2134 SER Chi-restraints excluded: chain B residue 2135 SER Chi-restraints excluded: chain B residue 2140 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2154 GLU Chi-restraints excluded: chain B residue 2211 THR Chi-restraints excluded: chain B residue 2250 GLN Chi-restraints excluded: chain B residue 2265 ILE Chi-restraints excluded: chain B residue 2270 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2340 SER Chi-restraints excluded: chain B residue 2354 ASN Chi-restraints excluded: chain B residue 2355 LEU Chi-restraints excluded: chain B residue 2372 LYS Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2405 VAL Chi-restraints excluded: chain B residue 2406 ILE Chi-restraints excluded: chain B residue 2414 ASP Chi-restraints excluded: chain B residue 2420 MET Chi-restraints excluded: chain B residue 2456 ARG Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2465 SER Chi-restraints excluded: chain B residue 2470 GLU Chi-restraints excluded: chain B residue 2477 ILE Chi-restraints excluded: chain B residue 2480 LEU Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2509 SER Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2512 THR Chi-restraints excluded: chain B residue 2513 MET Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 623 ARG Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 687 PRO Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 768 GLU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 917 PHE Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 999 CYS Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1015 VAL Chi-restraints excluded: chain D residue 1030 HIS Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1116 PHE Chi-restraints excluded: chain D residue 1155 LEU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1198 LEU Chi-restraints excluded: chain D residue 1205 GLN Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1214 LEU Chi-restraints excluded: chain D residue 1227 ILE Chi-restraints excluded: chain D residue 1286 ILE Chi-restraints excluded: chain D residue 1304 SER Chi-restraints excluded: chain D residue 1336 ILE Chi-restraints excluded: chain D residue 1544 ARG Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1556 GLN Chi-restraints excluded: chain D residue 1562 ARG Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1647 GLU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1656 ILE Chi-restraints excluded: chain D residue 1665 PHE Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1681 GLN Chi-restraints excluded: chain D residue 1690 LEU Chi-restraints excluded: chain D residue 1697 LEU Chi-restraints excluded: chain D residue 1699 HIS Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1783 ILE Chi-restraints excluded: chain D residue 1787 LEU Chi-restraints excluded: chain D residue 1793 LEU Chi-restraints excluded: chain D residue 1801 LEU Chi-restraints excluded: chain D residue 1803 TYR Chi-restraints excluded: chain D residue 1960 VAL Chi-restraints excluded: chain D residue 1974 ILE Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 1999 GLN Chi-restraints excluded: chain D residue 2006 VAL Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2077 SER Chi-restraints excluded: chain D residue 2080 GLN Chi-restraints excluded: chain D residue 2083 CYS Chi-restraints excluded: chain D residue 2094 LEU Chi-restraints excluded: chain D residue 2134 SER Chi-restraints excluded: chain D residue 2135 SER 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 2154 GLU Chi-restraints excluded: chain D residue 2250 GLN Chi-restraints excluded: chain D residue 2265 ILE Chi-restraints excluded: chain D residue 2270 ILE Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2340 SER Chi-restraints excluded: chain D residue 2354 ASN Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2372 LYS Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2405 VAL Chi-restraints excluded: chain D residue 2406 ILE Chi-restraints excluded: chain D residue 2414 ASP Chi-restraints excluded: chain D residue 2420 MET Chi-restraints excluded: chain D residue 2456 ARG Chi-restraints excluded: chain D residue 2462 ILE Chi-restraints excluded: chain D residue 2465 SER Chi-restraints excluded: chain D residue 2477 ILE Chi-restraints excluded: chain D residue 2480 LEU Chi-restraints excluded: chain D residue 2487 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2509 SER Chi-restraints excluded: chain D residue 2511 GLU Chi-restraints excluded: chain D residue 2512 THR Chi-restraints excluded: chain D residue 2513 MET Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 247 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 934 GLN A1009 GLN A1012 ASN A1052 GLN A1222 ASN A1409 HIS ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2011 GLN A2042 HIS A2080 GLN A2206 GLN A2250 GLN ** A2269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 934 GLN B1009 GLN B1012 ASN B1052 GLN B1114 GLN B1222 ASN B1409 HIS ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1699 HIS B2042 HIS B2080 GLN B2206 GLN B2250 GLN ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2375 GLN ** D 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 934 GLN D1009 GLN D1012 ASN D1052 GLN D1222 ASN D1409 HIS D1414 HIS ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1699 HIS D2042 HIS D2080 GLN D2206 GLN D2250 GLN ** D2331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.233572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.206643 restraints weight = 49892.712| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 1.97 r_work: 0.4051 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 32929 Z= 0.205 Angle : 0.927 55.403 44507 Z= 0.456 Chirality : 0.047 0.355 5046 Planarity : 0.006 0.102 5424 Dihedral : 14.731 97.162 5170 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.37 % Favored : 90.98 % Rotamer: Outliers : 10.75 % Allowed : 24.69 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.13), residues: 3801 helix: 0.26 (0.10), residues: 2550 sheet: -4.90 (0.31), residues: 135 loop : -4.02 (0.15), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 703 TYR 0.024 0.002 TYR B2293 PHE 0.026 0.002 PHE B 615 TRP 0.016 0.002 TRP B 622 HIS 0.011 0.002 HIS A2464 Details of bonding type rmsd covalent geometry : bond 0.00469 (32925) covalent geometry : angle 0.86518 (44499) SS BOND : bond 0.03542 ( 4) SS BOND : angle 24.92398 ( 8) hydrogen bonds : bond 0.04872 ( 1968) hydrogen bonds : angle 5.24545 ( 5796) *********************** 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 743 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 368 poor density : 375 time to evaluate : 1.091 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: A 920 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.2166 (mmm160) REVERT: A 1048 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6375 (t80) REVERT: A 1205 GLN cc_start: 0.3378 (OUTLIER) cc_final: 0.2351 (pm20) REVERT: A 1227 ILE cc_start: 0.8160 (tt) cc_final: 0.7934 (tt) REVERT: A 1546 GLU cc_start: 0.4063 (OUTLIER) cc_final: 0.0526 (mp0) REVERT: A 1681 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7090 (mm-40) REVERT: A 2080 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7886 (tp-100) REVERT: A 2153 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7473 (mmt180) REVERT: A 2189 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7555 (t80) REVERT: A 2375 GLN cc_start: 0.5001 (OUTLIER) cc_final: 0.4514 (mp10) REVERT: A 2387 ILE cc_start: 0.3170 (OUTLIER) cc_final: 0.2898 (tt) REVERT: A 2406 ILE cc_start: 0.4682 (OUTLIER) cc_final: 0.4442 (mt) REVERT: B 920 ARG cc_start: 0.4867 (OUTLIER) cc_final: 0.2253 (mmm160) REVERT: B 1205 GLN cc_start: 0.3154 (OUTLIER) cc_final: 0.2240 (pm20) REVERT: B 1227 ILE cc_start: 0.8140 (tt) cc_final: 0.7695 (pt) REVERT: B 1366 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6874 (mt0) REVERT: B 1546 GLU cc_start: 0.4078 (OUTLIER) cc_final: 0.0486 (mp0) REVERT: B 1681 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7176 (mm-40) REVERT: B 2023 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9073 (mt) REVERT: B 2045 MET cc_start: 0.6984 (mtp) cc_final: 0.6710 (mtp) REVERT: B 2064 GLN cc_start: 0.8351 (mt0) cc_final: 0.8128 (mm-40) REVERT: B 2153 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7471 (mmt180) REVERT: B 2175 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8126 (mtp) REVERT: B 2189 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7453 (t80) REVERT: B 2387 ILE cc_start: 0.3211 (OUTLIER) cc_final: 0.2686 (tt) REVERT: B 2480 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8394 (tp) REVERT: D 920 ARG cc_start: 0.4926 (OUTLIER) cc_final: 0.2125 (mmm160) REVERT: D 1048 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.5797 (t80) REVERT: D 1205 GLN cc_start: 0.3120 (OUTLIER) cc_final: 0.2156 (pm20) REVERT: D 1227 ILE cc_start: 0.8165 (tt) cc_final: 0.7945 (tt) REVERT: D 1546 GLU cc_start: 0.4182 (OUTLIER) cc_final: 0.0458 (mp0) REVERT: D 2023 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9118 (mt) REVERT: D 2064 GLN cc_start: 0.8405 (mt0) cc_final: 0.8120 (mm-40) REVERT: D 2080 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7897 (tp-100) REVERT: D 2153 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7326 (mmt180) REVERT: D 2480 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8748 (tp) REVERT: C 235 GLU cc_start: 0.8477 (tp30) cc_final: 0.7756 (tt0) REVERT: C 238 MET cc_start: 0.7963 (tpt) cc_final: 0.7566 (tpt) REVERT: F 235 GLU cc_start: 0.8185 (tp30) cc_final: 0.7626 (tt0) outliers start: 368 outliers final: 173 residues processed: 715 average time/residue: 0.1884 time to fit residues: 216.8619 Evaluate side-chains 503 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 300 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1556 GLN Chi-restraints excluded: chain A residue 1559 GLU Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1667 GLU Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1714 VAL Chi-restraints excluded: chain A residue 1721 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1803 TYR Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 1999 GLN Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2080 GLN Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2232 ILE Chi-restraints excluded: chain A residue 2250 GLN Chi-restraints excluded: chain A residue 2266 VAL Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2356 PHE Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2386 ARG 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 2405 VAL Chi-restraints excluded: chain A residue 2406 ILE Chi-restraints excluded: chain A residue 2407 GLU Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2480 LEU Chi-restraints excluded: chain A residue 2487 VAL Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1052 GLN Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1337 ASP Chi-restraints excluded: chain B residue 1366 GLN Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1556 GLN Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1665 PHE Chi-restraints excluded: chain B residue 1681 GLN Chi-restraints excluded: chain B residue 1721 SER Chi-restraints excluded: chain B residue 1803 TYR Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 1999 GLN Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2134 SER Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2175 MET Chi-restraints excluded: chain B residue 2189 PHE Chi-restraints excluded: chain B residue 2197 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2232 ILE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2355 LEU Chi-restraints excluded: chain B residue 2356 PHE Chi-restraints excluded: chain B residue 2360 ILE Chi-restraints excluded: chain B residue 2386 ARG 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 2405 VAL Chi-restraints excluded: chain B residue 2406 ILE Chi-restraints excluded: chain B residue 2412 ARG Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2480 LEU Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 679 GLU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 782 VAL Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 1030 HIS Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1052 GLN Chi-restraints excluded: chain D residue 1054 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1116 PHE Chi-restraints excluded: chain D residue 1155 LEU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1184 ILE Chi-restraints excluded: chain D residue 1205 GLN Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1336 ILE Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1556 GLN Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1665 PHE Chi-restraints excluded: chain D residue 1681 GLN Chi-restraints excluded: chain D residue 1803 TYR Chi-restraints excluded: chain D residue 1960 VAL Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 1999 GLN Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2080 GLN Chi-restraints excluded: chain D residue 2134 SER Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2197 VAL Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2356 PHE Chi-restraints excluded: chain D residue 2386 ARG Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2405 VAL Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2462 ILE Chi-restraints excluded: chain D residue 2480 LEU Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2516 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 360 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1052 GLN A1309 HIS ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1699 HIS ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2324 HIS A2331 ASN A2375 GLN B 932 HIS B1309 HIS ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2331 ASN D 932 HIS D1309 HIS D1353 GLN ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2250 GLN D2324 HIS ** D2331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 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 = 0.4545 r_free = 0.4545 target = 0.227032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.199503 restraints weight = 48223.033| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 1.94 r_work: 0.3942 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32929 Z= 0.159 Angle : 0.802 56.078 44507 Z= 0.393 Chirality : 0.043 0.339 5046 Planarity : 0.005 0.100 5424 Dihedral : 11.507 82.671 4763 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.37 % Favored : 91.11 % Rotamer: Outliers : 8.44 % Allowed : 25.36 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.14), residues: 3801 helix: 1.04 (0.10), residues: 2571 sheet: -4.92 (0.26), residues: 192 loop : -3.64 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1036 TYR 0.021 0.001 TYR D2293 PHE 0.032 0.002 PHE D1000 TRP 0.022 0.001 TRP D1168 HIS 0.007 0.001 HIS D2464 Details of bonding type rmsd covalent geometry : bond 0.00368 (32925) covalent geometry : angle 0.72796 (44499) SS BOND : bond 0.02233 ( 4) SS BOND : angle 25.15174 ( 8) hydrogen bonds : bond 0.04314 ( 1968) hydrogen bonds : angle 4.63027 ( 5796) *********************** 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 617 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 289 poor density : 328 time to evaluate : 0.791 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: A 768 GLU cc_start: 0.2771 (OUTLIER) cc_final: 0.2294 (pt0) REVERT: A 831 MET cc_start: 0.6828 (ppp) cc_final: 0.6493 (ppp) REVERT: A 920 ARG cc_start: 0.5000 (OUTLIER) cc_final: 0.2198 (mmm160) REVERT: A 1048 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7007 (t80) REVERT: A 1052 GLN cc_start: 0.5726 (OUTLIER) cc_final: 0.4667 (tt0) REVERT: A 1205 GLN cc_start: 0.3972 (OUTLIER) cc_final: 0.3084 (pm20) REVERT: A 1227 ILE cc_start: 0.8561 (tt) cc_final: 0.8113 (pt) REVERT: A 1342 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 1546 GLU cc_start: 0.4109 (OUTLIER) cc_final: 0.2379 (pm20) REVERT: A 1681 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: A 1788 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8404 (t) REVERT: A 2080 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8144 (tp40) REVERT: A 2153 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7643 (mmt180) REVERT: A 2225 MET cc_start: 0.4408 (tpp) cc_final: 0.3906 (tpt) REVERT: A 2375 GLN cc_start: 0.4559 (OUTLIER) cc_final: 0.4314 (mp10) REVERT: B 706 MET cc_start: -0.0413 (mmt) cc_final: -0.1087 (mmm) REVERT: B 768 GLU cc_start: 0.2510 (OUTLIER) cc_final: 0.1964 (pt0) REVERT: B 920 ARG cc_start: 0.4948 (OUTLIER) cc_final: 0.2292 (mmm160) REVERT: B 1157 MET cc_start: 0.7374 (tpp) cc_final: 0.7016 (mmp) REVERT: B 1205 GLN cc_start: 0.4033 (OUTLIER) cc_final: 0.3038 (pm20) REVERT: B 1227 ILE cc_start: 0.8594 (tt) cc_final: 0.8150 (pt) REVERT: B 1546 GLU cc_start: 0.4034 (OUTLIER) cc_final: 0.2376 (pm20) REVERT: B 2080 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8214 (tp40) REVERT: B 2153 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7488 (mmt180) REVERT: B 2226 SER cc_start: 0.2907 (OUTLIER) cc_final: 0.2470 (m) REVERT: B 2480 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8795 (tp) REVERT: D 700 TYR cc_start: 0.0058 (OUTLIER) cc_final: -0.1307 (m-80) REVERT: D 768 GLU cc_start: 0.2454 (OUTLIER) cc_final: 0.2056 (pt0) REVERT: D 920 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.2211 (mmm160) REVERT: D 1157 MET cc_start: 0.7502 (tpp) cc_final: 0.7193 (mmp) REVERT: D 1205 GLN cc_start: 0.3771 (OUTLIER) cc_final: 0.2914 (pm20) REVERT: D 1227 ILE cc_start: 0.8625 (tt) cc_final: 0.8180 (pt) REVERT: D 1546 GLU cc_start: 0.4308 (OUTLIER) cc_final: 0.2552 (pm20) REVERT: D 2004 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6715 (p90) REVERT: D 2064 GLN cc_start: 0.8592 (mt0) cc_final: 0.8385 (mt0) REVERT: D 2080 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8149 (tp40) REVERT: D 2153 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7661 (mmt180) REVERT: D 2288 MET cc_start: 0.2429 (ptm) cc_final: 0.1987 (ttt) outliers start: 289 outliers final: 154 residues processed: 589 average time/residue: 0.1835 time to fit residues: 177.0743 Evaluate side-chains 463 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 281 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1052 GLN Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1556 GLN Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1667 GLU Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1683 VAL Chi-restraints excluded: chain A residue 1788 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2080 GLN Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2386 ARG Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2420 MET Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1223 VAL Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1308 LEU Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1329 ASN Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1536 HIS Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1556 GLN Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1665 PHE Chi-restraints excluded: chain B residue 1681 GLN Chi-restraints excluded: chain B residue 1683 VAL Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2080 GLN Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2197 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2340 SER Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2355 LEU Chi-restraints excluded: chain B residue 2356 PHE Chi-restraints excluded: chain B residue 2386 ARG 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 2412 ARG Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2480 LEU Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 679 GLU Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 768 GLU Chi-restraints excluded: chain D residue 782 VAL Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 919 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 1030 HIS Chi-restraints excluded: chain D residue 1054 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1116 PHE Chi-restraints excluded: chain D residue 1155 LEU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1184 ILE Chi-restraints excluded: chain D residue 1205 GLN Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1308 LEU Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1408 ASP Chi-restraints excluded: chain D residue 1514 LEU Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1556 GLN Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1665 PHE Chi-restraints excluded: chain D residue 1681 GLN Chi-restraints excluded: chain D residue 1683 VAL Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1960 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 2080 GLN Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2197 VAL Chi-restraints excluded: chain D residue 2278 TRP Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2340 SER Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2356 PHE Chi-restraints excluded: chain D residue 2386 ARG Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2420 MET Chi-restraints excluded: chain D residue 2462 ILE Chi-restraints excluded: chain D residue 2487 VAL Chi-restraints excluded: chain D residue 2516 TRP Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 243 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 13 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 195 optimal weight: 1.9990 chunk 231 optimal weight: 30.0000 chunk 182 optimal weight: 0.6980 chunk 332 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 HIS A1040 ASN A1114 GLN ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2102 ASN A2107 GLN ** A2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2102 ASN B2107 GLN D1114 GLN ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2102 ASN ** D2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2331 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.221999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.193889 restraints weight = 47167.519| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.92 r_work: 0.3865 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.7967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 32929 Z= 0.164 Angle : 0.780 56.060 44507 Z= 0.381 Chirality : 0.042 0.366 5046 Planarity : 0.005 0.102 5424 Dihedral : 10.682 85.440 4706 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.29 % Favored : 92.24 % Rotamer: Outliers : 7.62 % Allowed : 25.80 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.14), residues: 3801 helix: 1.28 (0.10), residues: 2571 sheet: -4.61 (0.29), residues: 189 loop : -3.30 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1010 TYR 0.027 0.001 TYR A1051 PHE 0.032 0.002 PHE D1175 TRP 0.028 0.002 TRP A1168 HIS 0.011 0.001 HIS B1535 Details of bonding type rmsd covalent geometry : bond 0.00382 (32925) covalent geometry : angle 0.70408 (44499) SS BOND : bond 0.02409 ( 4) SS BOND : angle 25.09563 ( 8) hydrogen bonds : bond 0.04166 ( 1968) hydrogen bonds : angle 4.38399 ( 5796) *********************** 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 585 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 324 time to evaluate : 1.202 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: A 700 TYR cc_start: 0.0349 (OUTLIER) cc_final: -0.1143 (m-80) REVERT: A 706 MET cc_start: -0.1597 (mmm) cc_final: -0.1922 (mmm) REVERT: A 768 GLU cc_start: 0.2898 (OUTLIER) cc_final: 0.2520 (pt0) REVERT: A 920 ARG cc_start: 0.5054 (OUTLIER) cc_final: 0.2113 (mmm160) REVERT: A 1048 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7090 (t80) REVERT: A 1157 MET cc_start: 0.7537 (mmm) cc_final: 0.6968 (mmp) REVERT: A 1205 GLN cc_start: 0.4915 (OUTLIER) cc_final: 0.3833 (pt0) REVERT: A 1532 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7268 (t80) REVERT: A 1546 GLU cc_start: 0.4065 (OUTLIER) cc_final: 0.2319 (pm20) REVERT: A 1680 TYR cc_start: 0.7970 (t80) cc_final: 0.7706 (t80) REVERT: A 1722 ILE cc_start: 0.6345 (mm) cc_final: 0.6053 (mm) REVERT: A 2080 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7936 (tp40) REVERT: A 2153 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8002 (mmt-90) REVERT: A 2325 MET cc_start: 0.4365 (OUTLIER) cc_final: 0.3677 (tpt) REVERT: A 2375 GLN cc_start: 0.4651 (OUTLIER) cc_final: 0.4309 (mp10) REVERT: A 2511 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: B 700 TYR cc_start: 0.0354 (OUTLIER) cc_final: -0.1088 (m-80) REVERT: B 706 MET cc_start: 0.0072 (mmt) cc_final: -0.2406 (ttm) REVERT: B 768 GLU cc_start: 0.2751 (OUTLIER) cc_final: 0.2276 (pt0) REVERT: B 920 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.2261 (mmm160) REVERT: B 1047 LEU cc_start: 0.7365 (tt) cc_final: 0.6725 (mt) REVERT: B 1052 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.5955 (tt0) REVERT: B 1157 MET cc_start: 0.7603 (tpp) cc_final: 0.7239 (mmp) REVERT: B 1205 GLN cc_start: 0.4893 (OUTLIER) cc_final: 0.3701 (pt0) REVERT: B 1344 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 1368 ARG cc_start: 0.7395 (ttm170) cc_final: 0.7141 (ttm-80) REVERT: B 1680 TYR cc_start: 0.8049 (t80) cc_final: 0.7715 (t80) REVERT: B 2004 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6944 (p90) REVERT: B 2080 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8108 (tp-100) REVERT: B 2153 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7783 (mmt180) REVERT: B 2226 SER cc_start: 0.3206 (OUTLIER) cc_final: 0.2441 (m) REVERT: B 2288 MET cc_start: 0.2253 (ptm) cc_final: 0.1922 (ttt) REVERT: B 2325 MET cc_start: 0.4098 (OUTLIER) cc_final: 0.3493 (tpt) REVERT: B 2480 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8777 (tp) REVERT: D 700 TYR cc_start: 0.0202 (OUTLIER) cc_final: -0.1221 (m-80) REVERT: D 706 MET cc_start: -0.1733 (mmm) cc_final: -0.2194 (mmm) REVERT: D 768 GLU cc_start: 0.2605 (OUTLIER) cc_final: 0.2325 (pt0) REVERT: D 920 ARG cc_start: 0.5085 (OUTLIER) cc_final: 0.2238 (mmm160) REVERT: D 1047 LEU cc_start: 0.7398 (tt) cc_final: 0.6711 (mt) REVERT: D 1052 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5774 (tt0) REVERT: D 1157 MET cc_start: 0.7771 (tpp) cc_final: 0.7403 (mmp) REVERT: D 1205 GLN cc_start: 0.4806 (OUTLIER) cc_final: 0.3546 (pt0) REVERT: D 1532 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7018 (t80) REVERT: D 2004 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6921 (p90) REVERT: D 2080 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7978 (tp40) REVERT: D 2153 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8046 (mpt180) REVERT: D 2226 SER cc_start: 0.2758 (OUTLIER) cc_final: 0.2204 (m) REVERT: D 2288 MET cc_start: 0.2346 (ptm) cc_final: 0.1773 (ttm) REVERT: D 2325 MET cc_start: 0.4451 (OUTLIER) cc_final: 0.3878 (tpt) outliers start: 261 outliers final: 143 residues processed: 551 average time/residue: 0.1792 time to fit residues: 161.1257 Evaluate side-chains 457 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 280 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1556 GLN Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1667 GLU Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2080 GLN Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2325 MET Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2386 ARG Chi-restraints excluded: chain A residue 2389 LEU Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2487 VAL 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 700 TYR Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 848 MET Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1052 GLN Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1305 HIS Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1536 HIS Chi-restraints excluded: chain B residue 1553 GLU Chi-restraints excluded: chain B residue 1556 GLN Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1653 ARG Chi-restraints excluded: chain B residue 1665 PHE Chi-restraints excluded: chain B residue 1667 GLU Chi-restraints excluded: chain B residue 1681 GLN Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2080 GLN Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2194 MET Chi-restraints excluded: chain B residue 2197 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2325 MET Chi-restraints excluded: chain B residue 2340 SER Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2355 LEU Chi-restraints excluded: chain B residue 2356 PHE 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 2406 ILE Chi-restraints excluded: chain B residue 2412 ARG Chi-restraints excluded: chain B residue 2446 SER Chi-restraints excluded: chain B residue 2480 LEU Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 768 GLU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1030 HIS Chi-restraints excluded: chain D residue 1052 GLN Chi-restraints excluded: chain D residue 1054 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1116 PHE Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1184 ILE Chi-restraints excluded: chain D residue 1205 GLN Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1532 PHE Chi-restraints excluded: chain D residue 1553 GLU Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1665 PHE Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1681 GLN Chi-restraints excluded: chain D residue 1697 LEU Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1960 VAL Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2080 GLN Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2197 VAL Chi-restraints excluded: chain D residue 2226 SER Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2325 MET Chi-restraints excluded: chain D residue 2340 SER Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2355 LEU Chi-restraints excluded: chain D residue 2356 PHE Chi-restraints excluded: chain D residue 2386 ARG Chi-restraints excluded: chain D residue 2389 LEU Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2446 SER Chi-restraints excluded: chain D residue 2487 VAL 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 E residue 243 ILE Chi-restraints excluded: chain F residue 243 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 334 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 353 optimal weight: 7.9990 chunk 61 optimal weight: 0.0980 chunk 83 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 369 optimal weight: 20.0000 chunk 222 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** A1012 ASN ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2324 HIS ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 GLN D1111 GLN D1305 HIS D1535 HIS ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1951 HIS ** D2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.222320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.193113 restraints weight = 47314.717| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 1.95 r_work: 0.3805 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.8424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 32929 Z= 0.135 Angle : 0.732 56.062 44507 Z= 0.358 Chirality : 0.040 0.190 5046 Planarity : 0.005 0.099 5424 Dihedral : 10.191 83.890 4681 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.10 % Favored : 92.48 % Rotamer: Outliers : 7.25 % Allowed : 25.91 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.14), residues: 3801 helix: 1.52 (0.10), residues: 2568 sheet: -4.06 (0.35), residues: 153 loop : -3.15 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1534 TYR 0.014 0.001 TYR A2293 PHE 0.026 0.001 PHE B 615 TRP 0.052 0.001 TRP D2278 HIS 0.005 0.001 HIS B2464 Details of bonding type rmsd covalent geometry : bond 0.00314 (32925) covalent geometry : angle 0.65057 (44499) SS BOND : bond 0.02376 ( 4) SS BOND : angle 25.10024 ( 8) hydrogen bonds : bond 0.03793 ( 1968) hydrogen bonds : angle 4.20031 ( 5796) *********************** 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 550 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 302 time to evaluate : 1.074 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: A 700 TYR cc_start: 0.0286 (OUTLIER) cc_final: -0.1183 (m-80) REVERT: A 768 GLU cc_start: 0.3087 (OUTLIER) cc_final: 0.2605 (pt0) REVERT: A 1047 LEU cc_start: 0.7344 (tt) cc_final: 0.6725 (mt) REVERT: A 1048 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7269 (t80) REVERT: A 1154 TYR cc_start: 0.5924 (t80) cc_final: 0.5400 (t80) REVERT: A 1156 ASP cc_start: 0.5279 (OUTLIER) cc_final: 0.4747 (t0) REVERT: A 1157 MET cc_start: 0.7585 (mmm) cc_final: 0.7151 (mmp) REVERT: A 1205 GLN cc_start: 0.5069 (OUTLIER) cc_final: 0.3918 (pt0) REVERT: A 1344 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 1681 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: A 2004 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.7077 (p90) REVERT: A 2080 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8102 (tp40) REVERT: A 2153 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8064 (mmt-90) REVERT: A 2325 MET cc_start: 0.4917 (OUTLIER) cc_final: 0.4053 (tpt) REVERT: A 2375 GLN cc_start: 0.4586 (OUTLIER) cc_final: 0.4203 (mp10) REVERT: B 700 TYR cc_start: 0.0274 (OUTLIER) cc_final: -0.1168 (m-80) REVERT: B 706 MET cc_start: 0.0181 (mmt) cc_final: -0.1955 (ttm) REVERT: B 768 GLU cc_start: 0.3033 (OUTLIER) cc_final: 0.2387 (pt0) REVERT: B 1047 LEU cc_start: 0.7268 (tt) cc_final: 0.6744 (mt) REVERT: B 1157 MET cc_start: 0.7581 (tpp) cc_final: 0.7380 (mmp) REVERT: B 1205 GLN cc_start: 0.5191 (OUTLIER) cc_final: 0.3500 (pp30) REVERT: B 1207 ASP cc_start: 0.5183 (OUTLIER) cc_final: 0.4806 (t70) REVERT: B 1546 GLU cc_start: 0.3884 (OUTLIER) cc_final: 0.2182 (pm20) REVERT: B 1680 TYR cc_start: 0.8160 (t80) cc_final: 0.7887 (t80) REVERT: B 2080 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7945 (tp-100) REVERT: B 2153 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8075 (mmt-90) REVERT: B 2288 MET cc_start: 0.2548 (ptm) cc_final: 0.1879 (ttt) REVERT: B 2351 VAL cc_start: 0.4300 (OUTLIER) cc_final: 0.3554 (t) REVERT: B 2511 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: D 700 TYR cc_start: 0.0155 (OUTLIER) cc_final: -0.1831 (m-80) REVERT: D 706 MET cc_start: -0.1788 (OUTLIER) cc_final: -0.4307 (ttm) REVERT: D 768 GLU cc_start: 0.2908 (OUTLIER) cc_final: 0.2518 (pt0) REVERT: D 920 ARG cc_start: 0.4935 (OUTLIER) cc_final: 0.2120 (mmm160) REVERT: D 971 THR cc_start: 0.2410 (OUTLIER) cc_final: 0.1984 (p) REVERT: D 1047 LEU cc_start: 0.7249 (tt) cc_final: 0.6667 (mt) REVERT: D 1052 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.5987 (tt0) REVERT: D 1156 ASP cc_start: 0.5307 (OUTLIER) cc_final: 0.4606 (t0) REVERT: D 1205 GLN cc_start: 0.5145 (OUTLIER) cc_final: 0.4580 (pt0) REVERT: D 1217 CYS cc_start: 0.8111 (t) cc_final: 0.7889 (m) REVERT: D 1532 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7109 (t80) REVERT: D 1546 GLU cc_start: 0.4169 (OUTLIER) cc_final: 0.2288 (pm20) REVERT: D 1680 TYR cc_start: 0.8056 (t80) cc_final: 0.7781 (t80) REVERT: D 2004 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.7108 (p90) REVERT: D 2034 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8353 (tp40) REVERT: D 2080 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: D 2153 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8068 (mpt180) REVERT: D 2288 MET cc_start: 0.2515 (ptm) cc_final: 0.1835 (ttm) REVERT: D 2325 MET cc_start: 0.4832 (OUTLIER) cc_final: 0.3942 (tpt) outliers start: 248 outliers final: 152 residues processed: 523 average time/residue: 0.1766 time to fit residues: 152.0166 Evaluate side-chains 463 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 276 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1305 HIS Chi-restraints excluded: chain A residue 1311 ARG Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1553 GLU Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1960 VAL 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 2048 ILE Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2080 GLN Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2325 MET Chi-restraints excluded: chain A residue 2340 SER Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2386 ARG Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2420 MET Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2487 VAL Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1311 ARG Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1408 ASP Chi-restraints excluded: chain B residue 1536 HIS Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1665 PHE Chi-restraints excluded: chain B residue 1667 GLU Chi-restraints excluded: chain B residue 1681 GLN Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2080 GLN Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2197 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2355 LEU Chi-restraints excluded: chain B residue 2356 PHE Chi-restraints excluded: chain B residue 2389 LEU Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2412 ARG Chi-restraints excluded: chain B residue 2418 LEU Chi-restraints excluded: chain B residue 2446 SER Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 768 GLU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 935 VAL 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 1026 LEU Chi-restraints excluded: chain D residue 1030 HIS Chi-restraints excluded: chain D residue 1052 GLN Chi-restraints excluded: chain D residue 1054 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1155 LEU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1184 ILE Chi-restraints excluded: chain D residue 1205 GLN Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1305 HIS Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1532 PHE Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1553 GLU Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1665 PHE Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1681 GLN Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1960 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 2049 LEU Chi-restraints excluded: chain D residue 2080 GLN Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2197 VAL Chi-restraints excluded: chain D residue 2304 THR Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2325 MET Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2356 PHE Chi-restraints excluded: chain D residue 2386 ARG Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2467 MET Chi-restraints excluded: chain D residue 2487 VAL Chi-restraints excluded: chain D residue 2506 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 55 optimal weight: 6.9990 chunk 388 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 375 optimal weight: 0.0980 chunk 94 optimal weight: 0.7980 chunk 292 optimal weight: 0.0970 chunk 217 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1012 ASN ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1535 HIS ** A1556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1999 GLN ** A2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 GLN ** B1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2250 GLN D1012 ASN D1111 GLN ** D1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2161 GLN ** D2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2377 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.218965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.189387 restraints weight = 46405.012| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 1.92 r_work: 0.3777 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.8948 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= 0.175 Angle : 0.764 56.058 44507 Z= 0.374 Chirality : 0.041 0.183 5046 Planarity : 0.005 0.099 5424 Dihedral : 10.093 89.888 4659 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.52 % Favored : 92.08 % Rotamer: Outliers : 7.13 % Allowed : 26.23 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.14), residues: 3801 helix: 1.46 (0.10), residues: 2556 sheet: -3.79 (0.37), residues: 153 loop : -3.04 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1671 TYR 0.023 0.002 TYR D1306 PHE 0.032 0.002 PHE A2356 TRP 0.027 0.001 TRP D2278 HIS 0.024 0.001 HIS D1305 Details of bonding type rmsd covalent geometry : bond 0.00417 (32925) covalent geometry : angle 0.68603 (44499) SS BOND : bond 0.02387 ( 4) SS BOND : angle 25.09548 ( 8) hydrogen bonds : bond 0.04208 ( 1968) hydrogen bonds : angle 4.19247 ( 5796) *********************** 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 522 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 278 time to evaluate : 1.292 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: A 700 TYR cc_start: 0.0356 (OUTLIER) cc_final: -0.1161 (m-80) REVERT: A 706 MET cc_start: -0.1419 (mmm) cc_final: -0.1959 (mmm) REVERT: A 768 GLU cc_start: 0.3158 (OUTLIER) cc_final: 0.2720 (pt0) REVERT: A 1047 LEU cc_start: 0.7401 (tt) cc_final: 0.6797 (mt) REVERT: A 1048 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7269 (t80) REVERT: A 1052 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.5770 (tt0) REVERT: A 1157 MET cc_start: 0.7622 (mmm) cc_final: 0.7194 (mmp) REVERT: A 1532 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7544 (t80) REVERT: A 1546 GLU cc_start: 0.4019 (OUTLIER) cc_final: 0.3051 (pp20) REVERT: A 2004 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.7115 (p90) REVERT: A 2080 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7947 (tp40) REVERT: A 2153 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.7840 (mmt180) REVERT: A 2189 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7583 (t80) REVERT: A 2375 GLN cc_start: 0.4685 (OUTLIER) cc_final: 0.4329 (mp10) REVERT: A 2511 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: B 700 TYR cc_start: 0.0335 (OUTLIER) cc_final: -0.1240 (m-80) REVERT: B 706 MET cc_start: 0.0237 (mmt) cc_final: -0.1650 (ttt) REVERT: B 768 GLU cc_start: 0.3050 (OUTLIER) cc_final: 0.2502 (pt0) REVERT: B 920 ARG cc_start: 0.4872 (OUTLIER) cc_final: 0.2122 (mpp80) REVERT: B 1047 LEU cc_start: 0.7339 (tt) cc_final: 0.6842 (mt) REVERT: B 1052 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6032 (tt0) REVERT: B 1157 MET cc_start: 0.7621 (tpp) cc_final: 0.7390 (mmp) REVERT: B 1207 ASP cc_start: 0.5102 (OUTLIER) cc_final: 0.4619 (t0) REVERT: B 1366 GLN cc_start: 0.7590 (mm-40) cc_final: 0.6914 (mt0) REVERT: B 1532 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 1546 GLU cc_start: 0.4050 (OUTLIER) cc_final: 0.2260 (pm20) REVERT: B 2004 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7159 (p90) REVERT: B 2080 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: B 2153 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8027 (mpt180) REVERT: B 2288 MET cc_start: 0.2397 (ptm) cc_final: 0.1734 (ttt) REVERT: B 2351 VAL cc_start: 0.4122 (OUTLIER) cc_final: 0.3446 (t) REVERT: D 700 TYR cc_start: 0.0192 (OUTLIER) cc_final: -0.1968 (m-80) REVERT: D 706 MET cc_start: -0.1693 (OUTLIER) cc_final: -0.4099 (ttm) REVERT: D 768 GLU cc_start: 0.2900 (OUTLIER) cc_final: 0.2565 (pt0) REVERT: D 1047 LEU cc_start: 0.7279 (tt) cc_final: 0.6744 (mt) REVERT: D 1052 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6135 (tt0) REVERT: D 1532 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7223 (t80) REVERT: D 1546 GLU cc_start: 0.4274 (OUTLIER) cc_final: 0.2214 (pm20) REVERT: D 2004 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7046 (p90) REVERT: D 2080 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8022 (tp40) REVERT: D 2153 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8010 (mpt180) REVERT: D 2308 GLN cc_start: 0.6048 (tm-30) cc_final: 0.5761 (mm-40) outliers start: 244 outliers final: 158 residues processed: 495 average time/residue: 0.1807 time to fit residues: 146.8143 Evaluate side-chains 458 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 268 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1052 GLN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1305 HIS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1408 ASP Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1533 THR Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1553 GLU Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1960 VAL 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 2048 ILE Chi-restraints excluded: chain A residue 2080 GLN Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2355 LEU Chi-restraints excluded: chain A residue 2375 GLN Chi-restraints excluded: chain A residue 2386 ARG Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2487 VAL 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 694 CYS Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 946 TYR Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1052 GLN Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1305 HIS Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1553 GLU Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1667 GLU Chi-restraints excluded: chain B residue 1681 GLN Chi-restraints excluded: chain B residue 1697 LEU Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1960 VAL 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 2049 LEU Chi-restraints excluded: chain B residue 2080 GLN Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2197 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2355 LEU Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2412 ARG Chi-restraints excluded: chain B residue 2418 LEU Chi-restraints excluded: chain B residue 2446 SER Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 768 GLU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 1026 LEU Chi-restraints excluded: chain D residue 1030 HIS Chi-restraints excluded: chain D residue 1052 GLN Chi-restraints excluded: chain D residue 1054 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1155 LEU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1184 ILE Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1305 HIS Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1532 PHE Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1553 GLU Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1665 PHE Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1681 GLN Chi-restraints excluded: chain D residue 1697 LEU Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1960 VAL 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 2037 LEU Chi-restraints excluded: chain D residue 2080 GLN Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2197 VAL Chi-restraints excluded: chain D residue 2304 THR Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2386 ARG Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2446 SER Chi-restraints excluded: chain D residue 2487 VAL 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 F residue 243 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 15 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 247 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 chunk 386 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1519 GLN ** B1556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 HIS ** B2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1305 HIS D1519 GLN D1535 HIS ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.220055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.192648 restraints weight = 46686.039| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.87 r_work: 0.3902 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.9229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32929 Z= 0.146 Angle : 0.727 56.061 44507 Z= 0.355 Chirality : 0.040 0.194 5046 Planarity : 0.005 0.088 5424 Dihedral : 9.819 88.577 4646 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.79 % Favored : 92.82 % Rotamer: Outliers : 6.28 % Allowed : 27.08 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.14), residues: 3801 helix: 1.62 (0.10), residues: 2565 sheet: -3.63 (0.37), residues: 153 loop : -2.95 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1534 TYR 0.021 0.001 TYR B 985 PHE 0.025 0.001 PHE B 615 TRP 0.021 0.001 TRP D2278 HIS 0.006 0.001 HIS D2464 Details of bonding type rmsd covalent geometry : bond 0.00345 (32925) covalent geometry : angle 0.64509 (44499) SS BOND : bond 0.02384 ( 4) SS BOND : angle 25.09298 ( 8) hydrogen bonds : bond 0.03856 ( 1968) hydrogen bonds : angle 4.07789 ( 5796) *********************** 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 479 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 264 time to evaluate : 0.985 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 700 TYR cc_start: 0.0421 (OUTLIER) cc_final: -0.1618 (m-10) REVERT: A 706 MET cc_start: -0.1432 (mmm) cc_final: -0.1896 (mmm) REVERT: A 768 GLU cc_start: 0.2674 (OUTLIER) cc_final: 0.2455 (pt0) REVERT: A 920 ARG cc_start: 0.4744 (OUTLIER) cc_final: 0.1515 (mmm160) REVERT: A 1048 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 1052 GLN cc_start: 0.6668 (OUTLIER) cc_final: 0.6120 (tt0) REVERT: A 1157 MET cc_start: 0.7493 (mmm) cc_final: 0.7107 (mmp) REVERT: A 1361 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: A 1532 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 1546 GLU cc_start: 0.3888 (OUTLIER) cc_final: 0.1988 (pm20) REVERT: A 2004 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6975 (p90) REVERT: A 2080 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8053 (tp40) REVERT: A 2153 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7861 (mmt180) REVERT: A 2189 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7442 (t80) REVERT: B 700 TYR cc_start: 0.0362 (OUTLIER) cc_final: -0.1246 (m-80) REVERT: B 706 MET cc_start: 0.0119 (mmt) cc_final: -0.1521 (ttt) REVERT: B 768 GLU cc_start: 0.2631 (OUTLIER) cc_final: 0.2254 (pt0) REVERT: B 920 ARG cc_start: 0.4605 (OUTLIER) cc_final: 0.1467 (mmm160) REVERT: B 1047 LEU cc_start: 0.7437 (tt) cc_final: 0.7027 (mt) REVERT: B 1344 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 1514 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4616 (tt) REVERT: B 1532 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7187 (t80) REVERT: B 1546 GLU cc_start: 0.3955 (OUTLIER) cc_final: 0.2142 (pm20) REVERT: B 2080 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8230 (tp40) REVERT: B 2153 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8065 (mpt180) REVERT: B 2288 MET cc_start: 0.1863 (ptm) cc_final: 0.1368 (ttt) REVERT: B 2511 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8094 (mm-30) REVERT: D 700 TYR cc_start: 0.0251 (OUTLIER) cc_final: -0.2278 (m-10) REVERT: D 706 MET cc_start: -0.1580 (OUTLIER) cc_final: -0.3748 (ttm) REVERT: D 848 MET cc_start: 0.3715 (mmt) cc_final: 0.3454 (mmm) REVERT: D 920 ARG cc_start: 0.4821 (OUTLIER) cc_final: 0.2274 (mpp80) REVERT: D 1047 LEU cc_start: 0.7402 (tt) cc_final: 0.6905 (mt) REVERT: D 1361 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: D 1532 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6981 (t80) REVERT: D 1546 GLU cc_start: 0.4254 (OUTLIER) cc_final: 0.2337 (pm20) REVERT: D 2004 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6893 (p90) REVERT: D 2080 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8125 (tp40) REVERT: D 2153 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8032 (mpt180) REVERT: D 2288 MET cc_start: 0.1950 (ptm) cc_final: 0.1431 (ttt) outliers start: 215 outliers final: 139 residues processed: 460 average time/residue: 0.1696 time to fit residues: 128.8265 Evaluate side-chains 426 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 257 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1052 GLN Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1305 HIS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1361 GLN Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1533 THR Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1553 GLU Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1960 VAL 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 2048 ILE Chi-restraints excluded: chain A residue 2080 GLN Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2153 ARG Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2487 VAL Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1305 HIS Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1553 GLU Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1667 GLU Chi-restraints excluded: chain B residue 1681 GLN Chi-restraints excluded: chain B residue 1697 LEU Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2080 GLN Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2153 ARG Chi-restraints excluded: chain B residue 2197 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2412 ARG Chi-restraints excluded: chain B residue 2418 LEU Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 TYR Chi-restraints excluded: chain D residue 1026 LEU Chi-restraints excluded: chain D residue 1030 HIS Chi-restraints excluded: chain D residue 1054 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1155 LEU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1184 ILE Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1361 GLN Chi-restraints excluded: chain D residue 1532 PHE Chi-restraints excluded: chain D residue 1533 THR Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1553 GLU Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1665 PHE Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1681 GLN Chi-restraints excluded: chain D residue 1697 LEU Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1960 VAL Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2037 LEU Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2080 GLN Chi-restraints excluded: chain D residue 2153 ARG Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2197 VAL Chi-restraints excluded: chain D residue 2304 THR Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2386 ARG Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2467 MET Chi-restraints excluded: chain D residue 2487 VAL 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 243 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 278 optimal weight: 1.9990 chunk 330 optimal weight: 0.6980 chunk 268 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 GLN ** B1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 HIS ** B2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1052 GLN D1556 GLN ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2229 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 = 0.4477 r_free = 0.4477 target = 0.220193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190078 restraints weight = 46405.959| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 1.94 r_work: 0.3825 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.9481 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= 0.137 Angle : 0.721 56.057 44507 Z= 0.352 Chirality : 0.040 0.206 5046 Planarity : 0.005 0.085 5424 Dihedral : 9.448 89.815 4627 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.39 % Favored : 92.21 % Rotamer: Outliers : 5.99 % Allowed : 27.02 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.14), residues: 3801 helix: 1.67 (0.10), residues: 2583 sheet: -3.45 (0.39), residues: 153 loop : -2.96 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2386 TYR 0.017 0.001 TYR B1307 PHE 0.038 0.001 PHE A2356 TRP 0.019 0.001 TRP D2278 HIS 0.005 0.001 HIS D2464 Details of bonding type rmsd covalent geometry : bond 0.00319 (32925) covalent geometry : angle 0.63795 (44499) SS BOND : bond 0.02370 ( 4) SS BOND : angle 25.09711 ( 8) hydrogen bonds : bond 0.03757 ( 1968) hydrogen bonds : angle 3.98691 ( 5796) *********************** 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 470 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 265 time to evaluate : 1.117 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 700 TYR cc_start: 0.0355 (OUTLIER) cc_final: -0.1585 (m-10) REVERT: A 706 MET cc_start: -0.1460 (mmm) cc_final: -0.1842 (mmm) REVERT: A 768 GLU cc_start: 0.2970 (OUTLIER) cc_final: 0.2651 (pt0) REVERT: A 920 ARG cc_start: 0.4567 (OUTLIER) cc_final: 0.1412 (mmm160) REVERT: A 1048 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7395 (t80) REVERT: A 1052 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6167 (tt0) REVERT: A 1157 MET cc_start: 0.7587 (mmm) cc_final: 0.7156 (mmp) REVERT: A 1361 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8204 (mp10) REVERT: A 1532 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 1546 GLU cc_start: 0.3816 (OUTLIER) cc_final: 0.2650 (pp20) REVERT: A 2004 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.7169 (p90) REVERT: A 2080 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8096 (tp40) REVERT: A 2511 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.7908 (mm-30) REVERT: B 700 TYR cc_start: 0.0311 (OUTLIER) cc_final: -0.1289 (m-80) REVERT: B 706 MET cc_start: 0.0343 (mmt) cc_final: -0.1270 (ttt) REVERT: B 768 GLU cc_start: 0.3006 (OUTLIER) cc_final: 0.2545 (pt0) REVERT: B 920 ARG cc_start: 0.4561 (OUTLIER) cc_final: 0.2131 (mpp80) REVERT: B 1047 LEU cc_start: 0.7391 (tt) cc_final: 0.6929 (mt) REVERT: B 1532 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7127 (t80) REVERT: B 1546 GLU cc_start: 0.3828 (OUTLIER) cc_final: 0.2090 (pm20) REVERT: B 2080 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8218 (tp-100) REVERT: D 700 TYR cc_start: 0.0239 (OUTLIER) cc_final: -0.1853 (m-80) REVERT: D 706 MET cc_start: -0.1775 (OUTLIER) cc_final: -0.3961 (ttm) REVERT: D 848 MET cc_start: 0.3979 (OUTLIER) cc_final: 0.3584 (mmm) REVERT: D 920 ARG cc_start: 0.4694 (OUTLIER) cc_final: 0.2377 (mpp80) REVERT: D 1052 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6202 (tt0) REVERT: D 1361 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: D 1532 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6972 (t80) REVERT: D 1546 GLU cc_start: 0.4071 (OUTLIER) cc_final: 0.2265 (pm20) REVERT: D 2004 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.7037 (p90) REVERT: D 2080 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8244 (tp40) REVERT: D 2325 MET cc_start: 0.4612 (OUTLIER) cc_final: 0.3697 (tpt) outliers start: 205 outliers final: 139 residues processed: 445 average time/residue: 0.1715 time to fit residues: 127.1781 Evaluate side-chains 417 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 250 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1052 GLN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1305 HIS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1361 GLN Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1533 THR Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1553 GLU Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1960 VAL 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 2048 ILE Chi-restraints excluded: chain A residue 2080 GLN Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2487 VAL 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 694 CYS Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1305 HIS Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1553 GLU Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1667 GLU Chi-restraints excluded: chain B residue 1681 GLN Chi-restraints excluded: chain B residue 1697 LEU Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1951 HIS Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2049 LEU Chi-restraints excluded: chain B residue 2080 GLN Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2189 PHE Chi-restraints excluded: chain B residue 2197 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2406 ILE Chi-restraints excluded: chain B residue 2412 ARG Chi-restraints excluded: chain B residue 2446 SER Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 1026 LEU Chi-restraints excluded: chain D residue 1030 HIS Chi-restraints excluded: chain D residue 1052 GLN Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1155 LEU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1184 ILE Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1361 GLN Chi-restraints excluded: chain D residue 1532 PHE Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1553 GLU Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1681 GLN Chi-restraints excluded: chain D residue 1697 LEU Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1960 VAL 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 2037 LEU Chi-restraints excluded: chain D residue 2049 LEU Chi-restraints excluded: chain D residue 2080 GLN Chi-restraints excluded: chain D residue 2189 PHE Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2197 VAL Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2325 MET Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2386 ARG Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2467 MET Chi-restraints excluded: chain D residue 2487 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 231 optimal weight: 30.0000 chunk 378 optimal weight: 0.5980 chunk 368 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 279 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 351 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 HIS ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1519 GLN ** A1556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 HIS B 988 ASN ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 HIS ** B2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 HIS D1052 GLN D1305 HIS ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.215268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.186601 restraints weight = 45566.959| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.86 r_work: 0.3764 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.9812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 32929 Z= 0.263 Angle : 0.831 56.059 44507 Z= 0.409 Chirality : 0.045 0.196 5046 Planarity : 0.006 0.088 5424 Dihedral : 9.813 85.211 4609 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.02 % Favored : 91.55 % Rotamer: Outliers : 5.73 % Allowed : 27.23 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.14), residues: 3801 helix: 1.13 (0.10), residues: 2610 sheet: -3.38 (0.39), residues: 156 loop : -3.03 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1211 TYR 0.022 0.002 TYR B1307 PHE 0.046 0.002 PHE B2356 TRP 0.021 0.002 TRP D2278 HIS 0.012 0.002 HIS D2464 Details of bonding type rmsd covalent geometry : bond 0.00647 (32925) covalent geometry : angle 0.76051 (44499) SS BOND : bond 0.02409 ( 4) SS BOND : angle 25.08338 ( 8) hydrogen bonds : bond 0.04816 ( 1968) hydrogen bonds : angle 4.28815 ( 5796) *********************** 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 461 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 265 time to evaluate : 1.430 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 700 TYR cc_start: 0.0324 (OUTLIER) cc_final: -0.1630 (m-10) REVERT: A 706 MET cc_start: -0.1217 (mmm) cc_final: -0.1661 (mmm) REVERT: A 920 ARG cc_start: 0.4878 (OUTLIER) cc_final: 0.2178 (mpp80) REVERT: A 951 HIS cc_start: 0.3456 (OUTLIER) cc_final: 0.2907 (p-80) REVERT: A 1157 MET cc_start: 0.7593 (mmm) cc_final: 0.7128 (mmp) REVERT: A 1361 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8210 (mp10) REVERT: A 1532 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7461 (t80) REVERT: A 1546 GLU cc_start: 0.4188 (OUTLIER) cc_final: 0.3168 (pp20) REVERT: A 1681 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: A 2004 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7091 (p90) REVERT: A 2189 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7652 (t80) REVERT: A 2511 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.7853 (mm-30) REVERT: B 605 MET cc_start: 0.3650 (mmm) cc_final: 0.3426 (mmm) REVERT: B 920 ARG cc_start: 0.4728 (OUTLIER) cc_final: 0.2198 (mpp80) REVERT: B 951 HIS cc_start: 0.3811 (OUTLIER) cc_final: 0.2926 (p-80) REVERT: B 1532 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7211 (t80) REVERT: B 1546 GLU cc_start: 0.4314 (OUTLIER) cc_final: 0.3246 (pp20) REVERT: B 2080 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7915 (tp-100) REVERT: B 2511 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: D 700 TYR cc_start: 0.0289 (OUTLIER) cc_final: -0.2216 (m-10) REVERT: D 706 MET cc_start: -0.1403 (OUTLIER) cc_final: -0.3751 (ttm) REVERT: D 920 ARG cc_start: 0.4971 (OUTLIER) cc_final: 0.2217 (mpp80) REVERT: D 1047 LEU cc_start: 0.7367 (tt) cc_final: 0.6752 (mt) REVERT: D 1052 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6398 (tt0) REVERT: D 1361 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: D 1532 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7000 (t80) REVERT: D 1546 GLU cc_start: 0.4352 (OUTLIER) cc_final: 0.3224 (pp20) REVERT: D 2325 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.3762 (tpt) REVERT: D 2511 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.7885 (mm-30) outliers start: 196 outliers final: 133 residues processed: 437 average time/residue: 0.1768 time to fit residues: 127.2233 Evaluate side-chains 414 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 256 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 951 HIS Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1052 GLN Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1305 HIS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1361 GLN Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1553 GLU Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1960 VAL 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 2117 GLU Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2487 VAL 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 694 CYS Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1305 HIS Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1553 GLU Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1667 GLU Chi-restraints excluded: chain B residue 1697 LEU Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1951 HIS Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2080 GLN Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2189 PHE Chi-restraints excluded: chain B residue 2197 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2412 ARG Chi-restraints excluded: chain B residue 2446 SER Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 1026 LEU Chi-restraints excluded: chain D residue 1030 HIS Chi-restraints excluded: chain D residue 1052 GLN Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1155 LEU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1184 ILE Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1305 HIS Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1361 GLN Chi-restraints excluded: chain D residue 1532 PHE Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1553 GLU Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1697 LEU Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1960 VAL 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 2037 LEU Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2197 VAL Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2325 MET Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2404 TRP Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2446 SER Chi-restraints excluded: chain D residue 2487 VAL 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 F residue 243 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 265 optimal weight: 2.9990 chunk 389 optimal weight: 0.8980 chunk 243 optimal weight: 10.0000 chunk 360 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 chunk 251 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 316 optimal weight: 0.9980 chunk 375 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 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 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1361 GLN ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 HIS B1999 GLN ** B2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1052 GLN D1305 HIS ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.218924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.189778 restraints weight = 46263.993| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 1.90 r_work: 0.3834 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.9949 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= 0.146 Angle : 0.762 56.062 44507 Z= 0.370 Chirality : 0.041 0.220 5046 Planarity : 0.005 0.082 5424 Dihedral : 9.129 89.528 4595 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.84 % Favored : 92.77 % Rotamer: Outliers : 4.38 % Allowed : 28.37 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.14), residues: 3801 helix: 1.51 (0.10), residues: 2586 sheet: -3.27 (0.40), residues: 156 loop : -3.01 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1534 TYR 0.022 0.001 TYR A 799 PHE 0.030 0.001 PHE D2356 TRP 0.021 0.001 TRP D2278 HIS 0.017 0.001 HIS D1305 Details of bonding type rmsd covalent geometry : bond 0.00342 (32925) covalent geometry : angle 0.68327 (44499) SS BOND : bond 0.02373 ( 4) SS BOND : angle 25.09417 ( 8) hydrogen bonds : bond 0.03909 ( 1968) hydrogen bonds : angle 4.10217 ( 5796) ********************** 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 409 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 259 time to evaluate : 1.293 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: A 700 TYR cc_start: 0.0296 (OUTLIER) cc_final: -0.1672 (m-10) REVERT: A 706 MET cc_start: -0.1381 (mmm) cc_final: -0.1706 (mmm) REVERT: A 920 ARG cc_start: 0.4663 (OUTLIER) cc_final: 0.2341 (mpp80) REVERT: A 951 HIS cc_start: 0.3339 (OUTLIER) cc_final: 0.2953 (p-80) REVERT: A 1157 MET cc_start: 0.7508 (mmm) cc_final: 0.7121 (mmp) REVERT: A 1342 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8488 (tt) REVERT: A 1361 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: A 1532 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7321 (t80) REVERT: A 1546 GLU cc_start: 0.3824 (OUTLIER) cc_final: 0.2553 (pp20) REVERT: A 2004 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.7113 (p90) REVERT: B 700 TYR cc_start: 0.0304 (OUTLIER) cc_final: -0.0090 (m-80) REVERT: B 920 ARG cc_start: 0.4503 (OUTLIER) cc_final: 0.2358 (mpp80) REVERT: B 1532 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7125 (t80) REVERT: B 1546 GLU cc_start: 0.3933 (OUTLIER) cc_final: 0.2281 (pm20) REVERT: B 2080 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8287 (tp40) REVERT: B 2511 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8055 (mm-30) REVERT: D 706 MET cc_start: -0.1529 (OUTLIER) cc_final: -0.3749 (ttm) REVERT: D 920 ARG cc_start: 0.4678 (OUTLIER) cc_final: 0.2527 (mpp80) REVERT: D 1047 LEU cc_start: 0.7317 (tt) cc_final: 0.6808 (mt) REVERT: D 1052 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6289 (tt0) REVERT: D 1156 ASP cc_start: 0.5241 (OUTLIER) cc_final: 0.4999 (t0) REVERT: D 1341 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7611 (mtp-110) REVERT: D 1361 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: D 1546 GLU cc_start: 0.4053 (OUTLIER) cc_final: 0.2671 (pp20) REVERT: D 2004 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7029 (p90) REVERT: D 2325 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.3623 (tpt) outliers start: 150 outliers final: 121 residues processed: 394 average time/residue: 0.1834 time to fit residues: 118.3649 Evaluate side-chains 391 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 248 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 951 HIS Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1305 HIS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1361 GLN Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1553 GLU Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1681 GLN Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2278 TRP Chi-restraints excluded: chain A residue 2317 VAL Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2404 TRP Chi-restraints excluded: chain A residue 2412 ARG Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2487 VAL Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1030 HIS Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1305 HIS Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1361 GLN Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1553 GLU Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1667 GLU Chi-restraints excluded: chain B residue 1697 LEU Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2080 GLN Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2189 PHE Chi-restraints excluded: chain B residue 2197 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2278 TRP Chi-restraints excluded: chain B residue 2317 VAL Chi-restraints excluded: chain B residue 2345 THR Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2404 TRP Chi-restraints excluded: chain B residue 2412 ARG Chi-restraints excluded: chain B residue 2446 SER Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 920 ARG Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 1026 LEU Chi-restraints excluded: chain D residue 1030 HIS Chi-restraints excluded: chain D residue 1052 GLN Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1184 ILE Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1305 HIS Chi-restraints excluded: chain D residue 1322 SER Chi-restraints excluded: chain D residue 1361 GLN Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1548 TYR Chi-restraints excluded: chain D residue 1553 GLU Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1651 ASP Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1697 LEU Chi-restraints excluded: chain D residue 1722 ILE Chi-restraints excluded: chain D residue 1779 THR Chi-restraints excluded: chain D residue 1960 VAL Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2004 PHE Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2197 VAL Chi-restraints excluded: chain D residue 2317 VAL Chi-restraints excluded: chain D residue 2325 MET Chi-restraints excluded: chain D residue 2345 THR Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2412 ARG Chi-restraints excluded: chain D residue 2467 MET Chi-restraints excluded: chain D residue 2487 VAL 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 243 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 113 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 336 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1361 GLN ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 HIS ** B2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1052 GLN ** D1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2229 GLN ** 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 = 0.4459 r_free = 0.4459 target = 0.218516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.187550 restraints weight = 45808.270| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.96 r_work: 0.3797 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.9954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.333 32929 Z= 0.241 Angle : 0.904 59.182 44507 Z= 0.478 Chirality : 0.043 0.515 5046 Planarity : 0.006 0.196 5424 Dihedral : 9.128 89.629 4594 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.10 % Favored : 92.50 % Rotamer: Outliers : 4.67 % Allowed : 28.05 % Favored : 67.28 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3801 helix: 1.49 (0.10), residues: 2586 sheet: -3.26 (0.40), residues: 156 loop : -3.01 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 829 TYR 0.019 0.001 TYR A 799 PHE 0.028 0.001 PHE D2356 TRP 0.021 0.001 TRP A 819 HIS 0.328 0.003 HIS D1305 Details of bonding type rmsd covalent geometry : bond 0.00553 (32925) covalent geometry : angle 0.83909 (44499) SS BOND : bond 0.02383 ( 4) SS BOND : angle 25.08935 ( 8) hydrogen bonds : bond 0.04039 ( 1968) hydrogen bonds : angle 4.11403 ( 5796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11529.22 seconds wall clock time: 196 minutes 51.16 seconds (11811.16 seconds total)