Starting phenix.real_space_refine on Fri Jun 27 16:11:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yfg_39223/06_2025/8yfg_39223_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yfg_39223/06_2025/8yfg_39223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yfg_39223/06_2025/8yfg_39223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yfg_39223/06_2025/8yfg_39223.map" model { file = "/net/cci-nas-00/data/ceres_data/8yfg_39223/06_2025/8yfg_39223_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yfg_39223/06_2025/8yfg_39223_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 20847 2.51 5 N 5247 2.21 5 O 5301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31599 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 10394 Classifications: {'peptide': 1280} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1238} Chain breaks: 15 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 98 Chain: "B" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 10388 Classifications: {'peptide': 1280} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 41, 'TRANS': 1238} Chain breaks: 15 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 141 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 19} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 10394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 10394 Classifications: {'peptide': 1280} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1238} Chain breaks: 15 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 98 Chain: "E" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 141 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 19} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 141 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 19} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 23.58, per 1000 atoms: 0.75 Number of scatterers: 31599 At special positions: 0 Unit cell: (209.19, 208.62, 145.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 5301 8.00 N 5247 7.00 C 20847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A2411 " - pdb=" SG CYS A2415 " distance=2.04 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: 7.75 Conformation dependent library (CDL) restraints added in 3.8 seconds 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7452 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 9 sheets defined 69.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 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: 3.504A 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: 3.517A 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: 6.283A 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: 3.931A 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: 3.936A 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: 3.846A pdb=" N GLN A1205 " --> pdb=" O THR A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1231 removed outlier: 3.595A 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: 3.599A 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 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: 5.690A 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: 3.558A pdb=" N LYS A2096 " --> pdb=" O PHE A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2099 through 2112 removed outlier: 3.508A pdb=" N VAL A2112 " --> pdb=" O GLY A2108 " (cutoff:3.500A) 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: 4.497A pdb=" N PHE A2189 " --> pdb=" O ALA A2185 " (cutoff:3.500A) Proline residue: A2190 - end of helix Processing helix chain 'A' and resid 2236 through 2247 Processing helix chain 'A' and resid 2250 through 2260 Processing helix chain 'A' and resid 2283 through 2294 removed outlier: 3.769A pdb=" N GLN A2287 " --> pdb=" O PRO A2283 " (cutoff:3.500A) 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: 3.504A 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: 3.517A pdb=" N PHE B 690 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 4.106A 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: 4.071A 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: 4.249A 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: 3.931A 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: 3.846A pdb=" N GLN B1205 " --> pdb=" O THR B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1212 through 1231 removed outlier: 3.594A 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: 5.316A 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: 4.535A pdb=" N PHE B1665 " --> pdb=" O GLU B1661 " (cutoff:3.500A) removed outlier: 3.526A 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: 3.558A pdb=" N LYS B2096 " --> pdb=" O PHE B2093 " (cutoff:3.500A) Processing helix chain 'B' and resid 2099 through 2107 Processing helix chain 'B' and resid 2107 through 2112 removed outlier: 3.578A pdb=" N LEU B2111 " --> pdb=" O GLN B2107 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B2112 " --> pdb=" O GLY B2108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2107 through 2112' Processing helix chain 'B' and resid 2113 through 2127 removed outlier: 4.627A pdb=" N GLU B2117 " --> pdb=" O PRO B2113 " (cutoff:3.500A) Processing helix chain 'B' and resid 2132 through 2159 Processing helix chain 'B' and resid 2168 through 2200 removed outlier: 4.497A pdb=" N PHE B2189 " --> pdb=" O ALA B2185 " (cutoff:3.500A) Proline residue: B2190 - end of helix Processing helix chain 'B' and resid 2236 through 2247 Processing helix chain 'B' and resid 2250 through 2260 Processing helix chain 'B' and resid 2283 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 2469 removed outlier: 3.718A pdb=" N SER B2465 " --> pdb=" O ILE B2462 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B2466 " --> pdb=" O SER B2463 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N MET B2467 " --> pdb=" O HIS B2464 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B2469 " --> pdb=" O ILE B2466 " (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 'C' and resid 228 through 243 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: 3.504A 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: 3.517A pdb=" N PHE D 690 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 4.106A 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: 4.248A 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: 4.061A pdb=" N LYS D 993 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 6.283A 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: 3.931A 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: 3.936A 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: 3.594A 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: 3.740A 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: 5.691A 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: 3.558A pdb=" N LYS D2096 " --> pdb=" O PHE D2093 " (cutoff:3.500A) Processing helix chain 'D' and resid 2099 through 2112 removed outlier: 3.546A pdb=" N GLN D2107 " --> pdb=" O LEU D2103 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE D2109 " --> pdb=" O LEU D2105 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL D2112 " --> pdb=" O GLY D2108 " (cutoff:3.500A) 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: 4.497A pdb=" N PHE D2189 " --> pdb=" O ALA D2185 " (cutoff:3.500A) Proline residue: D2190 - end of helix Processing helix chain 'D' and resid 2236 through 2247 Processing helix chain 'D' and resid 2250 through 2260 Processing helix chain 'D' and resid 2284 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: 3.717A 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 'E' and resid 228 through 244 removed outlier: 3.613A pdb=" N CYS E 244 " --> pdb=" O CYS E 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 242 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: 3.541A 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: 3.541A pdb=" N VAL D2385 " --> pdb=" O ILE D2352 " (cutoff:3.500A) 1952 hydrogen bonds defined for protein. 5745 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: 13.46 Time building geometry restraints manager: 9.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4799 1.31 - 1.44: 9145 1.44 - 1.56: 18092 1.56 - 1.69: 9 1.69 - 1.81: 309 Bond restraints: 32354 Sorted by residual: bond pdb=" C PHE D2106 " pdb=" O PHE D2106 " ideal model delta sigma weight residual 1.237 1.316 -0.079 1.16e-02 7.43e+03 4.63e+01 bond pdb=" C SER D2281 " pdb=" O SER D2281 " ideal model delta sigma weight residual 1.235 1.185 0.051 8.20e-03 1.49e+04 3.83e+01 bond pdb=" CA VAL A1160 " pdb=" CB VAL A1160 " ideal model delta sigma weight residual 1.540 1.617 -0.078 1.29e-02 6.01e+03 3.64e+01 bond pdb=" CA VAL B1160 " pdb=" CB VAL B1160 " ideal model delta sigma weight residual 1.540 1.617 -0.078 1.29e-02 6.01e+03 3.63e+01 bond pdb=" CA VAL D1160 " pdb=" CB VAL D1160 " ideal model delta sigma weight residual 1.540 1.617 -0.077 1.29e-02 6.01e+03 3.60e+01 ... (remaining 32349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 42621 3.64 - 7.27: 1067 7.27 - 10.91: 158 10.91 - 14.54: 24 14.54 - 18.18: 2 Bond angle restraints: 43872 Sorted by residual: angle pdb=" N ILE F 243 " pdb=" CA ILE F 243 " pdb=" C ILE F 243 " ideal model delta sigma weight residual 113.71 95.53 18.18 9.50e-01 1.11e+00 3.66e+02 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 A 930 " pdb=" CA GLN A 930 " pdb=" C GLN A 930 " ideal model delta sigma weight residual 113.19 126.50 -13.31 1.19e+00 7.06e-01 1.25e+02 angle pdb=" N GLN D 930 " pdb=" CA GLN D 930 " pdb=" C GLN D 930 " ideal model delta sigma weight residual 113.19 126.47 -13.28 1.19e+00 7.06e-01 1.25e+02 angle pdb=" N GLY C 242 " pdb=" CA GLY C 242 " pdb=" C GLY C 242 " ideal model delta sigma weight residual 112.73 100.06 12.67 1.20e+00 6.94e-01 1.12e+02 ... (remaining 43867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 14480 17.72 - 35.44: 2088 35.44 - 53.16: 1732 53.16 - 70.88: 662 70.88 - 88.60: 62 Dihedral angle restraints: 19024 sinusoidal: 7555 harmonic: 11469 Sorted by residual: dihedral pdb=" C ILE E 243 " pdb=" N ILE E 243 " pdb=" CA ILE E 243 " pdb=" CB ILE E 243 " ideal model delta harmonic sigma weight residual -122.00 -140.71 18.71 0 2.50e+00 1.60e-01 5.60e+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 -145.51 59.51 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 -145.51 59.51 1 1.00e+01 1.00e-02 4.73e+01 ... (remaining 19021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 4484 0.143 - 0.287: 462 0.287 - 0.430: 71 0.430 - 0.574: 19 0.574 - 0.717: 7 Chirality restraints: 5043 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 1.28e+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 1.28e+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 1.28e+01 ... (remaining 5040 not shown) Planarity restraints: 5381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 686 " -0.112 5.00e-02 4.00e+02 1.70e-01 4.61e+01 pdb=" N PRO D 687 " 0.293 5.00e-02 4.00e+02 pdb=" CA PRO D 687 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO D 687 " -0.097 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 686 " 0.112 5.00e-02 4.00e+02 1.70e-01 4.61e+01 pdb=" N PRO A 687 " -0.293 5.00e-02 4.00e+02 pdb=" CA PRO A 687 " 0.084 5.00e-02 4.00e+02 pdb=" CD PRO A 687 " 0.097 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 686 " -0.112 5.00e-02 4.00e+02 1.70e-01 4.60e+01 pdb=" N PRO B 687 " 0.293 5.00e-02 4.00e+02 pdb=" CA PRO B 687 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO B 687 " -0.097 5.00e-02 4.00e+02 ... (remaining 5378 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 400 2.59 - 3.16: 26540 3.16 - 3.74: 56279 3.74 - 4.32: 79072 4.32 - 4.90: 117176 Nonbonded interactions: 279467 Sorted by model distance: nonbonded pdb=" CB LYS D2323 " pdb=" NZ LYS D2323 " model vdw 2.007 3.520 nonbonded pdb=" CB LYS B2323 " pdb=" NZ LYS B2323 " model vdw 2.007 3.520 nonbonded pdb=" CB LYS A2323 " pdb=" NZ LYS A2323 " model vdw 2.007 3.520 nonbonded pdb=" C LEU D2443 " pdb=" CD2 LEU D2443 " model vdw 2.098 3.690 nonbonded pdb=" C LEU A2443 " pdb=" CD2 LEU A2443 " model vdw 2.098 3.690 ... (remaining 279462 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 570 through 2113 or (resid 2114 and (name N or name CA or \ name C or name O or name CB )) or resid 2115 through 2521)) selection = chain 'B' selection = (chain 'D' and (resid 570 through 2113 or (resid 2114 and (name N or name CA or \ name C or name O or name CB )) or resid 2115 through 2521)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 77.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.760 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 76.010 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.200 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4094 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 : 0.008 0.079 32357 Z= 0.564 Angle : 1.378 18.181 43878 Z= 0.933 Chirality : 0.099 0.717 5043 Planarity : 0.009 0.170 5381 Dihedral : 25.965 88.599 11563 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 3.24 % Allowed : 11.15 % Favored : 85.61 % Rotamer: Outliers : 42.67 % Allowed : 14.57 % Favored : 42.76 % Cbeta Deviations : 0.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.11), residues: 3801 helix: -1.71 (0.09), residues: 2523 sheet: -5.37 (0.24), residues: 108 loop : -4.59 (0.14), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B1168 HIS 0.007 0.001 HIS A 951 PHE 0.030 0.002 PHE B 615 TYR 0.018 0.002 TYR B1165 ARG 0.007 0.001 ARG B1547 Details of bonding type rmsd hydrogen bonds : bond 0.17389 ( 1952) hydrogen bonds : angle 7.65452 ( 5745) SS BOND : bond 0.00498 ( 3) SS BOND : angle 0.86344 ( 6) covalent geometry : bond 0.00760 (32354) covalent geometry : angle 1.37792 (43872) *********************** 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 2073 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1441 poor density : 632 time to evaluate : 5.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 572 VAL cc_start: -0.0307 (OUTLIER) cc_final: -0.1574 (m) REVERT: A 596 ARG cc_start: 0.0260 (OUTLIER) cc_final: -0.1333 (tpt170) REVERT: A 638 MET cc_start: 0.1866 (OUTLIER) cc_final: -0.2500 (mtt) REVERT: A 768 GLU cc_start: 0.4610 (OUTLIER) cc_final: 0.2236 (pp20) REVERT: A 799 TYR cc_start: 0.2045 (OUTLIER) cc_final: 0.1684 (m-80) REVERT: A 806 LYS cc_start: 0.1598 (OUTLIER) cc_final: 0.0907 (mmmm) REVERT: A 843 ILE cc_start: -0.1403 (OUTLIER) cc_final: -0.4243 (tt) REVERT: A 853 LYS cc_start: 0.0484 (OUTLIER) cc_final: -0.0466 (mptt) REVERT: A 954 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.2840 (mtm-85) REVERT: A 978 ASP cc_start: 0.2420 (OUTLIER) cc_final: 0.0783 (t0) REVERT: A 1010 ARG cc_start: 0.4167 (OUTLIER) cc_final: 0.3747 (mtp180) REVERT: A 1048 PHE cc_start: 0.4235 (OUTLIER) cc_final: 0.3653 (t80) REVERT: A 1097 THR cc_start: 0.4603 (OUTLIER) cc_final: 0.4076 (p) REVERT: A 1116 PHE cc_start: 0.3752 (OUTLIER) cc_final: 0.2857 (m-80) REVERT: A 1208 THR cc_start: 0.4161 (OUTLIER) cc_final: 0.3752 (m) REVERT: A 1217 CYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6716 (p) REVERT: A 1409 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5917 (t-90) REVERT: A 1567 GLN cc_start: 0.3943 (OUTLIER) cc_final: 0.3154 (pt0) REVERT: A 1699 HIS cc_start: 0.4535 (OUTLIER) cc_final: 0.4161 (t70) REVERT: A 1716 LEU cc_start: 0.6535 (mt) cc_final: 0.5773 (mt) REVERT: A 1942 LEU cc_start: 0.2690 (OUTLIER) cc_final: 0.1419 (mm) REVERT: A 2008 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7737 (mp) REVERT: A 2011 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6700 (mt0) REVERT: A 2015 MET cc_start: 0.6542 (mtp) cc_final: 0.5267 (mtp) REVERT: A 2033 PHE cc_start: 0.6798 (t80) cc_final: 0.5738 (t80) REVERT: A 2048 ILE cc_start: 0.6231 (OUTLIER) cc_final: 0.5356 (pt) REVERT: A 2069 VAL cc_start: 0.8440 (t) cc_final: 0.8222 (t) REVERT: A 2117 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6702 (mt-10) REVERT: A 2121 VAL cc_start: 0.8680 (t) cc_final: 0.8384 (p) REVERT: A 2134 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.7360 (p) REVERT: A 2138 CYS cc_start: 0.7581 (m) cc_final: 0.7228 (m) REVERT: A 2148 ILE cc_start: 0.8558 (mt) cc_final: 0.8319 (tp) REVERT: A 2244 SER cc_start: 0.4285 (OUTLIER) cc_final: -0.1093 (t) REVERT: A 2280 ILE cc_start: 0.2831 (OUTLIER) cc_final: 0.1396 (pt) REVERT: A 2294 ASN cc_start: 0.7009 (OUTLIER) cc_final: 0.5984 (p0) REVERT: A 2364 ASN cc_start: 0.1437 (OUTLIER) cc_final: 0.1020 (p0) REVERT: A 2375 GLN cc_start: 0.2749 (OUTLIER) cc_final: 0.0065 (mp10) REVERT: A 2407 GLU cc_start: 0.3595 (OUTLIER) cc_final: 0.3137 (pt0) REVERT: A 2408 LEU cc_start: 0.1079 (OUTLIER) cc_final: 0.0207 (mt) REVERT: A 2467 MET cc_start: 0.6235 (ptp) cc_final: 0.5858 (ptp) REVERT: A 2477 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7848 (mm) REVERT: A 2487 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8640 (p) REVERT: A 2502 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8001 (ttmm) REVERT: A 2521 GLU cc_start: 0.2072 (OUTLIER) cc_final: -0.0856 (tm-30) REVERT: B 572 VAL cc_start: -0.0576 (OUTLIER) cc_final: -0.1654 (m) REVERT: B 596 ARG cc_start: 0.0123 (OUTLIER) cc_final: -0.1348 (tpt170) REVERT: B 638 MET cc_start: 0.1933 (OUTLIER) cc_final: -0.2299 (mtt) REVERT: B 768 GLU cc_start: 0.4441 (OUTLIER) cc_final: 0.2050 (pp20) REVERT: B 799 TYR cc_start: 0.1909 (OUTLIER) cc_final: 0.1638 (m-80) REVERT: B 806 LYS cc_start: 0.1619 (OUTLIER) cc_final: 0.0959 (mmmm) REVERT: B 843 ILE cc_start: -0.1475 (OUTLIER) cc_final: -0.4468 (tt) REVERT: B 853 LYS cc_start: 0.0470 (OUTLIER) cc_final: -0.0636 (mptt) REVERT: B 978 ASP cc_start: 0.2212 (OUTLIER) cc_final: 0.0585 (t0) REVERT: B 1034 ILE cc_start: 0.5678 (OUTLIER) cc_final: 0.5467 (mp) REVERT: B 1048 PHE cc_start: 0.4245 (OUTLIER) cc_final: 0.3818 (t80) REVERT: B 1097 THR cc_start: 0.4869 (OUTLIER) cc_final: 0.4266 (p) REVERT: B 1116 PHE cc_start: 0.3874 (OUTLIER) cc_final: 0.2908 (m-80) REVERT: B 1208 THR cc_start: 0.3956 (OUTLIER) cc_final: 0.3542 (m) REVERT: B 1217 CYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6689 (p) REVERT: B 1219 ILE cc_start: 0.6279 (OUTLIER) cc_final: 0.6015 (mp) REVERT: B 1699 HIS cc_start: 0.4459 (OUTLIER) cc_final: 0.3798 (t70) REVERT: B 1716 LEU cc_start: 0.6607 (mt) cc_final: 0.5795 (mt) REVERT: B 1942 LEU cc_start: 0.2818 (OUTLIER) cc_final: 0.1433 (mm) REVERT: B 2008 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7893 (mp) REVERT: B 2011 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6574 (mt0) REVERT: B 2015 MET cc_start: 0.6460 (mtp) cc_final: 0.5124 (mtp) REVERT: B 2048 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5465 (pt) REVERT: B 2069 VAL cc_start: 0.8446 (t) cc_final: 0.8182 (t) REVERT: B 2121 VAL cc_start: 0.8632 (t) cc_final: 0.8230 (p) REVERT: B 2134 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.7621 (p) REVERT: B 2138 CYS cc_start: 0.7700 (m) cc_final: 0.7215 (m) REVERT: B 2140 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: B 2175 MET cc_start: 0.5513 (mtp) cc_final: 0.5161 (mtp) REVERT: B 2223 PHE cc_start: 0.2630 (OUTLIER) cc_final: 0.1936 (t80) REVERT: B 2244 SER cc_start: 0.4289 (OUTLIER) cc_final: -0.1371 (t) REVERT: B 2280 ILE cc_start: 0.2555 (OUTLIER) cc_final: 0.1406 (pt) REVERT: B 2294 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6495 (p0) REVERT: B 2364 ASN cc_start: 0.1335 (OUTLIER) cc_final: 0.0965 (p0) REVERT: B 2375 GLN cc_start: 0.2626 (OUTLIER) cc_final: -0.0092 (mp10) REVERT: B 2407 GLU cc_start: 0.3575 (OUTLIER) cc_final: 0.3104 (pt0) REVERT: B 2408 LEU cc_start: 0.1226 (OUTLIER) cc_final: 0.0223 (mt) REVERT: B 2471 LEU cc_start: 0.8819 (mt) cc_final: 0.8248 (mp) REVERT: B 2477 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7641 (mm) REVERT: B 2487 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8669 (p) REVERT: B 2502 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8113 (ttmm) REVERT: C 229 GLU cc_start: 0.0993 (OUTLIER) cc_final: 0.0167 (pt0) REVERT: C 230 SER cc_start: 0.5846 (OUTLIER) cc_final: 0.5429 (t) REVERT: D 596 ARG cc_start: 0.0234 (OUTLIER) cc_final: -0.1523 (tpt170) REVERT: D 638 MET cc_start: 0.1905 (OUTLIER) cc_final: -0.2305 (mtt) REVERT: D 768 GLU cc_start: 0.4384 (OUTLIER) cc_final: 0.1953 (pp20) REVERT: D 799 TYR cc_start: 0.1934 (OUTLIER) cc_final: 0.1492 (m-80) REVERT: D 806 LYS cc_start: 0.1511 (OUTLIER) cc_final: 0.1021 (mmmm) REVERT: D 843 ILE cc_start: -0.1384 (OUTLIER) cc_final: -0.4305 (tt) REVERT: D 853 LYS cc_start: 0.0554 (OUTLIER) cc_final: -0.0809 (mptt) REVERT: D 855 VAL cc_start: 0.2846 (OUTLIER) cc_final: 0.2560 (t) REVERT: D 978 ASP cc_start: 0.2318 (OUTLIER) cc_final: 0.0586 (t0) REVERT: D 1048 PHE cc_start: 0.4242 (OUTLIER) cc_final: 0.3714 (t80) REVERT: D 1097 THR cc_start: 0.4556 (OUTLIER) cc_final: 0.3957 (p) REVERT: D 1116 PHE cc_start: 0.3955 (OUTLIER) cc_final: 0.3023 (m-80) REVERT: D 1208 THR cc_start: 0.4227 (OUTLIER) cc_final: 0.3951 (m) REVERT: D 1217 CYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6707 (p) REVERT: D 1219 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5946 (mp) REVERT: D 1567 GLN cc_start: 0.3970 (OUTLIER) cc_final: 0.3290 (pt0) REVERT: D 1669 GLN cc_start: 0.0777 (OUTLIER) cc_final: 0.0472 (mm110) REVERT: D 1699 HIS cc_start: 0.4463 (OUTLIER) cc_final: 0.3783 (t70) REVERT: D 1716 LEU cc_start: 0.6576 (mt) cc_final: 0.5650 (mt) REVERT: D 1942 LEU cc_start: 0.2505 (OUTLIER) cc_final: 0.1358 (mm) REVERT: D 2008 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7814 (mp) REVERT: D 2011 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6253 (mt0) REVERT: D 2015 MET cc_start: 0.6578 (mtp) cc_final: 0.5304 (mtp) REVERT: D 2033 PHE cc_start: 0.6898 (t80) cc_final: 0.5926 (t80) REVERT: D 2048 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5400 (pt) REVERT: D 2069 VAL cc_start: 0.8462 (t) cc_final: 0.8218 (t) REVERT: D 2117 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6545 (mt-10) REVERT: D 2121 VAL cc_start: 0.8647 (t) cc_final: 0.8403 (p) REVERT: D 2134 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.7374 (p) REVERT: D 2138 CYS cc_start: 0.8048 (m) cc_final: 0.7514 (m) REVERT: D 2140 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: D 2149 ILE cc_start: 0.8663 (mt) cc_final: 0.8364 (mm) REVERT: D 2175 MET cc_start: 0.5515 (mtp) cc_final: 0.5292 (mtm) REVERT: D 2244 SER cc_start: 0.4458 (OUTLIER) cc_final: -0.1165 (t) REVERT: D 2294 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.5961 (p0) REVERT: D 2340 SER cc_start: 0.6552 (OUTLIER) cc_final: 0.4700 (p) REVERT: D 2364 ASN cc_start: 0.1305 (OUTLIER) cc_final: 0.0962 (p0) REVERT: D 2375 GLN cc_start: 0.2785 (OUTLIER) cc_final: 0.0049 (mp10) REVERT: D 2407 GLU cc_start: 0.3659 (OUTLIER) cc_final: 0.3199 (pt0) REVERT: D 2408 LEU cc_start: 0.1159 (OUTLIER) cc_final: 0.0515 (mt) REVERT: D 2468 PHE cc_start: 0.7023 (m-80) cc_final: 0.6064 (m-10) REVERT: D 2477 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7574 (mm) REVERT: D 2478 LEU cc_start: 0.8938 (pp) cc_final: 0.8699 (pp) REVERT: D 2502 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8000 (ttmm) REVERT: D 2511 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6246 (mm-30) REVERT: D 2521 GLU cc_start: 0.1919 (OUTLIER) cc_final: -0.1038 (tm-30) REVERT: E 229 GLU cc_start: 0.1009 (OUTLIER) cc_final: 0.0310 (pt0) REVERT: E 230 SER cc_start: 0.5612 (OUTLIER) cc_final: 0.5300 (t) REVERT: F 229 GLU cc_start: 0.1017 (OUTLIER) cc_final: 0.0273 (pt0) REVERT: F 230 SER cc_start: 0.5673 (OUTLIER) cc_final: 0.5276 (t) outliers start: 1441 outliers final: 276 residues processed: 1852 average time/residue: 0.4616 time to fit residues: 1313.8134 Evaluate side-chains 840 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 388 poor density : 452 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 0.9980 chunk 295 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 118 optimal weight: 0.0770 chunk 185 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 354 optimal weight: 50.0000 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN ** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A 934 GLN A1009 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1309 HIS A1561 HIS A1669 GLN A1699 HIS A1947 HIS ** A2034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 HIS ** A2102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 GLN A2229 GLN ** A2269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2324 HIS ** A2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2464 HIS B 697 GLN B 851 GLN B 932 HIS B 934 GLN B1009 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1298 GLN B1309 HIS B1332 ASN B1561 HIS B1669 GLN ** B1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1947 HIS B2034 GLN B2042 HIS ** B2102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2206 GLN B2229 GLN B2324 HIS ** B2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2393 GLN B2464 HIS D 697 GLN D 851 GLN D 934 GLN D1009 GLN ** D1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1222 ASN D1309 HIS D1332 ASN D1561 HIS ** D1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1947 HIS ** D2034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2042 HIS D2206 GLN D2229 GLN D2324 HIS ** D2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2464 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.094326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.078770 restraints weight = 336999.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.080498 restraints weight = 181218.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.081650 restraints weight = 114168.183| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 32357 Z= 0.226 Angle : 0.946 14.472 43878 Z= 0.485 Chirality : 0.050 0.299 5043 Planarity : 0.008 0.110 5381 Dihedral : 5.765 61.687 4251 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.92 % Favored : 90.24 % Rotamer: Outliers : 0.83 % Allowed : 5.74 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.13), residues: 3801 helix: -0.44 (0.10), residues: 2577 sheet: -5.57 (0.28), residues: 78 loop : -4.21 (0.15), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B2404 HIS 0.017 0.002 HIS D2464 PHE 0.034 0.003 PHE D2189 TYR 0.025 0.002 TYR B1307 ARG 0.010 0.001 ARG B2386 Details of bonding type rmsd hydrogen bonds : bond 0.05420 ( 1952) hydrogen bonds : angle 5.59842 ( 5745) SS BOND : bond 0.00274 ( 3) SS BOND : angle 1.30668 ( 6) covalent geometry : bond 0.00506 (32354) covalent geometry : angle 0.94564 (43872) *********************** 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 543 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 515 time to evaluate : 3.649 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: A 1219 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7088 (mp) REVERT: A 1420 LEU cc_start: 0.8809 (tp) cc_final: 0.8481 (mt) REVERT: A 1681 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8578 (pm20) REVERT: A 1694 ILE cc_start: 0.9389 (mm) cc_final: 0.9111 (mm) REVERT: A 1696 ILE cc_start: 0.9315 (mm) cc_final: 0.8647 (mm) REVERT: A 1708 LEU cc_start: 0.9269 (tt) cc_final: 0.8797 (tp) REVERT: A 1716 LEU cc_start: 0.8491 (mt) cc_final: 0.8234 (mt) REVERT: A 1717 TRP cc_start: 0.8210 (t60) cc_final: 0.7365 (t60) REVERT: A 1719 MET cc_start: 0.7749 (ttt) cc_final: 0.7224 (ttt) REVERT: A 1724 ARG cc_start: 0.9092 (pmt-80) cc_final: 0.7763 (mmm160) REVERT: A 1729 PHE cc_start: 0.8726 (t80) cc_final: 0.8225 (t80) REVERT: A 1789 GLN cc_start: 0.9162 (tp40) cc_final: 0.8874 (mm110) REVERT: A 2070 LYS cc_start: 0.9168 (ptpp) cc_final: 0.8692 (pttm) REVERT: A 2138 CYS cc_start: 0.9163 (m) cc_final: 0.8549 (m) REVERT: A 2149 ILE cc_start: 0.9621 (mm) cc_final: 0.9364 (tp) REVERT: A 2175 MET cc_start: 0.8574 (mtt) cc_final: 0.8238 (tpp) REVERT: A 2288 MET cc_start: 0.2758 (mtt) cc_final: 0.2004 (ptt) REVERT: A 2343 GLU cc_start: 0.4781 (OUTLIER) cc_final: 0.4509 (mp0) REVERT: A 2356 PHE cc_start: 0.7917 (m-10) cc_final: 0.7573 (m-10) REVERT: A 2496 GLU cc_start: 0.9167 (pt0) cc_final: 0.8429 (mt-10) REVERT: B 1420 LEU cc_start: 0.8861 (tp) cc_final: 0.8541 (mt) REVERT: B 1690 LEU cc_start: 0.9010 (tp) cc_final: 0.8789 (tt) REVERT: B 1694 ILE cc_start: 0.9374 (mm) cc_final: 0.9094 (mm) REVERT: B 1696 ILE cc_start: 0.9317 (mm) cc_final: 0.8638 (mm) REVERT: B 1716 LEU cc_start: 0.8496 (mt) cc_final: 0.8223 (mt) REVERT: B 1719 MET cc_start: 0.7772 (ttt) cc_final: 0.7294 (ttt) REVERT: B 1724 ARG cc_start: 0.8567 (ptp90) cc_final: 0.7965 (mmp80) REVERT: B 1738 GLU cc_start: 0.9385 (pt0) cc_final: 0.9021 (pt0) REVERT: B 1789 GLN cc_start: 0.9132 (tp40) cc_final: 0.8848 (mm110) REVERT: B 2070 LYS cc_start: 0.9130 (ptpp) cc_final: 0.8803 (ptpp) REVERT: B 2280 ILE cc_start: 0.2099 (OUTLIER) cc_final: 0.1663 (pt) REVERT: B 2343 GLU cc_start: 0.4717 (OUTLIER) cc_final: 0.4385 (mp0) REVERT: B 2356 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7139 (m-10) REVERT: B 2467 MET cc_start: 0.6407 (mpp) cc_final: 0.5180 (mpp) REVERT: B 2496 GLU cc_start: 0.9156 (pt0) cc_final: 0.8751 (pt0) REVERT: C 240 CYS cc_start: 0.6176 (t) cc_final: 0.5440 (t) REVERT: D 1290 VAL cc_start: 0.7155 (t) cc_final: 0.6680 (t) REVERT: D 1294 PHE cc_start: 0.8015 (m-80) cc_final: 0.7750 (m-80) REVERT: D 1420 LEU cc_start: 0.8687 (tp) cc_final: 0.8396 (mt) REVERT: D 1681 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8567 (pm20) REVERT: D 1694 ILE cc_start: 0.9378 (mm) cc_final: 0.9101 (mm) REVERT: D 1696 ILE cc_start: 0.9311 (mm) cc_final: 0.8636 (mm) REVERT: D 1716 LEU cc_start: 0.8589 (mt) cc_final: 0.8344 (mt) REVERT: D 1719 MET cc_start: 0.7821 (ttt) cc_final: 0.7392 (ttt) REVERT: D 1724 ARG cc_start: 0.9098 (pmt-80) cc_final: 0.7840 (mmm160) REVERT: D 1789 GLN cc_start: 0.9143 (tp40) cc_final: 0.8846 (mm110) REVERT: D 2033 PHE cc_start: 0.8918 (t80) cc_final: 0.8411 (t80) REVERT: D 2037 LEU cc_start: 0.9594 (mp) cc_final: 0.9349 (mp) REVERT: D 2070 LYS cc_start: 0.9190 (ptpp) cc_final: 0.8710 (pttm) REVERT: D 2138 CYS cc_start: 0.9192 (m) cc_final: 0.8740 (m) REVERT: D 2142 ILE cc_start: 0.9674 (mt) cc_final: 0.9456 (mm) REVERT: D 2149 ILE cc_start: 0.9691 (mt) cc_final: 0.9487 (tp) REVERT: D 2224 THR cc_start: 0.9060 (t) cc_final: 0.8850 (p) REVERT: D 2343 GLU cc_start: 0.4604 (OUTLIER) cc_final: 0.4288 (mp0) REVERT: D 2356 PHE cc_start: 0.7928 (m-10) cc_final: 0.7546 (m-10) REVERT: D 2496 GLU cc_start: 0.9113 (pt0) cc_final: 0.8693 (pt0) outliers start: 28 outliers final: 6 residues processed: 542 average time/residue: 0.4088 time to fit residues: 362.5159 Evaluate side-chains 388 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 374 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 364 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 251 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 337 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 158 optimal weight: 0.0570 chunk 109 optimal weight: 1.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A1052 GLN A1111 GLN ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN ** A2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2364 ASN ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN B1052 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 ASN B1298 GLN B1353 GLN B1567 GLN B2102 ASN B2306 ASN B2364 ASN ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN D1052 GLN D1111 GLN ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1353 GLN D1567 GLN D2042 HIS D2102 ASN D2306 ASN D2364 ASN ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.093995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.079156 restraints weight = 337933.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.080653 restraints weight = 187537.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.081418 restraints weight = 125743.086| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.7447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32357 Z= 0.161 Angle : 0.786 11.575 43878 Z= 0.401 Chirality : 0.045 0.266 5043 Planarity : 0.006 0.105 5381 Dihedral : 5.439 50.071 4251 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.84 % Favored : 91.53 % Rotamer: Outliers : 0.56 % Allowed : 6.13 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3801 helix: 0.27 (0.10), residues: 2565 sheet: -4.84 (0.32), residues: 108 loop : -4.05 (0.15), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A2066 HIS 0.011 0.001 HIS D1030 PHE 0.033 0.002 PHE D 783 TYR 0.035 0.002 TYR B1692 ARG 0.013 0.001 ARG B1547 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 1952) hydrogen bonds : angle 4.98164 ( 5745) SS BOND : bond 0.00256 ( 3) SS BOND : angle 1.11932 ( 6) covalent geometry : bond 0.00363 (32354) covalent geometry : angle 0.78601 (43872) *********************** 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 510 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 491 time to evaluate : 3.760 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: A 1694 ILE cc_start: 0.9344 (mm) cc_final: 0.9080 (mm) REVERT: A 1696 ILE cc_start: 0.9237 (mm) cc_final: 0.8696 (mm) REVERT: A 1710 LEU cc_start: 0.9483 (mt) cc_final: 0.9156 (mt) REVERT: A 1717 TRP cc_start: 0.8074 (t60) cc_final: 0.7229 (t60) REVERT: A 1719 MET cc_start: 0.8001 (ttt) cc_final: 0.7566 (ttt) REVERT: A 1724 ARG cc_start: 0.9142 (pmt-80) cc_final: 0.7884 (mmm160) REVERT: A 1729 PHE cc_start: 0.8704 (t80) cc_final: 0.8050 (t80) REVERT: A 1736 PHE cc_start: 0.9214 (t80) cc_final: 0.8464 (t80) REVERT: A 1789 GLN cc_start: 0.9234 (tp40) cc_final: 0.8876 (mm110) REVERT: A 1964 MET cc_start: 0.9117 (mtp) cc_final: 0.8585 (mmm) REVERT: A 1968 ASP cc_start: 0.9112 (t0) cc_final: 0.8685 (t0) REVERT: A 2007 MET cc_start: 0.9207 (mmp) cc_final: 0.8877 (mmm) REVERT: A 2012 PHE cc_start: 0.9172 (t80) cc_final: 0.8949 (t80) REVERT: A 2015 MET cc_start: 0.9174 (mmt) cc_final: 0.8906 (mmt) REVERT: A 2033 PHE cc_start: 0.8760 (t80) cc_final: 0.8489 (t80) REVERT: A 2037 LEU cc_start: 0.9491 (mt) cc_final: 0.9289 (mt) REVERT: A 2070 LYS cc_start: 0.9114 (ptpp) cc_final: 0.8859 (pttm) REVERT: A 2076 LEU cc_start: 0.9437 (mt) cc_final: 0.9095 (mt) REVERT: A 2117 GLU cc_start: 0.8691 (mp0) cc_final: 0.8221 (mm-30) REVERT: A 2149 ILE cc_start: 0.9654 (mm) cc_final: 0.9377 (tp) REVERT: A 2175 MET cc_start: 0.8621 (mtt) cc_final: 0.8232 (tpp) REVERT: A 2288 MET cc_start: 0.2515 (mtt) cc_final: 0.1895 (ptt) REVERT: A 2356 PHE cc_start: 0.8109 (m-10) cc_final: 0.7599 (m-10) REVERT: A 2467 MET cc_start: 0.6976 (ptp) cc_final: 0.6317 (ttp) REVERT: A 2496 GLU cc_start: 0.9290 (pt0) cc_final: 0.8602 (mt-10) REVERT: B 711 MET cc_start: 0.8011 (mmp) cc_final: 0.7773 (mmm) REVERT: B 1690 LEU cc_start: 0.8953 (tp) cc_final: 0.8744 (tt) REVERT: B 1694 ILE cc_start: 0.9320 (mm) cc_final: 0.9030 (mm) REVERT: B 1696 ILE cc_start: 0.9158 (mm) cc_final: 0.8637 (mm) REVERT: B 1708 LEU cc_start: 0.9140 (tt) cc_final: 0.8758 (tp) REVERT: B 1719 MET cc_start: 0.8062 (ttt) cc_final: 0.7590 (ttt) REVERT: B 1789 GLN cc_start: 0.9305 (tp40) cc_final: 0.8900 (mm110) REVERT: B 1964 MET cc_start: 0.9113 (mtp) cc_final: 0.8640 (mmm) REVERT: B 2070 LYS cc_start: 0.9079 (ptpp) cc_final: 0.8864 (pttm) REVERT: B 2076 LEU cc_start: 0.9439 (mt) cc_final: 0.9120 (mt) REVERT: B 2225 MET cc_start: 0.5484 (mtm) cc_final: 0.5120 (mtt) REVERT: B 2356 PHE cc_start: 0.7950 (m-10) cc_final: 0.7634 (m-10) REVERT: B 2496 GLU cc_start: 0.9331 (pt0) cc_final: 0.8964 (pt0) REVERT: B 2506 LEU cc_start: 0.9532 (mm) cc_final: 0.9016 (mm) REVERT: B 2513 MET cc_start: 0.9237 (mmm) cc_final: 0.8987 (mmm) REVERT: C 240 CYS cc_start: 0.6034 (t) cc_final: 0.5712 (t) REVERT: D 1420 LEU cc_start: 0.8689 (tp) cc_final: 0.8466 (mt) REVERT: D 1422 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6956 (tp30) REVERT: D 1694 ILE cc_start: 0.9336 (mm) cc_final: 0.9088 (mm) REVERT: D 1696 ILE cc_start: 0.9166 (mm) cc_final: 0.8654 (mm) REVERT: D 1708 LEU cc_start: 0.9144 (tt) cc_final: 0.8753 (tp) REVERT: D 1710 LEU cc_start: 0.9479 (mt) cc_final: 0.9157 (mt) REVERT: D 1716 LEU cc_start: 0.8494 (mt) cc_final: 0.8241 (mp) REVERT: D 1719 MET cc_start: 0.8026 (ttt) cc_final: 0.7552 (ttt) REVERT: D 1724 ARG cc_start: 0.9183 (pmt-80) cc_final: 0.7972 (mmm160) REVERT: D 1736 PHE cc_start: 0.9165 (t80) cc_final: 0.8444 (t80) REVERT: D 1789 GLN cc_start: 0.9295 (tp40) cc_final: 0.8915 (mm110) REVERT: D 1964 MET cc_start: 0.9122 (mtp) cc_final: 0.8651 (mmm) REVERT: D 1968 ASP cc_start: 0.9107 (t0) cc_final: 0.8632 (t0) REVERT: D 2007 MET cc_start: 0.9176 (mmp) cc_final: 0.8902 (mmm) REVERT: D 2015 MET cc_start: 0.9173 (mmt) cc_final: 0.8914 (mmt) REVERT: D 2033 PHE cc_start: 0.8937 (t80) cc_final: 0.8382 (t80) REVERT: D 2037 LEU cc_start: 0.9527 (mp) cc_final: 0.9254 (mp) REVERT: D 2070 LYS cc_start: 0.9106 (ptpp) cc_final: 0.8886 (pttm) REVERT: D 2076 LEU cc_start: 0.9464 (mt) cc_final: 0.9148 (mt) REVERT: D 2117 GLU cc_start: 0.8643 (mp0) cc_final: 0.8245 (mm-30) REVERT: D 2149 ILE cc_start: 0.9711 (mt) cc_final: 0.9439 (tp) REVERT: D 2225 MET cc_start: 0.3930 (mpp) cc_final: 0.3682 (mpp) REVERT: D 2356 PHE cc_start: 0.7954 (m-10) cc_final: 0.7716 (m-10) REVERT: D 2467 MET cc_start: 0.5968 (pmm) cc_final: 0.4855 (pmm) REVERT: D 2468 PHE cc_start: 0.8238 (m-10) cc_final: 0.6983 (m-10) REVERT: D 2496 GLU cc_start: 0.9312 (pt0) cc_final: 0.8863 (pt0) outliers start: 19 outliers final: 1 residues processed: 510 average time/residue: 0.4467 time to fit residues: 374.3963 Evaluate side-chains 364 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 362 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 42 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 370 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 273 optimal weight: 30.0000 chunk 101 optimal weight: 0.0270 chunk 123 optimal weight: 1.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A1005 ASN A1111 GLN ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1353 GLN A1567 GLN ** A2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2102 ASN A2306 ASN ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN B1005 ASN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2206 GLN ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2377 ASN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN D1111 GLN D1353 GLN ** D2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2377 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.093476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.078461 restraints weight = 336936.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.079889 restraints weight = 189863.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.081009 restraints weight = 123988.832| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.7966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 32357 Z= 0.148 Angle : 0.747 11.423 43878 Z= 0.377 Chirality : 0.044 0.274 5043 Planarity : 0.006 0.107 5381 Dihedral : 5.248 42.771 4251 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.13 % Favored : 92.29 % Rotamer: Outliers : 0.27 % Allowed : 4.32 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3801 helix: 0.53 (0.10), residues: 2574 sheet: -4.45 (0.33), residues: 108 loop : -3.87 (0.15), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B1215 HIS 0.008 0.001 HIS D1030 PHE 0.044 0.002 PHE A2356 TYR 0.067 0.001 TYR D2507 ARG 0.007 0.001 ARG D1164 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 1952) hydrogen bonds : angle 4.74557 ( 5745) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.98000 ( 6) covalent geometry : bond 0.00331 (32354) covalent geometry : angle 0.74648 (43872) *********************** 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 478 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 469 time to evaluate : 4.198 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 1694 ILE cc_start: 0.9350 (mm) cc_final: 0.9115 (mm) REVERT: A 1696 ILE cc_start: 0.9206 (mm) cc_final: 0.8681 (mm) REVERT: A 1710 LEU cc_start: 0.9512 (mt) cc_final: 0.9176 (mt) REVERT: A 1716 LEU cc_start: 0.8477 (mp) cc_final: 0.8260 (mp) REVERT: A 1719 MET cc_start: 0.8123 (ttt) cc_final: 0.7504 (ttt) REVERT: A 1724 ARG cc_start: 0.9041 (pmt-80) cc_final: 0.7857 (mmm160) REVERT: A 1736 PHE cc_start: 0.9182 (t80) cc_final: 0.8555 (t80) REVERT: A 1789 GLN cc_start: 0.9288 (tp40) cc_final: 0.8916 (mm110) REVERT: A 1964 MET cc_start: 0.9033 (mtp) cc_final: 0.8554 (mmm) REVERT: A 1968 ASP cc_start: 0.9146 (t0) cc_final: 0.8614 (t0) REVERT: A 2007 MET cc_start: 0.9148 (mmp) cc_final: 0.8838 (mmm) REVERT: A 2033 PHE cc_start: 0.8838 (t80) cc_final: 0.8622 (t80) REVERT: A 2076 LEU cc_start: 0.9465 (mt) cc_final: 0.9108 (mt) REVERT: A 2117 GLU cc_start: 0.8822 (mp0) cc_final: 0.8370 (mm-30) REVERT: A 2133 LEU cc_start: 0.9458 (tp) cc_final: 0.9230 (tp) REVERT: A 2149 ILE cc_start: 0.9629 (mm) cc_final: 0.9360 (tp) REVERT: A 2175 MET cc_start: 0.8518 (mtm) cc_final: 0.8119 (tpp) REVERT: A 2288 MET cc_start: 0.2476 (mtt) cc_final: 0.2032 (ptt) REVERT: A 2356 PHE cc_start: 0.7879 (m-10) cc_final: 0.7403 (m-10) REVERT: A 2466 ILE cc_start: 0.9446 (pt) cc_final: 0.9085 (pt) REVERT: A 2496 GLU cc_start: 0.9289 (pt0) cc_final: 0.8670 (mt-10) REVERT: B 1690 LEU cc_start: 0.8977 (tp) cc_final: 0.8725 (tp) REVERT: B 1694 ILE cc_start: 0.9338 (mm) cc_final: 0.8912 (mm) REVERT: B 1696 ILE cc_start: 0.9219 (mm) cc_final: 0.8763 (mm) REVERT: B 1710 LEU cc_start: 0.9504 (mt) cc_final: 0.9235 (mt) REVERT: B 1719 MET cc_start: 0.8123 (ttt) cc_final: 0.7584 (ttt) REVERT: B 1736 PHE cc_start: 0.9248 (t80) cc_final: 0.8537 (t80) REVERT: B 1789 GLN cc_start: 0.9320 (tp40) cc_final: 0.8933 (tp40) REVERT: B 1964 MET cc_start: 0.9039 (mtp) cc_final: 0.8561 (mmm) REVERT: B 2007 MET cc_start: 0.9169 (mmp) cc_final: 0.8896 (mmm) REVERT: B 2012 PHE cc_start: 0.9218 (t80) cc_final: 0.8992 (t80) REVERT: B 2015 MET cc_start: 0.9101 (mmt) cc_final: 0.8784 (mmt) REVERT: B 2076 LEU cc_start: 0.9463 (mt) cc_final: 0.9146 (mt) REVERT: B 2138 CYS cc_start: 0.9534 (m) cc_final: 0.9287 (t) REVERT: B 2356 PHE cc_start: 0.7888 (m-10) cc_final: 0.7092 (m-10) REVERT: B 2467 MET cc_start: 0.9284 (tmm) cc_final: 0.9002 (tmm) REVERT: B 2479 LYS cc_start: 0.9627 (pptt) cc_final: 0.9245 (ptpp) REVERT: B 2496 GLU cc_start: 0.9360 (pt0) cc_final: 0.8842 (mt-10) REVERT: B 2506 LEU cc_start: 0.9537 (mm) cc_final: 0.9150 (mm) REVERT: B 2513 MET cc_start: 0.9289 (mmm) cc_final: 0.9033 (mmm) REVERT: C 240 CYS cc_start: 0.6030 (t) cc_final: 0.5414 (p) REVERT: D 711 MET cc_start: 0.8497 (mmp) cc_final: 0.8188 (mmm) REVERT: D 1420 LEU cc_start: 0.8625 (tp) cc_final: 0.8386 (mt) REVERT: D 1694 ILE cc_start: 0.9336 (mm) cc_final: 0.8988 (mm) REVERT: D 1696 ILE cc_start: 0.9221 (mm) cc_final: 0.8763 (mm) REVERT: D 1710 LEU cc_start: 0.9498 (mt) cc_final: 0.9193 (mt) REVERT: D 1719 MET cc_start: 0.8120 (ttt) cc_final: 0.7412 (ttt) REVERT: D 1724 ARG cc_start: 0.9110 (pmt-80) cc_final: 0.7948 (mmm160) REVERT: D 1736 PHE cc_start: 0.9213 (t80) cc_final: 0.8602 (t80) REVERT: D 1789 GLN cc_start: 0.9324 (tp40) cc_final: 0.8988 (tp40) REVERT: D 1964 MET cc_start: 0.9057 (mtp) cc_final: 0.8588 (mmm) REVERT: D 1968 ASP cc_start: 0.9162 (t0) cc_final: 0.8533 (t0) REVERT: D 2007 MET cc_start: 0.9170 (mmp) cc_final: 0.8903 (mmm) REVERT: D 2015 MET cc_start: 0.9054 (mmt) cc_final: 0.8851 (mmt) REVERT: D 2033 PHE cc_start: 0.8944 (t80) cc_final: 0.8482 (t80) REVERT: D 2037 LEU cc_start: 0.9500 (mp) cc_final: 0.9154 (mp) REVERT: D 2076 LEU cc_start: 0.9476 (mt) cc_final: 0.9150 (mt) REVERT: D 2117 GLU cc_start: 0.8811 (mp0) cc_final: 0.8257 (mm-30) REVERT: D 2133 LEU cc_start: 0.9379 (tp) cc_final: 0.9113 (tp) REVERT: D 2137 MET cc_start: 0.9089 (mtm) cc_final: 0.8770 (mtm) REVERT: D 2149 ILE cc_start: 0.9710 (mt) cc_final: 0.9449 (tp) REVERT: D 2356 PHE cc_start: 0.7927 (m-10) cc_final: 0.7267 (m-10) REVERT: D 2467 MET cc_start: 0.6220 (pmm) cc_final: 0.5644 (pmm) REVERT: D 2468 PHE cc_start: 0.8358 (m-10) cc_final: 0.7669 (m-10) REVERT: D 2496 GLU cc_start: 0.9314 (pt0) cc_final: 0.8738 (mt-10) outliers start: 9 outliers final: 0 residues processed: 478 average time/residue: 0.4075 time to fit residues: 321.8048 Evaluate side-chains 351 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 364 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 1 optimal weight: 40.0000 chunk 365 optimal weight: 0.0770 chunk 352 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 chunk 299 optimal weight: 6.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 HIS A2206 GLN ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2042 HIS ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1353 GLN ** D2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2206 GLN ** D2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 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 = 0.4206 r_free = 0.4206 target = 0.093041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.078152 restraints weight = 336809.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.080154 restraints weight = 178756.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.080624 restraints weight = 104322.363| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.8350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 32357 Z= 0.137 Angle : 0.728 11.818 43878 Z= 0.363 Chirality : 0.043 0.213 5043 Planarity : 0.006 0.110 5381 Dihedral : 5.091 36.817 4251 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.34 % Favored : 92.03 % Rotamer: Outliers : 0.18 % Allowed : 3.55 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3801 helix: 0.62 (0.10), residues: 2601 sheet: -4.59 (0.26), residues: 165 loop : -3.65 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A2305 HIS 0.009 0.001 HIS D1030 PHE 0.042 0.002 PHE D2356 TYR 0.035 0.001 TYR D1692 ARG 0.007 0.000 ARG A 703 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1952) hydrogen bonds : angle 4.57357 ( 5745) SS BOND : bond 0.00072 ( 3) SS BOND : angle 0.82674 ( 6) covalent geometry : bond 0.00315 (32354) covalent geometry : angle 0.72753 (43872) *********************** 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 473 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 467 time to evaluate : 4.028 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 1694 ILE cc_start: 0.9336 (mm) cc_final: 0.8982 (mm) REVERT: A 1696 ILE cc_start: 0.9179 (mm) cc_final: 0.8695 (mm) REVERT: A 1710 LEU cc_start: 0.9502 (mt) cc_final: 0.9210 (mt) REVERT: A 1719 MET cc_start: 0.8136 (ttt) cc_final: 0.7461 (ttt) REVERT: A 1724 ARG cc_start: 0.8965 (pmt-80) cc_final: 0.7850 (mmm160) REVERT: A 1736 PHE cc_start: 0.9142 (t80) cc_final: 0.8568 (t80) REVERT: A 1789 GLN cc_start: 0.9264 (tp40) cc_final: 0.8925 (tp40) REVERT: A 1964 MET cc_start: 0.8932 (mtp) cc_final: 0.8433 (mmm) REVERT: A 2007 MET cc_start: 0.9092 (mmp) cc_final: 0.8786 (mmm) REVERT: A 2047 PHE cc_start: 0.8673 (t80) cc_final: 0.8291 (t80) REVERT: A 2076 LEU cc_start: 0.9475 (mt) cc_final: 0.9143 (mt) REVERT: A 2117 GLU cc_start: 0.8864 (mp0) cc_final: 0.8463 (mm-30) REVERT: A 2123 ASP cc_start: 0.9240 (m-30) cc_final: 0.8654 (m-30) REVERT: A 2137 MET cc_start: 0.9023 (mtm) cc_final: 0.8662 (mtp) REVERT: A 2175 MET cc_start: 0.8468 (mtm) cc_final: 0.8109 (tpp) REVERT: A 2356 PHE cc_start: 0.7902 (m-10) cc_final: 0.7493 (m-10) REVERT: A 2466 ILE cc_start: 0.9369 (pt) cc_final: 0.8927 (pt) REVERT: A 2496 GLU cc_start: 0.9391 (tt0) cc_final: 0.8869 (mt-10) REVERT: B 711 MET cc_start: 0.8154 (mmp) cc_final: 0.7898 (mmm) REVERT: B 1690 LEU cc_start: 0.8978 (tp) cc_final: 0.8717 (tp) REVERT: B 1694 ILE cc_start: 0.9355 (mm) cc_final: 0.8924 (mm) REVERT: B 1710 LEU cc_start: 0.9490 (mt) cc_final: 0.9189 (mt) REVERT: B 1719 MET cc_start: 0.8127 (ttt) cc_final: 0.7609 (ttt) REVERT: B 1736 PHE cc_start: 0.9255 (t80) cc_final: 0.8616 (t80) REVERT: B 1789 GLN cc_start: 0.9273 (tp40) cc_final: 0.8883 (tp40) REVERT: B 1964 MET cc_start: 0.8972 (mtp) cc_final: 0.8496 (mmm) REVERT: B 1968 ASP cc_start: 0.9175 (t70) cc_final: 0.8762 (t0) REVERT: B 2007 MET cc_start: 0.9118 (mmp) cc_final: 0.8864 (mmm) REVERT: B 2047 PHE cc_start: 0.8677 (t80) cc_final: 0.8292 (t80) REVERT: B 2068 PHE cc_start: 0.8434 (m-10) cc_final: 0.8232 (m-10) REVERT: B 2076 LEU cc_start: 0.9436 (mt) cc_final: 0.9105 (mt) REVERT: B 2288 MET cc_start: 0.1587 (mtt) cc_final: 0.0902 (ptt) REVERT: B 2496 GLU cc_start: 0.9352 (pt0) cc_final: 0.9053 (pt0) REVERT: B 2506 LEU cc_start: 0.9535 (mm) cc_final: 0.9131 (mm) REVERT: C 240 CYS cc_start: 0.6128 (t) cc_final: 0.5328 (p) REVERT: D 711 MET cc_start: 0.8504 (mmp) cc_final: 0.8286 (mmm) REVERT: D 1420 LEU cc_start: 0.8638 (tp) cc_final: 0.8385 (mt) REVERT: D 1694 ILE cc_start: 0.9349 (mm) cc_final: 0.9013 (mm) REVERT: D 1696 ILE cc_start: 0.9182 (mm) cc_final: 0.8711 (mm) REVERT: D 1710 LEU cc_start: 0.9505 (mt) cc_final: 0.9248 (mt) REVERT: D 1719 MET cc_start: 0.8180 (ttt) cc_final: 0.7649 (ttt) REVERT: D 1724 ARG cc_start: 0.9117 (pmt-80) cc_final: 0.7975 (mmm160) REVERT: D 1736 PHE cc_start: 0.9179 (t80) cc_final: 0.8636 (t80) REVERT: D 1789 GLN cc_start: 0.9323 (tp40) cc_final: 0.9011 (tp40) REVERT: D 1964 MET cc_start: 0.8964 (mtp) cc_final: 0.8512 (mmm) REVERT: D 2007 MET cc_start: 0.9129 (mmp) cc_final: 0.8868 (mmm) REVERT: D 2033 PHE cc_start: 0.8873 (t80) cc_final: 0.8565 (t80) REVERT: D 2047 PHE cc_start: 0.8654 (t80) cc_final: 0.8275 (t80) REVERT: D 2076 LEU cc_start: 0.9449 (mt) cc_final: 0.9103 (mt) REVERT: D 2117 GLU cc_start: 0.8830 (mp0) cc_final: 0.8356 (mm-30) REVERT: D 2123 ASP cc_start: 0.9448 (m-30) cc_final: 0.8793 (m-30) REVERT: D 2137 MET cc_start: 0.9130 (mtm) cc_final: 0.8753 (ttt) REVERT: D 2149 ILE cc_start: 0.9741 (mt) cc_final: 0.9476 (tp) REVERT: D 2356 PHE cc_start: 0.7701 (m-10) cc_final: 0.7487 (m-10) REVERT: D 2467 MET cc_start: 0.6339 (pmm) cc_final: 0.5872 (pmm) REVERT: D 2468 PHE cc_start: 0.8368 (m-10) cc_final: 0.7729 (m-10) REVERT: D 2496 GLU cc_start: 0.9297 (pt0) cc_final: 0.8956 (pt0) outliers start: 6 outliers final: 0 residues processed: 473 average time/residue: 0.4425 time to fit residues: 351.1891 Evaluate side-chains 334 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 270 optimal weight: 6.9990 chunk 262 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 250 optimal weight: 0.0060 chunk 359 optimal weight: 0.3980 chunk 331 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 336 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 overall best weight: 2.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A1112 GLN A1409 HIS A2034 GLN A2060 ASN ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2364 ASN ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN B 932 HIS ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1699 HIS B2060 ASN B2364 ASN ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1353 GLN D2034 GLN D2042 HIS D2060 ASN ** D2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2364 ASN ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.089425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.074464 restraints weight = 342969.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.075396 restraints weight = 201922.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.075546 restraints weight = 121934.958| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.8880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32357 Z= 0.174 Angle : 0.733 9.010 43878 Z= 0.375 Chirality : 0.043 0.253 5043 Planarity : 0.006 0.114 5381 Dihedral : 5.015 29.779 4251 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.60 % Favored : 91.82 % Rotamer: Outliers : 0.15 % Allowed : 3.76 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3801 helix: 0.62 (0.10), residues: 2589 sheet: -4.40 (0.26), residues: 183 loop : -3.37 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B2305 HIS 0.007 0.001 HIS D1030 PHE 0.035 0.002 PHE B2033 TYR 0.053 0.002 TYR D2507 ARG 0.013 0.001 ARG D1547 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 1952) hydrogen bonds : angle 4.60342 ( 5745) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.82387 ( 6) covalent geometry : bond 0.00383 (32354) covalent geometry : angle 0.73318 (43872) *********************** 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 438 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 433 time to evaluate : 3.828 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: A 1694 ILE cc_start: 0.9417 (mm) cc_final: 0.8958 (mm) REVERT: A 1710 LEU cc_start: 0.9496 (mt) cc_final: 0.9146 (mt) REVERT: A 1719 MET cc_start: 0.8317 (ttt) cc_final: 0.8003 (ttt) REVERT: A 1724 ARG cc_start: 0.9048 (pmt-80) cc_final: 0.7983 (mmm160) REVERT: A 1736 PHE cc_start: 0.9039 (t80) cc_final: 0.8619 (t80) REVERT: A 1964 MET cc_start: 0.9020 (mtp) cc_final: 0.8608 (mmm) REVERT: A 1966 LEU cc_start: 0.9163 (mm) cc_final: 0.8512 (tt) REVERT: A 2007 MET cc_start: 0.9128 (mmp) cc_final: 0.8797 (mmm) REVERT: A 2018 ASP cc_start: 0.8979 (m-30) cc_final: 0.8758 (m-30) REVERT: A 2033 PHE cc_start: 0.8830 (t80) cc_final: 0.8249 (t80) REVERT: A 2037 LEU cc_start: 0.9436 (mt) cc_final: 0.8639 (mt) REVERT: A 2047 PHE cc_start: 0.8809 (t80) cc_final: 0.8369 (t80) REVERT: A 2068 PHE cc_start: 0.8571 (m-10) cc_final: 0.8336 (m-10) REVERT: A 2076 LEU cc_start: 0.9534 (mt) cc_final: 0.9220 (mt) REVERT: A 2117 GLU cc_start: 0.9027 (mp0) cc_final: 0.8502 (mp0) REVERT: A 2137 MET cc_start: 0.8976 (mtm) cc_final: 0.8505 (mtp) REVERT: A 2175 MET cc_start: 0.8662 (mtm) cc_final: 0.8205 (mpp) REVERT: A 2181 LEU cc_start: 0.9379 (mm) cc_final: 0.9061 (pp) REVERT: A 2182 PHE cc_start: 0.9537 (t80) cc_final: 0.9315 (t80) REVERT: A 2356 PHE cc_start: 0.8032 (m-10) cc_final: 0.7685 (m-10) REVERT: A 2420 MET cc_start: 0.6272 (mmt) cc_final: 0.5241 (mmt) REVERT: A 2467 MET cc_start: 0.7229 (ptp) cc_final: 0.6476 (ptp) REVERT: A 2496 GLU cc_start: 0.9346 (tt0) cc_final: 0.8336 (tp30) REVERT: A 2506 LEU cc_start: 0.9632 (mm) cc_final: 0.9290 (mm) REVERT: B 711 MET cc_start: 0.8227 (mmp) cc_final: 0.7981 (mmm) REVERT: B 1290 VAL cc_start: 0.7435 (t) cc_final: 0.6952 (t) REVERT: B 1291 CYS cc_start: 0.8074 (t) cc_final: 0.7873 (t) REVERT: B 1690 LEU cc_start: 0.9071 (tp) cc_final: 0.8851 (tp) REVERT: B 1694 ILE cc_start: 0.9442 (mm) cc_final: 0.8986 (mm) REVERT: B 1710 LEU cc_start: 0.9574 (mt) cc_final: 0.9240 (mt) REVERT: B 1719 MET cc_start: 0.8314 (ttt) cc_final: 0.7891 (ttt) REVERT: B 1736 PHE cc_start: 0.9235 (t80) cc_final: 0.8623 (t80) REVERT: B 1789 GLN cc_start: 0.9116 (tp40) cc_final: 0.8802 (tp-100) REVERT: B 2047 PHE cc_start: 0.8772 (t80) cc_final: 0.8371 (t80) REVERT: B 2356 PHE cc_start: 0.8091 (m-10) cc_final: 0.7824 (m-80) REVERT: B 2467 MET cc_start: 0.9451 (tmm) cc_final: 0.9198 (tmm) REVERT: B 2496 GLU cc_start: 0.9299 (pt0) cc_final: 0.8338 (tt0) REVERT: B 2506 LEU cc_start: 0.9664 (mm) cc_final: 0.9360 (mm) REVERT: B 2513 MET cc_start: 0.9490 (mmm) cc_final: 0.9261 (mmm) REVERT: C 240 CYS cc_start: 0.6572 (t) cc_final: 0.5705 (p) REVERT: D 711 MET cc_start: 0.8480 (mmp) cc_final: 0.8247 (mmm) REVERT: D 831 MET cc_start: 0.3745 (ptp) cc_final: 0.3535 (mtm) REVERT: D 1420 LEU cc_start: 0.8706 (tp) cc_final: 0.8504 (mt) REVERT: D 1690 LEU cc_start: 0.9198 (tt) cc_final: 0.8921 (pp) REVERT: D 1694 ILE cc_start: 0.9422 (mm) cc_final: 0.9032 (mm) REVERT: D 1719 MET cc_start: 0.8394 (ttt) cc_final: 0.8016 (ttt) REVERT: D 1724 ARG cc_start: 0.9125 (pmt-80) cc_final: 0.8071 (mmm160) REVERT: D 2007 MET cc_start: 0.9194 (mmp) cc_final: 0.8877 (mmm) REVERT: D 2033 PHE cc_start: 0.8832 (t80) cc_final: 0.8311 (t80) REVERT: D 2037 LEU cc_start: 0.9522 (mp) cc_final: 0.9021 (mp) REVERT: D 2047 PHE cc_start: 0.8802 (t80) cc_final: 0.8393 (t80) REVERT: D 2068 PHE cc_start: 0.8590 (m-10) cc_final: 0.8372 (m-10) REVERT: D 2070 LYS cc_start: 0.9161 (ptpp) cc_final: 0.8734 (ptpp) REVERT: D 2117 GLU cc_start: 0.9064 (mp0) cc_final: 0.8544 (mm-30) REVERT: D 2137 MET cc_start: 0.9189 (mtm) cc_final: 0.8689 (ttt) REVERT: D 2140 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8726 (mm-30) REVERT: D 2149 ILE cc_start: 0.9765 (mt) cc_final: 0.9509 (tp) REVERT: D 2356 PHE cc_start: 0.8152 (m-10) cc_final: 0.7853 (m-10) REVERT: D 2467 MET cc_start: 0.7044 (pmm) cc_final: 0.6392 (pmm) REVERT: D 2468 PHE cc_start: 0.8597 (m-10) cc_final: 0.7905 (m-10) REVERT: D 2496 GLU cc_start: 0.9222 (pt0) cc_final: 0.8330 (tt0) outliers start: 5 outliers final: 0 residues processed: 438 average time/residue: 0.3960 time to fit residues: 289.2469 Evaluate side-chains 318 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 100 optimal weight: 0.0060 chunk 67 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A1699 HIS A1789 GLN A2042 HIS ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 ASN B1699 HIS B2042 HIS ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1699 HIS D1951 HIS ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.090057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.075721 restraints weight = 342877.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.076077 restraints weight = 203003.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.076639 restraints weight = 124272.601| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.9183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 32357 Z= 0.142 Angle : 0.721 9.347 43878 Z= 0.364 Chirality : 0.042 0.196 5043 Planarity : 0.006 0.115 5381 Dihedral : 4.914 25.616 4251 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.68 % Favored : 91.74 % Rotamer: Outliers : 0.12 % Allowed : 2.64 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3801 helix: 0.79 (0.10), residues: 2583 sheet: -4.13 (0.28), residues: 183 loop : -3.25 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1215 HIS 0.008 0.001 HIS D1030 PHE 0.037 0.002 PHE A2356 TYR 0.027 0.001 TYR D1692 ARG 0.010 0.000 ARG A 703 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1952) hydrogen bonds : angle 4.47399 ( 5745) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.78997 ( 6) covalent geometry : bond 0.00324 (32354) covalent geometry : angle 0.72095 (43872) *********************** 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 442 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 438 time to evaluate : 3.753 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: A 1694 ILE cc_start: 0.9194 (mm) cc_final: 0.8960 (mm) REVERT: A 1719 MET cc_start: 0.8445 (ttt) cc_final: 0.7949 (ttt) REVERT: A 1724 ARG cc_start: 0.9060 (pmt-80) cc_final: 0.8066 (mmm160) REVERT: A 1964 MET cc_start: 0.8879 (mtp) cc_final: 0.8425 (mmm) REVERT: A 1966 LEU cc_start: 0.9104 (mm) cc_final: 0.8414 (tt) REVERT: A 2007 MET cc_start: 0.9102 (mmp) cc_final: 0.8803 (mmm) REVERT: A 2018 ASP cc_start: 0.9039 (m-30) cc_final: 0.8796 (m-30) REVERT: A 2033 PHE cc_start: 0.8899 (t80) cc_final: 0.8345 (t80) REVERT: A 2037 LEU cc_start: 0.9335 (mt) cc_final: 0.8645 (mt) REVERT: A 2047 PHE cc_start: 0.8730 (t80) cc_final: 0.8347 (t80) REVERT: A 2076 LEU cc_start: 0.9473 (mt) cc_final: 0.9151 (mt) REVERT: A 2095 THR cc_start: 0.8602 (p) cc_final: 0.8386 (t) REVERT: A 2117 GLU cc_start: 0.9068 (mp0) cc_final: 0.8518 (mp0) REVERT: A 2118 LEU cc_start: 0.9561 (pp) cc_final: 0.9340 (pp) REVERT: A 2123 ASP cc_start: 0.9491 (m-30) cc_final: 0.8809 (m-30) REVERT: A 2137 MET cc_start: 0.9140 (mtm) cc_final: 0.8671 (mtp) REVERT: A 2138 CYS cc_start: 0.9530 (m) cc_final: 0.9297 (t) REVERT: A 2175 MET cc_start: 0.8566 (mtm) cc_final: 0.8132 (mmp) REVERT: A 2181 LEU cc_start: 0.9385 (mm) cc_final: 0.9123 (pp) REVERT: A 2182 PHE cc_start: 0.9528 (t80) cc_final: 0.9300 (t80) REVERT: A 2420 MET cc_start: 0.5643 (mmt) cc_final: 0.5381 (mmt) REVERT: A 2496 GLU cc_start: 0.9304 (tt0) cc_final: 0.8898 (mt-10) REVERT: A 2499 LEU cc_start: 0.9768 (tt) cc_final: 0.9511 (tp) REVERT: A 2506 LEU cc_start: 0.9508 (mm) cc_final: 0.9194 (mm) REVERT: A 2513 MET cc_start: 0.9315 (mmt) cc_final: 0.8926 (mmt) REVERT: B 711 MET cc_start: 0.7932 (mmp) cc_final: 0.7629 (mmm) REVERT: B 1166 LEU cc_start: 0.6386 (tt) cc_final: 0.6112 (tt) REVERT: B 1690 LEU cc_start: 0.9036 (tp) cc_final: 0.8797 (tt) REVERT: B 1694 ILE cc_start: 0.9408 (mm) cc_final: 0.9113 (mm) REVERT: B 1710 LEU cc_start: 0.9598 (mt) cc_final: 0.9254 (mt) REVERT: B 1719 MET cc_start: 0.8397 (ttt) cc_final: 0.7852 (ttt) REVERT: B 1736 PHE cc_start: 0.9214 (t80) cc_final: 0.8597 (t80) REVERT: B 1964 MET cc_start: 0.9015 (mtp) cc_final: 0.8672 (mmm) REVERT: B 1966 LEU cc_start: 0.9080 (mm) cc_final: 0.8374 (tt) REVERT: B 2007 MET cc_start: 0.9151 (mmp) cc_final: 0.8866 (mmm) REVERT: B 2033 PHE cc_start: 0.8984 (t80) cc_final: 0.8663 (t80) REVERT: B 2037 LEU cc_start: 0.9499 (mt) cc_final: 0.9175 (mt) REVERT: B 2047 PHE cc_start: 0.8755 (t80) cc_final: 0.8358 (t80) REVERT: B 2076 LEU cc_start: 0.9516 (mt) cc_final: 0.9258 (mt) REVERT: B 2219 TYR cc_start: 0.7281 (m-80) cc_final: 0.7049 (m-80) REVERT: B 2356 PHE cc_start: 0.7942 (m-10) cc_final: 0.7711 (m-80) REVERT: B 2479 LYS cc_start: 0.9581 (pptt) cc_final: 0.9365 (pptt) REVERT: B 2496 GLU cc_start: 0.9237 (pt0) cc_final: 0.8632 (pt0) REVERT: B 2506 LEU cc_start: 0.9669 (mm) cc_final: 0.9305 (mm) REVERT: B 2513 MET cc_start: 0.9419 (mmm) cc_final: 0.8984 (mmp) REVERT: C 240 CYS cc_start: 0.6541 (t) cc_final: 0.5626 (p) REVERT: D 605 MET cc_start: 0.1526 (tpt) cc_final: 0.1304 (mtm) REVERT: D 711 MET cc_start: 0.8242 (mmp) cc_final: 0.7953 (mmm) REVERT: D 1420 LEU cc_start: 0.8631 (tp) cc_final: 0.8418 (mt) REVERT: D 1690 LEU cc_start: 0.9138 (tt) cc_final: 0.8836 (pp) REVERT: D 1710 LEU cc_start: 0.9609 (mt) cc_final: 0.9368 (mt) REVERT: D 1719 MET cc_start: 0.8401 (ttt) cc_final: 0.8046 (ttt) REVERT: D 1724 ARG cc_start: 0.9098 (pmt-80) cc_final: 0.8078 (mmm160) REVERT: D 1736 PHE cc_start: 0.9058 (t80) cc_final: 0.8712 (t80) REVERT: D 1964 MET cc_start: 0.8985 (mtp) cc_final: 0.8693 (mmm) REVERT: D 2007 MET cc_start: 0.9108 (mmp) cc_final: 0.8839 (mmm) REVERT: D 2047 PHE cc_start: 0.8708 (t80) cc_final: 0.8344 (t80) REVERT: D 2070 LYS cc_start: 0.9134 (ptpp) cc_final: 0.8817 (ptpp) REVERT: D 2076 LEU cc_start: 0.9521 (mt) cc_final: 0.9288 (mt) REVERT: D 2117 GLU cc_start: 0.8929 (mp0) cc_final: 0.8414 (mp0) REVERT: D 2123 ASP cc_start: 0.9271 (m-30) cc_final: 0.8503 (m-30) REVERT: D 2137 MET cc_start: 0.9170 (mtm) cc_final: 0.8675 (ttt) REVERT: D 2140 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8686 (mm-30) REVERT: D 2149 ILE cc_start: 0.9782 (mt) cc_final: 0.9530 (tp) REVERT: D 2175 MET cc_start: 0.9067 (tpt) cc_final: 0.8764 (tpp) REVERT: D 2356 PHE cc_start: 0.8001 (m-10) cc_final: 0.7628 (m-10) REVERT: D 2466 ILE cc_start: 0.9562 (pt) cc_final: 0.8893 (pt) REVERT: D 2467 MET cc_start: 0.7166 (pmm) cc_final: 0.6564 (pmm) REVERT: D 2468 PHE cc_start: 0.8583 (m-10) cc_final: 0.7956 (m-10) REVERT: D 2496 GLU cc_start: 0.9152 (pt0) cc_final: 0.8619 (pt0) REVERT: D 2513 MET cc_start: 0.9232 (mmm) cc_final: 0.8909 (mmm) outliers start: 4 outliers final: 0 residues processed: 441 average time/residue: 0.4308 time to fit residues: 317.4171 Evaluate side-chains 329 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 285 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 43 optimal weight: 0.0570 chunk 50 optimal weight: 0.9990 chunk 128 optimal weight: 50.0000 chunk 343 optimal weight: 10.0000 chunk 371 optimal weight: 2.9990 chunk 298 optimal weight: 30.0000 chunk 351 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN ** A1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2042 HIS ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1222 ASN ** D1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1789 GLN D1951 HIS D2042 HIS ** D2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 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 = 0.4100 r_free = 0.4100 target = 0.086289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.071688 restraints weight = 346984.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.071779 restraints weight = 207989.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.071916 restraints weight = 138168.753| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.9712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 32357 Z= 0.221 Angle : 0.788 11.552 43878 Z= 0.409 Chirality : 0.045 0.201 5043 Planarity : 0.006 0.119 5381 Dihedral : 5.145 24.182 4251 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.71 % Favored : 91.69 % Rotamer: Outliers : 0.09 % Allowed : 2.07 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3801 helix: 0.56 (0.10), residues: 2577 sheet: -4.04 (0.29), residues: 186 loop : -3.27 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 802 HIS 0.009 0.002 HIS B1699 PHE 0.040 0.002 PHE B1302 TYR 0.038 0.002 TYR B2507 ARG 0.009 0.001 ARG B2245 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 1952) hydrogen bonds : angle 4.71318 ( 5745) SS BOND : bond 0.01198 ( 3) SS BOND : angle 1.08339 ( 6) covalent geometry : bond 0.00454 (32354) covalent geometry : angle 0.78760 (43872) *********************** 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 414 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 411 time to evaluate : 3.499 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 605 MET cc_start: 0.1430 (tpt) cc_final: 0.1144 (mtm) REVERT: A 711 MET cc_start: 0.7442 (mmp) cc_final: 0.7188 (mmm) REVERT: A 1290 VAL cc_start: 0.7444 (t) cc_final: 0.7052 (t) REVERT: A 1690 LEU cc_start: 0.9209 (tt) cc_final: 0.8947 (pp) REVERT: A 1719 MET cc_start: 0.8470 (ttt) cc_final: 0.7939 (ttt) REVERT: A 1791 MET cc_start: 0.8710 (ppp) cc_final: 0.8508 (ppp) REVERT: A 1964 MET cc_start: 0.9007 (mtp) cc_final: 0.8587 (mmm) REVERT: A 1966 LEU cc_start: 0.9237 (mm) cc_final: 0.8579 (tt) REVERT: A 2007 MET cc_start: 0.9238 (mmp) cc_final: 0.8973 (mmm) REVERT: A 2033 PHE cc_start: 0.8981 (t80) cc_final: 0.8716 (t80) REVERT: A 2037 LEU cc_start: 0.9553 (mt) cc_final: 0.9224 (mt) REVERT: A 2047 PHE cc_start: 0.8832 (t80) cc_final: 0.8447 (t80) REVERT: A 2076 LEU cc_start: 0.9535 (mt) cc_final: 0.9246 (mt) REVERT: A 2117 GLU cc_start: 0.9201 (mp0) cc_final: 0.8806 (mp0) REVERT: A 2123 ASP cc_start: 0.9224 (m-30) cc_final: 0.8694 (m-30) REVERT: A 2137 MET cc_start: 0.9120 (mtm) cc_final: 0.8553 (mtp) REVERT: A 2138 CYS cc_start: 0.9346 (m) cc_final: 0.9143 (t) REVERT: A 2175 MET cc_start: 0.8676 (mtm) cc_final: 0.8298 (mmp) REVERT: A 2182 PHE cc_start: 0.9545 (t80) cc_final: 0.9325 (t80) REVERT: A 2288 MET cc_start: 0.1327 (mtt) cc_final: 0.0954 (ptt) REVERT: A 2420 MET cc_start: 0.6476 (mmt) cc_final: 0.5530 (mmt) REVERT: A 2496 GLU cc_start: 0.9257 (tt0) cc_final: 0.8349 (tp30) REVERT: B 1694 ILE cc_start: 0.9570 (mm) cc_final: 0.9234 (mm) REVERT: B 1710 LEU cc_start: 0.9604 (mt) cc_final: 0.9249 (mt) REVERT: B 1736 PHE cc_start: 0.9213 (t80) cc_final: 0.8581 (t80) REVERT: B 1789 GLN cc_start: 0.9110 (tp40) cc_final: 0.8748 (mm110) REVERT: B 1964 MET cc_start: 0.9095 (mtp) cc_final: 0.8712 (mmm) REVERT: B 2007 MET cc_start: 0.9256 (mmp) cc_final: 0.9029 (mmm) REVERT: B 2047 PHE cc_start: 0.8849 (t80) cc_final: 0.8476 (t80) REVERT: B 2061 VAL cc_start: 0.8406 (m) cc_final: 0.8176 (p) REVERT: B 2070 LYS cc_start: 0.9089 (ptpp) cc_final: 0.8854 (ptpp) REVERT: B 2076 LEU cc_start: 0.9552 (mt) cc_final: 0.9339 (mt) REVERT: B 2325 MET cc_start: 0.8952 (pmm) cc_final: 0.7860 (tpt) REVERT: B 2356 PHE cc_start: 0.8066 (m-10) cc_final: 0.7821 (m-80) REVERT: B 2478 LEU cc_start: 0.9790 (tp) cc_final: 0.9512 (pp) REVERT: B 2496 GLU cc_start: 0.9176 (pt0) cc_final: 0.8518 (mt-10) REVERT: C 240 CYS cc_start: 0.6666 (t) cc_final: 0.5717 (p) REVERT: D 711 MET cc_start: 0.8086 (mmp) cc_final: 0.7771 (mmm) REVERT: D 1719 MET cc_start: 0.8548 (ttt) cc_final: 0.8044 (ttt) REVERT: D 1724 ARG cc_start: 0.9147 (pmt-80) cc_final: 0.8168 (mmm160) REVERT: D 1791 MET cc_start: 0.8714 (ppp) cc_final: 0.8509 (ppp) REVERT: D 1964 MET cc_start: 0.9101 (mtp) cc_final: 0.8753 (mmm) REVERT: D 2007 MET cc_start: 0.9282 (mmp) cc_final: 0.9047 (mmm) REVERT: D 2033 PHE cc_start: 0.8835 (t80) cc_final: 0.8608 (t80) REVERT: D 2037 LEU cc_start: 0.9532 (mp) cc_final: 0.9313 (mt) REVERT: D 2047 PHE cc_start: 0.8839 (t80) cc_final: 0.8482 (t80) REVERT: D 2070 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8737 (pttm) REVERT: D 2076 LEU cc_start: 0.9560 (mt) cc_final: 0.9348 (mt) REVERT: D 2117 GLU cc_start: 0.9194 (mp0) cc_final: 0.8822 (mp0) REVERT: D 2123 ASP cc_start: 0.9295 (m-30) cc_final: 0.8612 (m-30) REVERT: D 2137 MET cc_start: 0.9200 (mtm) cc_final: 0.8708 (ttt) REVERT: D 2149 ILE cc_start: 0.9833 (mt) cc_final: 0.9612 (tp) REVERT: D 2466 ILE cc_start: 0.9399 (pt) cc_final: 0.9009 (pt) REVERT: D 2496 GLU cc_start: 0.9145 (pt0) cc_final: 0.8495 (mt-10) REVERT: D 2513 MET cc_start: 0.9370 (mmm) cc_final: 0.8947 (mmp) outliers start: 3 outliers final: 1 residues processed: 413 average time/residue: 0.3893 time to fit residues: 269.1422 Evaluate side-chains 316 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 328 optimal weight: 3.9990 chunk 359 optimal weight: 0.0370 chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 40.0000 chunk 135 optimal weight: 6.9990 chunk 305 optimal weight: 20.0000 chunk 89 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 265 optimal weight: 20.0000 chunk 300 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 GLN A2042 HIS ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1699 HIS B2042 HIS ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 HIS ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1699 HIS D1789 GLN D2042 HIS ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2456 HIS ** 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 = 0.4137 r_free = 0.4137 target = 0.088295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.072391 restraints weight = 342814.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.073656 restraints weight = 184970.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.074168 restraints weight = 126771.310| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.9875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 32357 Z= 0.142 Angle : 0.746 15.529 43878 Z= 0.376 Chirality : 0.044 0.242 5043 Planarity : 0.006 0.118 5381 Dihedral : 5.012 24.291 4251 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.13 % Favored : 92.32 % Rotamer: Outliers : 0.06 % Allowed : 1.01 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3801 helix: 0.74 (0.10), residues: 2556 sheet: -3.93 (0.30), residues: 186 loop : -3.16 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D2066 HIS 0.008 0.001 HIS D2456 PHE 0.039 0.002 PHE B2189 TYR 0.032 0.002 TYR B2067 ARG 0.010 0.001 ARG B2245 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1952) hydrogen bonds : angle 4.51716 ( 5745) SS BOND : bond 0.00115 ( 3) SS BOND : angle 1.28112 ( 6) covalent geometry : bond 0.00323 (32354) covalent geometry : angle 0.74586 (43872) *********************** 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 422 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 420 time to evaluate : 3.543 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: A 605 MET cc_start: 0.1355 (tpt) cc_final: 0.1050 (mtm) REVERT: A 848 MET cc_start: -0.2373 (mmp) cc_final: -0.2711 (mmp) REVERT: A 1694 ILE cc_start: 0.9191 (mm) cc_final: 0.8961 (mm) REVERT: A 1719 MET cc_start: 0.8570 (ttt) cc_final: 0.8112 (ttt) REVERT: A 1736 PHE cc_start: 0.9046 (t80) cc_final: 0.8640 (t80) REVERT: A 1966 LEU cc_start: 0.9122 (mm) cc_final: 0.8478 (tt) REVERT: A 2007 MET cc_start: 0.9149 (mmp) cc_final: 0.8917 (mmm) REVERT: A 2033 PHE cc_start: 0.8867 (t80) cc_final: 0.8537 (t80) REVERT: A 2037 LEU cc_start: 0.9511 (mt) cc_final: 0.9165 (mt) REVERT: A 2047 PHE cc_start: 0.8765 (t80) cc_final: 0.8470 (t80) REVERT: A 2117 GLU cc_start: 0.9187 (mp0) cc_final: 0.8652 (mp0) REVERT: A 2123 ASP cc_start: 0.9208 (m-30) cc_final: 0.8466 (m-30) REVERT: A 2137 MET cc_start: 0.9071 (mtm) cc_final: 0.8571 (mtp) REVERT: A 2175 MET cc_start: 0.8532 (mtm) cc_final: 0.8172 (mmp) REVERT: A 2182 PHE cc_start: 0.9517 (t80) cc_final: 0.9280 (t80) REVERT: A 2288 MET cc_start: 0.1121 (mtt) cc_final: 0.0830 (ptt) REVERT: A 2420 MET cc_start: 0.6235 (mmt) cc_final: 0.5346 (mmt) REVERT: A 2466 ILE cc_start: 0.9568 (pt) cc_final: 0.9050 (pt) REVERT: A 2496 GLU cc_start: 0.9319 (tt0) cc_final: 0.8918 (mt-10) REVERT: A 2499 LEU cc_start: 0.9798 (tt) cc_final: 0.9534 (tp) REVERT: A 2506 LEU cc_start: 0.9647 (mm) cc_final: 0.9293 (mm) REVERT: A 2513 MET cc_start: 0.9480 (mmt) cc_final: 0.8924 (mmt) REVERT: B 605 MET cc_start: 0.1645 (tpt) cc_final: 0.1357 (mtm) REVERT: B 1167 PHE cc_start: 0.6948 (t80) cc_final: 0.6394 (m-80) REVERT: B 1694 ILE cc_start: 0.9491 (mm) cc_final: 0.9169 (mm) REVERT: B 1710 LEU cc_start: 0.9594 (mt) cc_final: 0.9240 (mt) REVERT: B 1719 MET cc_start: 0.8316 (ttt) cc_final: 0.7618 (ttt) REVERT: B 1736 PHE cc_start: 0.9222 (t80) cc_final: 0.8599 (t80) REVERT: B 1789 GLN cc_start: 0.9085 (tp40) cc_final: 0.8718 (mm110) REVERT: B 1964 MET cc_start: 0.9038 (mtp) cc_final: 0.8671 (mmm) REVERT: B 1966 LEU cc_start: 0.9149 (mm) cc_final: 0.8464 (tt) REVERT: B 2007 MET cc_start: 0.9167 (mmp) cc_final: 0.8829 (mmm) REVERT: B 2033 PHE cc_start: 0.9111 (t80) cc_final: 0.8328 (t80) REVERT: B 2037 LEU cc_start: 0.9561 (mt) cc_final: 0.9169 (mt) REVERT: B 2047 PHE cc_start: 0.8749 (t80) cc_final: 0.8427 (t80) REVERT: B 2061 VAL cc_start: 0.8305 (m) cc_final: 0.8067 (p) REVERT: B 2076 LEU cc_start: 0.9526 (mt) cc_final: 0.9283 (mt) REVERT: B 2325 MET cc_start: 0.8995 (pmm) cc_final: 0.7939 (tpt) REVERT: B 2478 LEU cc_start: 0.9766 (tp) cc_final: 0.9503 (pp) REVERT: B 2496 GLU cc_start: 0.9224 (pt0) cc_final: 0.8468 (mt-10) REVERT: B 2506 LEU cc_start: 0.9627 (mm) cc_final: 0.9308 (mm) REVERT: B 2513 MET cc_start: 0.9338 (mmp) cc_final: 0.8998 (mmm) REVERT: C 240 CYS cc_start: 0.6504 (t) cc_final: 0.5652 (p) REVERT: D 706 MET cc_start: -0.1101 (mmp) cc_final: -0.1371 (tpt) REVERT: D 1290 VAL cc_start: 0.7472 (t) cc_final: 0.7096 (t) REVERT: D 1694 ILE cc_start: 0.9231 (mm) cc_final: 0.8960 (mm) REVERT: D 1719 MET cc_start: 0.8476 (ttt) cc_final: 0.8005 (ttt) REVERT: D 1724 ARG cc_start: 0.9107 (pmt-80) cc_final: 0.8215 (mmm160) REVERT: D 1964 MET cc_start: 0.9007 (mtp) cc_final: 0.8727 (mmm) REVERT: D 2007 MET cc_start: 0.9214 (mmp) cc_final: 0.8877 (mmm) REVERT: D 2018 ASP cc_start: 0.8824 (m-30) cc_final: 0.8395 (m-30) REVERT: D 2033 PHE cc_start: 0.8787 (t80) cc_final: 0.8288 (t80) REVERT: D 2037 LEU cc_start: 0.9465 (mp) cc_final: 0.8891 (mp) REVERT: D 2047 PHE cc_start: 0.8733 (t80) cc_final: 0.8441 (t80) REVERT: D 2117 GLU cc_start: 0.9150 (mp0) cc_final: 0.8622 (mp0) REVERT: D 2137 MET cc_start: 0.9219 (mtm) cc_final: 0.8660 (ttt) REVERT: D 2140 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8627 (mm-30) REVERT: D 2149 ILE cc_start: 0.9814 (mt) cc_final: 0.9601 (tp) REVERT: D 2466 ILE cc_start: 0.9504 (pt) cc_final: 0.9097 (pt) REVERT: D 2479 LYS cc_start: 0.9636 (pptt) cc_final: 0.9365 (pptt) REVERT: D 2496 GLU cc_start: 0.9209 (pt0) cc_final: 0.8455 (mt-10) REVERT: D 2506 LEU cc_start: 0.9525 (mm) cc_final: 0.9060 (mm) REVERT: D 2513 MET cc_start: 0.9305 (mmm) cc_final: 0.8784 (mmp) outliers start: 2 outliers final: 0 residues processed: 422 average time/residue: 0.4014 time to fit residues: 281.6098 Evaluate side-chains 323 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 157 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 332 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 GLN A2034 GLN A2042 HIS ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1699 HIS B2042 HIS ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1112 GLN ** D1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1789 GLN ** D2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2456 HIS ** 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 = 0.4113 r_free = 0.4113 target = 0.086910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.071729 restraints weight = 343053.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.072122 restraints weight = 210360.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.072704 restraints weight = 128511.851| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 1.0179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 32357 Z= 0.169 Angle : 0.757 14.109 43878 Z= 0.385 Chirality : 0.044 0.225 5043 Planarity : 0.006 0.119 5381 Dihedral : 5.046 26.361 4251 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.50 % Favored : 91.90 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3801 helix: 0.71 (0.10), residues: 2550 sheet: -3.82 (0.30), residues: 186 loop : -3.11 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B2516 HIS 0.008 0.002 HIS D2456 PHE 0.034 0.002 PHE D2356 TYR 0.032 0.002 TYR D1692 ARG 0.014 0.001 ARG B2198 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 1952) hydrogen bonds : angle 4.58499 ( 5745) SS BOND : bond 0.00107 ( 3) SS BOND : angle 1.00296 ( 6) covalent geometry : bond 0.00369 (32354) covalent geometry : angle 0.75649 (43872) ********************** 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 407 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 405 time to evaluate : 3.512 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 605 MET cc_start: 0.1266 (tpt) cc_final: 0.0999 (mtm) REVERT: A 848 MET cc_start: -0.1806 (mmp) cc_final: -0.2114 (mmp) REVERT: A 1412 VAL cc_start: 0.8485 (p) cc_final: 0.8222 (m) REVERT: A 1690 LEU cc_start: 0.9126 (tt) cc_final: 0.8851 (pp) REVERT: A 1719 MET cc_start: 0.8529 (ttt) cc_final: 0.8058 (ttt) REVERT: A 1736 PHE cc_start: 0.9078 (t80) cc_final: 0.8743 (t80) REVERT: A 1964 MET cc_start: 0.9086 (mtp) cc_final: 0.8806 (mmm) REVERT: A 1966 LEU cc_start: 0.9143 (mm) cc_final: 0.8527 (tt) REVERT: A 2007 MET cc_start: 0.9183 (mmp) cc_final: 0.8916 (mmm) REVERT: A 2033 PHE cc_start: 0.8910 (t80) cc_final: 0.8556 (t80) REVERT: A 2037 LEU cc_start: 0.9516 (mt) cc_final: 0.9188 (mt) REVERT: A 2117 GLU cc_start: 0.9231 (mp0) cc_final: 0.8808 (mp0) REVERT: A 2123 ASP cc_start: 0.9225 (m-30) cc_final: 0.8539 (m-30) REVERT: A 2137 MET cc_start: 0.9077 (mtm) cc_final: 0.8671 (mtp) REVERT: A 2175 MET cc_start: 0.8560 (mtm) cc_final: 0.8225 (mmp) REVERT: A 2181 LEU cc_start: 0.9392 (mm) cc_final: 0.9113 (pp) REVERT: A 2182 PHE cc_start: 0.9568 (t80) cc_final: 0.9290 (t80) REVERT: A 2288 MET cc_start: 0.1197 (mtt) cc_final: 0.0888 (ptm) REVERT: A 2420 MET cc_start: 0.6447 (mmt) cc_final: 0.5538 (mmt) REVERT: A 2496 GLU cc_start: 0.9284 (tt0) cc_final: 0.8932 (mt-10) REVERT: A 2499 LEU cc_start: 0.9766 (tt) cc_final: 0.9522 (tp) REVERT: A 2506 LEU cc_start: 0.9628 (mm) cc_final: 0.9332 (mm) REVERT: A 2513 MET cc_start: 0.9198 (mmt) cc_final: 0.8809 (mmt) REVERT: B 605 MET cc_start: 0.1663 (tpt) cc_final: 0.1412 (mtm) REVERT: B 848 MET cc_start: -0.2458 (mmp) cc_final: -0.2743 (mmp) REVERT: B 1694 ILE cc_start: 0.9496 (mm) cc_final: 0.9158 (mm) REVERT: B 1710 LEU cc_start: 0.9618 (mt) cc_final: 0.9234 (mt) REVERT: B 1719 MET cc_start: 0.8368 (ttt) cc_final: 0.7728 (ttt) REVERT: B 1736 PHE cc_start: 0.9214 (t80) cc_final: 0.8590 (t80) REVERT: B 1789 GLN cc_start: 0.9081 (tp40) cc_final: 0.8849 (mm110) REVERT: B 1964 MET cc_start: 0.9066 (mtp) cc_final: 0.8676 (mmm) REVERT: B 2007 MET cc_start: 0.9186 (mmp) cc_final: 0.8947 (mmm) REVERT: B 2033 PHE cc_start: 0.9169 (t80) cc_final: 0.8471 (t80) REVERT: B 2037 LEU cc_start: 0.9573 (mt) cc_final: 0.9149 (mt) REVERT: B 2047 PHE cc_start: 0.8782 (t80) cc_final: 0.8466 (t80) REVERT: B 2061 VAL cc_start: 0.8378 (m) cc_final: 0.8160 (p) REVERT: B 2070 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8792 (pttm) REVERT: B 2076 LEU cc_start: 0.9535 (mt) cc_final: 0.9328 (mt) REVERT: B 2325 MET cc_start: 0.9040 (pmm) cc_final: 0.8016 (tpt) REVERT: B 2478 LEU cc_start: 0.9731 (tp) cc_final: 0.9527 (pp) REVERT: B 2479 LYS cc_start: 0.9595 (pptt) cc_final: 0.9369 (pptt) REVERT: B 2496 GLU cc_start: 0.9158 (pt0) cc_final: 0.8504 (mt-10) REVERT: B 2506 LEU cc_start: 0.9653 (mm) cc_final: 0.9410 (mm) REVERT: B 2513 MET cc_start: 0.9486 (mmp) cc_final: 0.9012 (mmm) REVERT: C 240 CYS cc_start: 0.6604 (t) cc_final: 0.5606 (p) REVERT: D 711 MET cc_start: 0.8350 (mmp) cc_final: 0.8146 (mmm) REVERT: D 831 MET cc_start: 0.3437 (ptp) cc_final: 0.3196 (mtt) REVERT: D 1719 MET cc_start: 0.8411 (ttt) cc_final: 0.7880 (ttt) REVERT: D 1964 MET cc_start: 0.9044 (mtp) cc_final: 0.8780 (mmm) REVERT: D 2007 MET cc_start: 0.9226 (mmp) cc_final: 0.8993 (mmm) REVERT: D 2018 ASP cc_start: 0.8891 (m-30) cc_final: 0.8442 (m-30) REVERT: D 2033 PHE cc_start: 0.8736 (t80) cc_final: 0.8245 (t80) REVERT: D 2037 LEU cc_start: 0.9482 (mp) cc_final: 0.8864 (mp) REVERT: D 2070 LYS cc_start: 0.9004 (ptpp) cc_final: 0.8616 (ptpp) REVERT: D 2117 GLU cc_start: 0.9199 (mp0) cc_final: 0.8830 (mp0) REVERT: D 2123 ASP cc_start: 0.9313 (m-30) cc_final: 0.8509 (m-30) REVERT: D 2137 MET cc_start: 0.9123 (mtm) cc_final: 0.8486 (ttt) REVERT: D 2140 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8743 (mm-30) REVERT: D 2149 ILE cc_start: 0.9837 (mt) cc_final: 0.9604 (tp) REVERT: D 2175 MET cc_start: 0.8687 (mmm) cc_final: 0.8418 (mmt) REVERT: D 2479 LYS cc_start: 0.9602 (pptt) cc_final: 0.9335 (pptt) REVERT: D 2496 GLU cc_start: 0.9130 (pt0) cc_final: 0.8460 (mt-10) REVERT: D 2506 LEU cc_start: 0.9573 (mm) cc_final: 0.9310 (mm) REVERT: D 2513 MET cc_start: 0.9286 (mmm) cc_final: 0.8905 (mmp) outliers start: 2 outliers final: 0 residues processed: 407 average time/residue: 0.3832 time to fit residues: 259.4018 Evaluate side-chains 317 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 371 optimal weight: 7.9990 chunk 376 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 30.0000 chunk 240 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 195 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 GLN ** A2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2456 HIS ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2042 HIS ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 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 = 0.4096 r_free = 0.4096 target = 0.085761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.071211 restraints weight = 344410.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.070303 restraints weight = 197177.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.071321 restraints weight = 133785.277| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 1.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32357 Z= 0.190 Angle : 0.765 10.946 43878 Z= 0.394 Chirality : 0.044 0.239 5043 Planarity : 0.006 0.121 5381 Dihedral : 5.149 26.795 4251 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.63 % Favored : 91.74 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3801 helix: 0.60 (0.10), residues: 2568 sheet: -3.81 (0.30), residues: 186 loop : -3.10 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D2066 HIS 0.027 0.002 HIS B1699 PHE 0.033 0.002 PHE A2356 TYR 0.034 0.002 TYR A1692 ARG 0.011 0.001 ARG B1724 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 1952) hydrogen bonds : angle 4.64828 ( 5745) SS BOND : bond 0.00141 ( 3) SS BOND : angle 1.01971 ( 6) covalent geometry : bond 0.00406 (32354) covalent geometry : angle 0.76484 (43872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18691.84 seconds wall clock time: 325 minutes 45.15 seconds (19545.15 seconds total)