Starting phenix.real_space_refine on Tue Aug 26 00:30:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yfg_39223/08_2025/8yfg_39223_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yfg_39223/08_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_39223/08_2025/8yfg_39223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yfg_39223/08_2025/8yfg_39223.map" model { file = "/net/cci-nas-00/data/ceres_data/8yfg_39223/08_2025/8yfg_39223_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yfg_39223/08_2025/8yfg_39223_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'PHE:plan': 5, 'TYR:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 3, 'TRP:plan': 1} 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: {'PHE:plan': 6, 'TYR:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 3, 'TRP:plan': 1} 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: {'PHE:plan': 5, 'TYR:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 3, 'TRP:plan': 1} 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: 7.95, per 1000 atoms: 0.25 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: 3.15 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.4 microseconds 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: 1.19 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: 7.02 Time building geometry restraints manager: 4.12 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: 36.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.360 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.270 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (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 ARG 0.007 0.001 ARG B1547 TYR 0.018 0.002 TYR B1165 PHE 0.030 0.002 PHE B 615 TRP 0.022 0.002 TRP B1168 HIS 0.007 0.001 HIS A 951 Details of bonding type rmsd covalent geometry : bond 0.00760 (32354) covalent geometry : angle 1.37792 (43872) SS BOND : bond 0.00498 ( 3) SS BOND : angle 0.86344 ( 6) hydrogen bonds : bond 0.17389 ( 1952) hydrogen bonds : angle 7.65452 ( 5745) *********************** 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 : 1.352 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: -0.1577 (m) REVERT: A 596 ARG cc_start: 0.0260 (OUTLIER) cc_final: -0.1335 (tpt170) REVERT: A 638 MET cc_start: 0.1866 (OUTLIER) cc_final: -0.2499 (mtt) REVERT: A 768 GLU cc_start: 0.4610 (OUTLIER) cc_final: 0.2237 (pp20) REVERT: A 799 TYR cc_start: 0.2045 (OUTLIER) cc_final: 0.1677 (m-80) REVERT: A 806 LYS cc_start: 0.1598 (OUTLIER) cc_final: 0.0917 (mmmm) REVERT: A 843 ILE cc_start: -0.1403 (OUTLIER) cc_final: -0.4247 (tt) REVERT: A 853 LYS cc_start: 0.0484 (OUTLIER) cc_final: -0.0464 (mptt) REVERT: A 954 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.2832 (mtm-85) REVERT: A 978 ASP cc_start: 0.2420 (OUTLIER) cc_final: 0.0788 (t0) REVERT: A 1010 ARG cc_start: 0.4167 (OUTLIER) cc_final: 0.3749 (mtp180) REVERT: A 1048 PHE cc_start: 0.4235 (OUTLIER) cc_final: 0.3651 (t80) REVERT: A 1097 THR cc_start: 0.4603 (OUTLIER) cc_final: 0.4077 (p) REVERT: A 1116 PHE cc_start: 0.3752 (OUTLIER) cc_final: 0.2854 (m-80) REVERT: A 1208 THR cc_start: 0.4161 (OUTLIER) cc_final: 0.3742 (m) REVERT: A 1217 CYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6718 (p) REVERT: A 1409 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5921 (t-90) REVERT: A 1567 GLN cc_start: 0.3943 (OUTLIER) cc_final: 0.3153 (pt0) REVERT: A 1699 HIS cc_start: 0.4535 (OUTLIER) cc_final: 0.4160 (t70) REVERT: A 1716 LEU cc_start: 0.6535 (mt) cc_final: 0.5777 (mt) REVERT: A 1942 LEU cc_start: 0.2690 (OUTLIER) cc_final: 0.1421 (mm) REVERT: A 2008 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7735 (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: 0.5264 (mtp) REVERT: A 2033 PHE cc_start: 0.6798 (t80) cc_final: 0.5739 (t80) REVERT: A 2048 ILE cc_start: 0.6231 (OUTLIER) cc_final: 0.5353 (pt) REVERT: A 2069 VAL cc_start: 0.8440 (t) cc_final: 0.8221 (t) REVERT: A 2117 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: A 2121 VAL cc_start: 0.8680 (t) cc_final: 0.8382 (p) REVERT: A 2134 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.7359 (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: 0.8320 (tp) REVERT: A 2244 SER cc_start: 0.4285 (OUTLIER) cc_final: -0.1090 (t) REVERT: A 2280 ILE cc_start: 0.2831 (OUTLIER) cc_final: 0.1395 (pt) REVERT: A 2294 ASN cc_start: 0.7009 (OUTLIER) cc_final: 0.5985 (p0) REVERT: A 2364 ASN cc_start: 0.1437 (OUTLIER) cc_final: 0.1021 (p0) REVERT: A 2375 GLN cc_start: 0.2749 (OUTLIER) cc_final: 0.0062 (mp10) REVERT: A 2407 GLU cc_start: 0.3595 (OUTLIER) cc_final: 0.3134 (pt0) REVERT: A 2408 LEU cc_start: 0.1079 (OUTLIER) cc_final: 0.0206 (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: 0.8000 (ttmm) REVERT: A 2521 GLU cc_start: 0.2072 (OUTLIER) cc_final: -0.0857 (tm-30) REVERT: B 572 VAL cc_start: -0.0576 (OUTLIER) cc_final: -0.1655 (m) REVERT: B 596 ARG cc_start: 0.0123 (OUTLIER) cc_final: -0.1347 (tpt170) REVERT: B 638 MET cc_start: 0.1933 (OUTLIER) cc_final: -0.2300 (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: 0.0960 (mmmm) REVERT: B 843 ILE cc_start: -0.1475 (OUTLIER) cc_final: -0.4470 (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: 0.0589 (t0) REVERT: B 1034 ILE cc_start: 0.5678 (OUTLIER) cc_final: 0.5426 (mp) REVERT: B 1048 PHE cc_start: 0.4245 (OUTLIER) cc_final: 0.3819 (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: 0.2904 (m-80) REVERT: B 1208 THR cc_start: 0.3956 (OUTLIER) cc_final: 0.3535 (m) REVERT: B 1217 CYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6692 (p) REVERT: B 1219 ILE cc_start: 0.6279 (OUTLIER) cc_final: 0.6012 (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: 0.5797 (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: 0.6573 (mt0) REVERT: B 2015 MET cc_start: 0.6460 (mtp) cc_final: 0.5122 (mtp) REVERT: B 2048 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5467 (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: 0.8228 (p) REVERT: B 2134 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.7619 (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: 0.7202 (mm-30) REVERT: B 2175 MET cc_start: 0.5513 (mtp) cc_final: 0.5158 (mtp) REVERT: B 2223 PHE cc_start: 0.2630 (OUTLIER) cc_final: 0.1935 (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: 0.1408 (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: 0.0966 (p0) REVERT: B 2375 GLN cc_start: 0.2626 (OUTLIER) cc_final: -0.0095 (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: 0.0221 (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: 0.7642 (mm) REVERT: B 2487 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8670 (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: 0.5431 (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: 0.1954 (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: 0.1026 (mmmm) REVERT: D 843 ILE cc_start: -0.1384 (OUTLIER) cc_final: -0.4303 (tt) REVERT: D 853 LYS cc_start: 0.0554 (OUTLIER) cc_final: -0.0808 (mptt) REVERT: D 855 VAL cc_start: 0.2846 (OUTLIER) cc_final: 0.2564 (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: 0.3764 (t80) REVERT: D 1097 THR cc_start: 0.4556 (OUTLIER) cc_final: 0.3944 (p) REVERT: D 1116 PHE cc_start: 0.3955 (OUTLIER) cc_final: 0.3020 (m-80) REVERT: D 1208 THR cc_start: 0.4227 (OUTLIER) cc_final: 0.3952 (m) REVERT: D 1217 CYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6712 (p) REVERT: D 1219 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5978 (mp) REVERT: D 1567 GLN cc_start: 0.3970 (OUTLIER) cc_final: 0.3289 (pt0) REVERT: D 1669 GLN cc_start: 0.0777 (OUTLIER) cc_final: 0.0471 (mm110) REVERT: D 1699 HIS cc_start: 0.4463 (OUTLIER) cc_final: 0.3786 (t70) REVERT: D 1716 LEU cc_start: 0.6576 (mt) cc_final: 0.5653 (mt) REVERT: D 1942 LEU cc_start: 0.2505 (OUTLIER) cc_final: 0.1359 (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: 0.6251 (mt0) REVERT: D 2015 MET cc_start: 0.6578 (mtp) cc_final: 0.5303 (mtp) REVERT: D 2033 PHE cc_start: 0.6898 (t80) cc_final: 0.5925 (t80) REVERT: D 2048 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5398 (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: 0.6546 (mt-10) REVERT: D 2121 VAL cc_start: 0.8647 (t) cc_final: 0.8401 (p) REVERT: D 2134 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.7372 (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: 0.7228 (mm-30) REVERT: D 2149 ILE cc_start: 0.8663 (mt) cc_final: 0.8365 (mm) REVERT: D 2175 MET cc_start: 0.5515 (mtp) cc_final: 0.5290 (mtm) REVERT: D 2244 SER cc_start: 0.4458 (OUTLIER) cc_final: -0.1164 (t) REVERT: D 2294 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.5960 (p0) REVERT: D 2340 SER cc_start: 0.6552 (OUTLIER) cc_final: 0.4698 (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: 0.3198 (pt0) REVERT: D 2408 LEU cc_start: 0.1159 (OUTLIER) cc_final: 0.0514 (mt) REVERT: D 2468 PHE cc_start: 0.7023 (m-80) cc_final: 0.6065 (m-10) REVERT: D 2477 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7576 (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: 0.7999 (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: -0.1039 (tm-30) REVERT: E 229 GLU cc_start: 0.1009 (OUTLIER) cc_final: 0.0312 (pt0) REVERT: E 230 SER cc_start: 0.5612 (OUTLIER) cc_final: 0.5301 (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: 277 residues processed: 1852 average time/residue: 0.2168 time to fit residues: 620.2831 Evaluate side-chains 840 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 389 poor density : 451 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ** 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 A2100 HIS ** A2102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 GLN A2229 GLN A2269 GLN 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** B1309 HIS B1332 ASN B1409 HIS B1561 HIS B1669 GLN ** B1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1947 HIS B2034 GLN B2042 HIS B2100 HIS ** B2102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2206 GLN ** B2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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 D2100 HIS D2206 GLN ** D2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.095102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.079670 restraints weight = 339047.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.081476 restraints weight = 180332.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.082648 restraints weight = 114004.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.083234 restraints weight = 82777.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.083806 restraints weight = 68150.545| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 32357 Z= 0.214 Angle : 0.936 15.169 43878 Z= 0.478 Chirality : 0.050 0.307 5043 Planarity : 0.008 0.109 5381 Dihedral : 5.735 61.400 4251 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.73 % Favored : 90.42 % Rotamer: Outliers : 0.80 % Allowed : 5.66 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.13), residues: 3801 helix: -0.39 (0.10), residues: 2577 sheet: -5.57 (0.28), residues: 78 loop : -4.20 (0.15), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B2386 TYR 0.024 0.002 TYR B1961 PHE 0.035 0.003 PHE D2189 TRP 0.052 0.002 TRP B2404 HIS 0.019 0.002 HIS D2464 Details of bonding type rmsd covalent geometry : bond 0.00480 (32354) covalent geometry : angle 0.93631 (43872) SS BOND : bond 0.00264 ( 3) SS BOND : angle 1.36979 ( 6) hydrogen bonds : bond 0.05426 ( 1952) hydrogen bonds : angle 5.56171 ( 5745) *********************** 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 549 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 522 time to evaluate : 0.984 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: A 1219 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7057 (mp) REVERT: A 1420 LEU cc_start: 0.8745 (tp) cc_final: 0.8451 (mt) REVERT: A 1694 ILE cc_start: 0.9373 (mm) cc_final: 0.8882 (mm) REVERT: A 1696 ILE cc_start: 0.9291 (mm) cc_final: 0.8613 (mm) REVERT: A 1708 LEU cc_start: 0.9248 (tt) cc_final: 0.8777 (tp) REVERT: A 1716 LEU cc_start: 0.8429 (mt) cc_final: 0.8145 (mt) REVERT: A 1717 TRP cc_start: 0.8049 (t60) cc_final: 0.7218 (t60) REVERT: A 1719 MET cc_start: 0.7630 (ttt) cc_final: 0.7121 (ttt) REVERT: A 1724 ARG cc_start: 0.9002 (pmt-80) cc_final: 0.7689 (mmm160) REVERT: A 1729 PHE cc_start: 0.8624 (t80) cc_final: 0.8142 (t80) REVERT: A 1789 GLN cc_start: 0.9182 (tp40) cc_final: 0.8924 (tp40) REVERT: A 2007 MET cc_start: 0.9248 (mmp) cc_final: 0.8938 (mmm) REVERT: A 2070 LYS cc_start: 0.9155 (ptpp) cc_final: 0.8605 (pttm) REVERT: A 2138 CYS cc_start: 0.9200 (m) cc_final: 0.8572 (m) REVERT: A 2149 ILE cc_start: 0.9610 (mm) cc_final: 0.9336 (tp) REVERT: A 2175 MET cc_start: 0.8522 (mtt) cc_final: 0.8159 (tpp) REVERT: A 2288 MET cc_start: 0.2757 (mtt) cc_final: 0.2012 (ptt) REVERT: A 2343 GLU cc_start: 0.4738 (OUTLIER) cc_final: 0.4418 (mp0) REVERT: A 2496 GLU cc_start: 0.9145 (pt0) cc_final: 0.8393 (mt-10) REVERT: B 1420 LEU cc_start: 0.8793 (tp) cc_final: 0.8504 (mt) REVERT: B 1694 ILE cc_start: 0.9352 (mm) cc_final: 0.9032 (mm) REVERT: B 1696 ILE cc_start: 0.9276 (mm) cc_final: 0.8581 (mm) REVERT: B 1716 LEU cc_start: 0.8436 (mt) cc_final: 0.8166 (mt) REVERT: B 1717 TRP cc_start: 0.8020 (t60) cc_final: 0.7126 (t60) REVERT: B 1719 MET cc_start: 0.7639 (ttt) cc_final: 0.7133 (ttt) REVERT: B 1724 ARG cc_start: 0.8445 (ptp90) cc_final: 0.7968 (mmm160) REVERT: B 1729 PHE cc_start: 0.8604 (t80) cc_final: 0.8115 (t80) REVERT: B 1738 GLU cc_start: 0.9382 (pt0) cc_final: 0.9024 (pt0) REVERT: B 1789 GLN cc_start: 0.9155 (tp40) cc_final: 0.8884 (mm-40) REVERT: B 2070 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8753 (ptpp) REVERT: B 2280 ILE cc_start: 0.2079 (OUTLIER) cc_final: 0.1623 (pt) REVERT: B 2343 GLU cc_start: 0.4672 (OUTLIER) cc_final: 0.4336 (mp0) REVERT: B 2356 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7117 (m-10) REVERT: B 2496 GLU cc_start: 0.9133 (pt0) cc_final: 0.8707 (pt0) REVERT: C 240 CYS cc_start: 0.6002 (t) cc_final: 0.5299 (t) REVERT: D 1420 LEU cc_start: 0.8628 (tp) cc_final: 0.8353 (mt) REVERT: D 1681 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8546 (pm20) REVERT: D 1694 ILE cc_start: 0.9361 (mm) cc_final: 0.9037 (mm) REVERT: D 1696 ILE cc_start: 0.9299 (mm) cc_final: 0.8615 (mm) REVERT: D 1716 LEU cc_start: 0.8512 (mt) cc_final: 0.8256 (mt) REVERT: D 1717 TRP cc_start: 0.8075 (t60) cc_final: 0.7295 (t60) REVERT: D 1719 MET cc_start: 0.7736 (ttt) cc_final: 0.7280 (ttt) REVERT: D 1724 ARG cc_start: 0.9013 (pmt-80) cc_final: 0.7762 (mmm160) REVERT: D 1729 PHE cc_start: 0.8602 (t80) cc_final: 0.8080 (t80) REVERT: D 1789 GLN cc_start: 0.9182 (tp40) cc_final: 0.8914 (mm-40) REVERT: D 2070 LYS cc_start: 0.9168 (ptpp) cc_final: 0.8664 (pttm) REVERT: D 2138 CYS cc_start: 0.9229 (m) cc_final: 0.8802 (m) REVERT: D 2149 ILE cc_start: 0.9670 (mt) cc_final: 0.9468 (tp) REVERT: D 2343 GLU cc_start: 0.4572 (OUTLIER) cc_final: 0.4248 (mp0) REVERT: D 2356 PHE cc_start: 0.7914 (m-10) cc_final: 0.7576 (m-10) REVERT: D 2496 GLU cc_start: 0.9098 (pt0) cc_final: 0.8465 (mt-10) outliers start: 27 outliers final: 6 residues processed: 548 average time/residue: 0.1819 time to fit residues: 162.2757 Evaluate side-chains 389 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 376 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 137 optimal weight: 6.9990 chunk 281 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 364 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 295 optimal weight: 8.9990 chunk 319 optimal weight: 20.0000 chunk 351 optimal weight: 6.9990 chunk 366 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 A1567 GLN A2034 GLN A2042 HIS A2060 ASN ** A2102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 GLN A2306 ASN ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN B1052 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 ASN B1353 GLN B1409 HIS B1567 GLN B2042 HIS B2060 ASN ** B2102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2206 GLN B2229 GLN B2306 ASN ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN D1052 GLN D1111 GLN ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1567 GLN D2034 GLN D2042 HIS D2060 ASN D2206 GLN ** D2229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2306 ASN ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.089244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.073704 restraints weight = 342321.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.074709 restraints weight = 188774.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.075468 restraints weight = 128177.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.075749 restraints weight = 96339.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.076235 restraints weight = 75958.073| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.7680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 32357 Z= 0.249 Angle : 0.835 12.112 43878 Z= 0.439 Chirality : 0.047 0.272 5043 Planarity : 0.007 0.108 5381 Dihedral : 5.591 49.125 4251 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 25.50 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.87 % Favored : 90.45 % Rotamer: Outliers : 0.62 % Allowed : 6.04 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.13), residues: 3801 helix: 0.04 (0.10), residues: 2541 sheet: -4.71 (0.28), residues: 138 loop : -4.13 (0.14), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1547 TYR 0.046 0.002 TYR D2507 PHE 0.029 0.003 PHE B2004 TRP 0.029 0.002 TRP A2124 HIS 0.010 0.002 HIS D1364 Details of bonding type rmsd covalent geometry : bond 0.00527 (32354) covalent geometry : angle 0.83483 (43872) SS BOND : bond 0.00112 ( 3) SS BOND : angle 0.89209 ( 6) hydrogen bonds : bond 0.04800 ( 1952) hydrogen bonds : angle 5.25607 ( 5745) *********************** 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 476 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 455 time to evaluate : 1.363 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 1290 VAL cc_start: 0.7208 (t) cc_final: 0.6881 (t) REVERT: A 1694 ILE cc_start: 0.9448 (mm) cc_final: 0.9034 (mm) REVERT: A 1696 ILE cc_start: 0.9316 (mm) cc_final: 0.8728 (mm) REVERT: A 1710 LEU cc_start: 0.9553 (mt) cc_final: 0.9218 (mt) REVERT: A 1719 MET cc_start: 0.8239 (ttt) cc_final: 0.7760 (ttt) REVERT: A 1724 ARG cc_start: 0.9178 (pmt-80) cc_final: 0.7969 (mmm160) REVERT: A 1736 PHE cc_start: 0.9154 (t80) cc_final: 0.8526 (t80) REVERT: A 1964 MET cc_start: 0.9276 (mtp) cc_final: 0.8754 (mmm) REVERT: A 1968 ASP cc_start: 0.9065 (t0) cc_final: 0.8823 (t0) REVERT: A 2007 MET cc_start: 0.9482 (mmp) cc_final: 0.9180 (mmm) REVERT: A 2012 PHE cc_start: 0.9369 (t80) cc_final: 0.9137 (t80) REVERT: A 2033 PHE cc_start: 0.8902 (t80) cc_final: 0.8606 (t80) REVERT: A 2037 LEU cc_start: 0.9674 (mt) cc_final: 0.9419 (mt) REVERT: A 2076 LEU cc_start: 0.9535 (mt) cc_final: 0.9151 (mt) REVERT: A 2117 GLU cc_start: 0.8976 (mp0) cc_final: 0.8464 (mm-30) REVERT: A 2118 LEU cc_start: 0.9514 (mt) cc_final: 0.9239 (mt) REVERT: A 2123 ASP cc_start: 0.9478 (m-30) cc_final: 0.8583 (m-30) REVERT: A 2133 LEU cc_start: 0.9540 (tt) cc_final: 0.9141 (tt) REVERT: A 2175 MET cc_start: 0.8788 (mtm) cc_final: 0.8366 (mmt) REVERT: A 2181 LEU cc_start: 0.9392 (mm) cc_final: 0.9187 (pp) REVERT: A 2182 PHE cc_start: 0.9560 (t80) cc_final: 0.9345 (t80) REVERT: A 2496 GLU cc_start: 0.9344 (pt0) cc_final: 0.8700 (mt-10) REVERT: B 711 MET cc_start: 0.8287 (mmp) cc_final: 0.8087 (mmm) REVERT: B 1290 VAL cc_start: 0.7321 (t) cc_final: 0.6931 (t) REVERT: B 1694 ILE cc_start: 0.9438 (mm) cc_final: 0.9035 (mm) REVERT: B 1696 ILE cc_start: 0.9284 (mm) cc_final: 0.8717 (mm) REVERT: B 1710 LEU cc_start: 0.9570 (mt) cc_final: 0.9218 (mt) REVERT: B 1719 MET cc_start: 0.8240 (ttt) cc_final: 0.7726 (ttt) REVERT: B 1724 ARG cc_start: 0.8687 (ptp90) cc_final: 0.8418 (mmm160) REVERT: B 1736 PHE cc_start: 0.9181 (t80) cc_final: 0.8493 (t80) REVERT: B 1964 MET cc_start: 0.9288 (mtp) cc_final: 0.8732 (mmm) REVERT: B 2007 MET cc_start: 0.9464 (mmp) cc_final: 0.9237 (mmm) REVERT: B 2012 PHE cc_start: 0.9356 (t80) cc_final: 0.9085 (t80) REVERT: B 2015 MET cc_start: 0.9302 (mtt) cc_final: 0.9011 (tmm) REVERT: B 2037 LEU cc_start: 0.9574 (mt) cc_final: 0.9369 (mt) REVERT: B 2076 LEU cc_start: 0.9533 (mt) cc_final: 0.9199 (mt) REVERT: B 2223 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7628 (m-10) REVERT: B 2225 MET cc_start: 0.5547 (mtm) cc_final: 0.4557 (mtt) REVERT: B 2317 VAL cc_start: 0.7144 (t) cc_final: 0.6877 (p) REVERT: B 2356 PHE cc_start: 0.8027 (m-10) cc_final: 0.7751 (m-10) REVERT: B 2466 ILE cc_start: 0.9669 (pt) cc_final: 0.9164 (pt) REVERT: B 2470 GLU cc_start: 0.8394 (pm20) cc_final: 0.8090 (pm20) REVERT: B 2496 GLU cc_start: 0.9349 (pt0) cc_final: 0.9069 (pt0) REVERT: B 2506 LEU cc_start: 0.9663 (mm) cc_final: 0.9362 (mm) REVERT: B 2513 MET cc_start: 0.9521 (mmm) cc_final: 0.9096 (mmm) REVERT: C 240 CYS cc_start: 0.6053 (t) cc_final: 0.4879 (t) REVERT: D 1290 VAL cc_start: 0.7091 (t) cc_final: 0.6689 (t) REVERT: D 1694 ILE cc_start: 0.9464 (mm) cc_final: 0.9038 (mm) REVERT: D 1696 ILE cc_start: 0.9331 (mm) cc_final: 0.8744 (mm) REVERT: D 1710 LEU cc_start: 0.9563 (mt) cc_final: 0.9207 (mt) REVERT: D 1719 MET cc_start: 0.8171 (ttt) cc_final: 0.7728 (ttt) REVERT: D 1724 ARG cc_start: 0.9199 (pmt-80) cc_final: 0.8003 (mmm160) REVERT: D 1736 PHE cc_start: 0.9112 (t80) cc_final: 0.8552 (t80) REVERT: D 1968 ASP cc_start: 0.9076 (t0) cc_final: 0.8841 (t0) REVERT: D 2007 MET cc_start: 0.9461 (mmp) cc_final: 0.9209 (mmm) REVERT: D 2012 PHE cc_start: 0.9370 (t80) cc_final: 0.9132 (t80) REVERT: D 2033 PHE cc_start: 0.8997 (t80) cc_final: 0.8753 (t80) REVERT: D 2037 LEU cc_start: 0.9702 (mt) cc_final: 0.9476 (mt) REVERT: D 2117 GLU cc_start: 0.9018 (mp0) cc_final: 0.8452 (mm-30) REVERT: D 2118 LEU cc_start: 0.9488 (mt) cc_final: 0.9234 (mt) REVERT: D 2123 ASP cc_start: 0.9475 (m-30) cc_final: 0.8550 (m-30) REVERT: D 2149 ILE cc_start: 0.9746 (mt) cc_final: 0.9478 (tp) REVERT: D 2356 PHE cc_start: 0.8157 (m-10) cc_final: 0.7938 (m-10) REVERT: D 2467 MET cc_start: 0.6904 (pmm) cc_final: 0.5962 (pmm) REVERT: D 2468 PHE cc_start: 0.8540 (m-10) cc_final: 0.7728 (m-10) REVERT: D 2496 GLU cc_start: 0.9303 (pt0) cc_final: 0.8976 (pt0) outliers start: 21 outliers final: 1 residues processed: 476 average time/residue: 0.1758 time to fit residues: 139.4415 Evaluate side-chains 345 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 343 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 46 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 382 optimal weight: 2.9990 chunk 370 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 290 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 284 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 HIS A 851 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1353 GLN A1409 HIS ** A2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 ASN ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN ** B2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2102 ASN B2306 ASN ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2377 ASN D 702 HIS D 851 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2229 GLN D2306 ASN ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2377 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.090390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.075570 restraints weight = 336937.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.076843 restraints weight = 180482.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.078054 restraints weight = 101626.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.077912 restraints weight = 85746.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.077900 restraints weight = 79179.209| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.8163 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= 0.161 Angle : 0.762 11.103 43878 Z= 0.386 Chirality : 0.044 0.260 5043 Planarity : 0.006 0.110 5381 Dihedral : 5.322 34.131 4251 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.39 % Favored : 92.05 % Rotamer: Outliers : 0.30 % Allowed : 4.32 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.13), residues: 3801 helix: 0.44 (0.10), residues: 2565 sheet: -4.73 (0.25), residues: 171 loop : -3.92 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1547 TYR 0.030 0.001 TYR D1961 PHE 0.032 0.002 PHE B2033 TRP 0.027 0.002 TRP D2066 HIS 0.007 0.001 HIS D1699 Details of bonding type rmsd covalent geometry : bond 0.00358 (32354) covalent geometry : angle 0.76203 (43872) SS BOND : bond 0.00102 ( 3) SS BOND : angle 1.09219 ( 6) hydrogen bonds : bond 0.04145 ( 1952) hydrogen bonds : angle 4.87837 ( 5745) *********************** 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 472 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 462 time to evaluate : 1.415 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: A 1694 ILE cc_start: 0.9154 (mm) cc_final: 0.8912 (mm) REVERT: A 1696 ILE cc_start: 0.9294 (mm) cc_final: 0.8807 (mm) REVERT: A 1710 LEU cc_start: 0.9562 (mt) cc_final: 0.9324 (mt) REVERT: A 1716 LEU cc_start: 0.8640 (mp) cc_final: 0.8416 (mp) REVERT: A 1719 MET cc_start: 0.8293 (ttt) cc_final: 0.7776 (ttt) REVERT: A 1724 ARG cc_start: 0.9109 (pmt-80) cc_final: 0.7998 (mmm160) REVERT: A 1736 PHE cc_start: 0.9107 (t80) cc_final: 0.8519 (t80) REVERT: A 1964 MET cc_start: 0.9138 (mtp) cc_final: 0.8643 (mmm) REVERT: A 1968 ASP cc_start: 0.9023 (t0) cc_final: 0.8737 (t0) REVERT: A 2007 MET cc_start: 0.9252 (mmp) cc_final: 0.8884 (mmm) REVERT: A 2037 LEU cc_start: 0.9548 (mt) cc_final: 0.9333 (mt) REVERT: A 2047 PHE cc_start: 0.8747 (t80) cc_final: 0.8267 (t80) REVERT: A 2076 LEU cc_start: 0.9513 (mt) cc_final: 0.9190 (mt) REVERT: A 2095 THR cc_start: 0.8558 (p) cc_final: 0.8272 (t) REVERT: A 2117 GLU cc_start: 0.9072 (mp0) cc_final: 0.8583 (mp0) REVERT: A 2123 ASP cc_start: 0.9288 (m-30) cc_final: 0.8657 (m-30) REVERT: A 2175 MET cc_start: 0.8650 (mtm) cc_final: 0.8296 (tpp) REVERT: A 2181 LEU cc_start: 0.9397 (mm) cc_final: 0.9092 (pp) REVERT: A 2182 PHE cc_start: 0.9545 (t80) cc_final: 0.9341 (t80) REVERT: A 2288 MET cc_start: 0.2198 (mtt) cc_final: 0.1390 (ptt) REVERT: A 2420 MET cc_start: 0.4778 (mmt) cc_final: 0.3857 (mmt) REVERT: A 2469 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8373 (tm-30) REVERT: A 2496 GLU cc_start: 0.9295 (pt0) cc_final: 0.8883 (pt0) REVERT: B 1694 ILE cc_start: 0.9152 (mm) cc_final: 0.8905 (mm) REVERT: B 1696 ILE cc_start: 0.9298 (mm) cc_final: 0.8862 (mm) REVERT: B 1710 LEU cc_start: 0.9570 (mt) cc_final: 0.9327 (mt) REVERT: B 1719 MET cc_start: 0.8283 (ttt) cc_final: 0.7664 (ttt) REVERT: B 1736 PHE cc_start: 0.9159 (t80) cc_final: 0.8561 (t80) REVERT: B 1964 MET cc_start: 0.9115 (mtp) cc_final: 0.8634 (mmm) REVERT: B 1968 ASP cc_start: 0.9230 (t70) cc_final: 0.8987 (t0) REVERT: B 2012 PHE cc_start: 0.9247 (t80) cc_final: 0.8987 (t80) REVERT: B 2015 MET cc_start: 0.9009 (mtt) cc_final: 0.8785 (mtt) REVERT: B 2037 LEU cc_start: 0.9523 (mt) cc_final: 0.9283 (mt) REVERT: B 2420 MET cc_start: 0.4859 (mmt) cc_final: 0.3879 (mmt) REVERT: B 2496 GLU cc_start: 0.9318 (pt0) cc_final: 0.8913 (pt0) REVERT: B 2513 MET cc_start: 0.9543 (mmm) cc_final: 0.9296 (mmm) REVERT: C 240 CYS cc_start: 0.6115 (t) cc_final: 0.5398 (p) REVERT: C 247 SER cc_start: 0.4081 (t) cc_final: 0.2514 (t) REVERT: D 1694 ILE cc_start: 0.9155 (mm) cc_final: 0.8903 (mm) REVERT: D 1696 ILE cc_start: 0.9284 (mm) cc_final: 0.8820 (mm) REVERT: D 1716 LEU cc_start: 0.8605 (mp) cc_final: 0.8398 (mp) REVERT: D 1719 MET cc_start: 0.8196 (ttt) cc_final: 0.7517 (ttt) REVERT: D 1724 ARG cc_start: 0.9127 (pmt-80) cc_final: 0.8048 (mmm160) REVERT: D 1964 MET cc_start: 0.9169 (mtp) cc_final: 0.8732 (mmm) REVERT: D 1968 ASP cc_start: 0.9021 (t0) cc_final: 0.8768 (t0) REVERT: D 2018 ASP cc_start: 0.9017 (m-30) cc_final: 0.8815 (m-30) REVERT: D 2033 PHE cc_start: 0.8926 (t80) cc_final: 0.8258 (t80) REVERT: D 2037 LEU cc_start: 0.9583 (mt) cc_final: 0.8807 (mt) REVERT: D 2047 PHE cc_start: 0.8713 (t80) cc_final: 0.8227 (t80) REVERT: D 2076 LEU cc_start: 0.9542 (mt) cc_final: 0.9284 (mt) REVERT: D 2117 GLU cc_start: 0.9005 (mp0) cc_final: 0.8548 (mm-30) REVERT: D 2123 ASP cc_start: 0.9352 (m-30) cc_final: 0.8771 (m-30) REVERT: D 2149 ILE cc_start: 0.9749 (mt) cc_final: 0.9528 (tp) REVERT: D 2356 PHE cc_start: 0.8013 (m-10) cc_final: 0.7596 (m-10) REVERT: D 2466 ILE cc_start: 0.9535 (pt) cc_final: 0.9100 (pt) REVERT: D 2467 MET cc_start: 0.7105 (pmm) cc_final: 0.6447 (pmm) REVERT: D 2468 PHE cc_start: 0.8469 (m-10) cc_final: 0.8003 (m-10) REVERT: D 2496 GLU cc_start: 0.9282 (pt0) cc_final: 0.8951 (pt0) outliers start: 10 outliers final: 0 residues processed: 472 average time/residue: 0.1810 time to fit residues: 142.9693 Evaluate side-chains 348 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 290 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 291 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 355 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN A 932 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2102 ASN ** 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 ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN D 932 HIS ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1222 ASN ** D2102 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.086875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.069505 restraints weight = 342735.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.071462 restraints weight = 175973.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.072504 restraints weight = 110023.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.073245 restraints weight = 81568.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.073549 restraints weight = 66930.021| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.8867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 32357 Z= 0.216 Angle : 0.775 14.022 43878 Z= 0.404 Chirality : 0.044 0.223 5043 Planarity : 0.006 0.114 5381 Dihedral : 5.350 34.672 4251 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.47 % Favored : 90.92 % Rotamer: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.13), residues: 3801 helix: 0.42 (0.10), residues: 2586 sheet: -4.38 (0.31), residues: 141 loop : -3.75 (0.16), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2508 TYR 0.029 0.002 TYR A1961 PHE 0.049 0.002 PHE D2356 TRP 0.024 0.002 TRP B2516 HIS 0.008 0.002 HIS B 932 Details of bonding type rmsd covalent geometry : bond 0.00457 (32354) covalent geometry : angle 0.77528 (43872) SS BOND : bond 0.00148 ( 3) SS BOND : angle 0.61133 ( 6) hydrogen bonds : bond 0.04249 ( 1952) hydrogen bonds : angle 4.93626 ( 5745) *********************** 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 438 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 435 time to evaluate : 1.229 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: A 1420 LEU cc_start: 0.8433 (mt) cc_final: 0.8028 (mt) REVERT: A 1694 ILE cc_start: 0.9284 (mm) cc_final: 0.9062 (mm) REVERT: A 1696 ILE cc_start: 0.9332 (mm) cc_final: 0.8742 (mm) REVERT: A 1710 LEU cc_start: 0.9622 (mt) cc_final: 0.9341 (mt) REVERT: A 1719 MET cc_start: 0.8497 (ttt) cc_final: 0.8034 (ttt) REVERT: A 1724 ARG cc_start: 0.9133 (pmt-80) cc_final: 0.8117 (mmm160) REVERT: A 1736 PHE cc_start: 0.9118 (t80) cc_final: 0.8595 (t80) REVERT: A 1791 MET cc_start: 0.8691 (ppp) cc_final: 0.8488 (ppp) REVERT: A 2007 MET cc_start: 0.9354 (mmp) cc_final: 0.9058 (mmm) REVERT: A 2047 PHE cc_start: 0.8845 (t80) cc_final: 0.8358 (t80) REVERT: A 2070 LYS cc_start: 0.9203 (ptpp) cc_final: 0.8859 (pttm) REVERT: A 2117 GLU cc_start: 0.9259 (mp0) cc_final: 0.8832 (mp0) REVERT: A 2123 ASP cc_start: 0.9258 (m-30) cc_final: 0.8680 (m-30) REVERT: A 2175 MET cc_start: 0.8708 (mtm) cc_final: 0.8459 (tpp) REVERT: A 2317 VAL cc_start: 0.7913 (t) cc_final: 0.7650 (p) REVERT: A 2356 PHE cc_start: 0.8000 (m-10) cc_final: 0.7791 (m-80) REVERT: A 2420 MET cc_start: 0.5487 (mmt) cc_final: 0.4352 (mmt) REVERT: A 2496 GLU cc_start: 0.9325 (pt0) cc_final: 0.9061 (pt0) REVERT: A 2506 LEU cc_start: 0.9566 (mm) cc_final: 0.8987 (mm) REVERT: B 1694 ILE cc_start: 0.9283 (mm) cc_final: 0.9051 (mm) REVERT: B 1696 ILE cc_start: 0.9327 (mm) cc_final: 0.8794 (mm) REVERT: B 1710 LEU cc_start: 0.9632 (mt) cc_final: 0.9350 (mt) REVERT: B 1719 MET cc_start: 0.8407 (ttt) cc_final: 0.7883 (ttt) REVERT: B 1736 PHE cc_start: 0.9161 (t80) cc_final: 0.8597 (t80) REVERT: B 1791 MET cc_start: 0.8732 (ppp) cc_final: 0.8531 (ppp) REVERT: B 1964 MET cc_start: 0.9123 (mtp) cc_final: 0.8625 (mmm) REVERT: B 2007 MET cc_start: 0.9387 (mmp) cc_final: 0.9169 (mmm) REVERT: B 2012 PHE cc_start: 0.9277 (t80) cc_final: 0.8928 (t80) REVERT: B 2015 MET cc_start: 0.9116 (mtt) cc_final: 0.8755 (tmm) REVERT: B 2016 VAL cc_start: 0.9710 (t) cc_final: 0.9067 (t) REVERT: B 2047 PHE cc_start: 0.8845 (t80) cc_final: 0.8353 (t80) REVERT: B 2076 LEU cc_start: 0.9557 (mt) cc_final: 0.9324 (mt) REVERT: B 2143 TYR cc_start: 0.8953 (t80) cc_final: 0.8752 (t80) REVERT: B 2420 MET cc_start: 0.5401 (mmt) cc_final: 0.4246 (mmt) REVERT: B 2496 GLU cc_start: 0.9386 (pt0) cc_final: 0.9013 (pt0) REVERT: B 2506 LEU cc_start: 0.9696 (mm) cc_final: 0.9118 (mm) REVERT: B 2513 MET cc_start: 0.9479 (mmm) cc_final: 0.9030 (mmp) REVERT: C 240 CYS cc_start: 0.6272 (t) cc_final: 0.5524 (p) REVERT: C 247 SER cc_start: 0.4792 (t) cc_final: 0.4517 (t) REVERT: D 1694 ILE cc_start: 0.9276 (mm) cc_final: 0.9051 (mm) REVERT: D 1696 ILE cc_start: 0.9301 (mm) cc_final: 0.8721 (mm) REVERT: D 1710 LEU cc_start: 0.9632 (mt) cc_final: 0.9378 (mt) REVERT: D 1719 MET cc_start: 0.8439 (ttt) cc_final: 0.7839 (ttt) REVERT: D 1724 ARG cc_start: 0.9155 (pmt-80) cc_final: 0.8185 (mmm160) REVERT: D 1736 PHE cc_start: 0.9100 (t80) cc_final: 0.8617 (t80) REVERT: D 1791 MET cc_start: 0.8743 (ppp) cc_final: 0.8521 (ppp) REVERT: D 1964 MET cc_start: 0.9199 (mtp) cc_final: 0.8738 (mmm) REVERT: D 2007 MET cc_start: 0.9346 (mmp) cc_final: 0.9104 (mmm) REVERT: D 2018 ASP cc_start: 0.9015 (m-30) cc_final: 0.8753 (m-30) REVERT: D 2033 PHE cc_start: 0.8939 (t80) cc_final: 0.8328 (t80) REVERT: D 2037 LEU cc_start: 0.9616 (mt) cc_final: 0.8876 (mt) REVERT: D 2047 PHE cc_start: 0.8793 (t80) cc_final: 0.8291 (t80) REVERT: D 2076 LEU cc_start: 0.9589 (mt) cc_final: 0.9359 (mt) REVERT: D 2117 GLU cc_start: 0.9225 (mp0) cc_final: 0.8844 (mp0) REVERT: D 2123 ASP cc_start: 0.9252 (m-30) cc_final: 0.8667 (m-30) REVERT: D 2137 MET cc_start: 0.9175 (mtm) cc_final: 0.8733 (mtp) REVERT: D 2149 ILE cc_start: 0.9822 (mt) cc_final: 0.9609 (tp) REVERT: D 2356 PHE cc_start: 0.7834 (m-10) cc_final: 0.7286 (m-80) REVERT: D 2496 GLU cc_start: 0.9317 (pt0) cc_final: 0.8971 (pt0) REVERT: D 2506 LEU cc_start: 0.9474 (mm) cc_final: 0.9173 (mm) REVERT: D 2513 MET cc_start: 0.9312 (mmt) cc_final: 0.9088 (mmp) outliers start: 3 outliers final: 0 residues processed: 438 average time/residue: 0.1924 time to fit residues: 140.4137 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 : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 118 optimal weight: 7.9990 chunk 376 optimal weight: 0.0020 chunk 242 optimal weight: 0.9980 chunk 307 optimal weight: 0.9990 chunk 296 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 153 optimal weight: 0.0070 chunk 365 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 HIS A 851 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 GLN A2042 HIS A2102 ASN ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 HIS B 851 GLN B 932 HIS ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN ** B1535 HIS ** 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 851 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN ** D1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1789 GLN D2042 HIS ** D2102 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.089772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.075060 restraints weight = 336723.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.076167 restraints weight = 180183.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.077706 restraints weight = 104269.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.077342 restraints weight = 91862.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.077291 restraints weight = 83991.540| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.9066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 32357 Z= 0.141 Angle : 0.740 9.869 43878 Z= 0.370 Chirality : 0.043 0.227 5043 Planarity : 0.006 0.114 5381 Dihedral : 5.162 27.677 4251 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.39 % Favored : 92.00 % Rotamer: Outliers : 0.18 % Allowed : 3.44 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 3801 helix: 0.70 (0.10), residues: 2580 sheet: -4.14 (0.30), residues: 153 loop : -3.58 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D1671 TYR 0.041 0.001 TYR D2507 PHE 0.031 0.002 PHE B 990 TRP 0.031 0.001 TRP B1215 HIS 0.020 0.001 HIS D1535 Details of bonding type rmsd covalent geometry : bond 0.00321 (32354) covalent geometry : angle 0.73952 (43872) SS BOND : bond 0.00115 ( 3) SS BOND : angle 1.27089 ( 6) hydrogen bonds : bond 0.03880 ( 1952) hydrogen bonds : angle 4.54726 ( 5745) *********************** 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 451 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 445 time to evaluate : 1.234 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: A 1694 ILE cc_start: 0.9183 (mm) cc_final: 0.8953 (mm) REVERT: A 1696 ILE cc_start: 0.9247 (mm) cc_final: 0.8680 (mm) REVERT: A 1719 MET cc_start: 0.8490 (ttt) cc_final: 0.7904 (ttt) REVERT: A 1724 ARG cc_start: 0.9068 (pmt-80) cc_final: 0.8346 (mmm160) REVERT: A 1964 MET cc_start: 0.9048 (mtp) cc_final: 0.8698 (mmm) REVERT: A 2015 MET cc_start: 0.9134 (mmt) cc_final: 0.8587 (mmt) REVERT: A 2033 PHE cc_start: 0.8752 (t80) cc_final: 0.8384 (t80) REVERT: A 2037 LEU cc_start: 0.9475 (mt) cc_final: 0.9133 (mp) REVERT: A 2047 PHE cc_start: 0.8777 (t80) cc_final: 0.8373 (t80) REVERT: A 2070 LYS cc_start: 0.9152 (ptpp) cc_final: 0.8802 (pttm) REVERT: A 2117 GLU cc_start: 0.9220 (mp0) cc_final: 0.8643 (mp0) REVERT: A 2138 CYS cc_start: 0.9468 (m) cc_final: 0.9158 (t) REVERT: A 2175 MET cc_start: 0.8699 (mtm) cc_final: 0.8372 (mmp) REVERT: A 2181 LEU cc_start: 0.9342 (mm) cc_final: 0.9111 (pp) REVERT: A 2182 PHE cc_start: 0.9546 (t80) cc_final: 0.9329 (t80) REVERT: A 2420 MET cc_start: 0.5005 (mmt) cc_final: 0.4050 (mmt) REVERT: A 2466 ILE cc_start: 0.9704 (pt) cc_final: 0.9398 (pt) REVERT: A 2496 GLU cc_start: 0.9273 (pt0) cc_final: 0.8985 (pt0) REVERT: A 2506 LEU cc_start: 0.9547 (mm) cc_final: 0.9200 (mm) REVERT: B 711 MET cc_start: 0.7913 (mmp) cc_final: 0.7651 (mmp) REVERT: B 1690 LEU cc_start: 0.9083 (tt) cc_final: 0.8877 (tt) REVERT: B 1694 ILE cc_start: 0.9150 (mm) cc_final: 0.8896 (mm) REVERT: B 1696 ILE cc_start: 0.9258 (mm) cc_final: 0.8762 (mm) REVERT: B 1710 LEU cc_start: 0.9611 (mt) cc_final: 0.9390 (mt) REVERT: B 1716 LEU cc_start: 0.8794 (mp) cc_final: 0.8593 (mp) REVERT: B 1719 MET cc_start: 0.8455 (ttt) cc_final: 0.7891 (ttt) REVERT: B 1736 PHE cc_start: 0.9222 (t80) cc_final: 0.8743 (t80) REVERT: B 1964 MET cc_start: 0.8996 (mtp) cc_final: 0.8599 (mmm) REVERT: B 2012 PHE cc_start: 0.9199 (t80) cc_final: 0.8894 (t80) REVERT: B 2047 PHE cc_start: 0.8801 (t80) cc_final: 0.8359 (t80) REVERT: B 2070 LYS cc_start: 0.9199 (ptpp) cc_final: 0.8922 (ptpp) REVERT: B 2420 MET cc_start: 0.4769 (mmt) cc_final: 0.3986 (mmt) REVERT: B 2496 GLU cc_start: 0.9369 (pt0) cc_final: 0.9026 (pt0) REVERT: C 240 CYS cc_start: 0.6149 (t) cc_final: 0.5203 (p) REVERT: C 243 ILE cc_start: 0.7347 (tp) cc_final: 0.7133 (mt) REVERT: D 1694 ILE cc_start: 0.9176 (mm) cc_final: 0.8944 (mm) REVERT: D 1696 ILE cc_start: 0.9203 (mm) cc_final: 0.8696 (mm) REVERT: D 1716 LEU cc_start: 0.8748 (mp) cc_final: 0.8544 (mp) REVERT: D 1719 MET cc_start: 0.8431 (ttt) cc_final: 0.7899 (ttt) REVERT: D 1724 ARG cc_start: 0.9112 (pmt-80) cc_final: 0.8424 (mmm160) REVERT: D 1964 MET cc_start: 0.8966 (mtp) cc_final: 0.8673 (mmm) REVERT: D 2015 MET cc_start: 0.9149 (mmt) cc_final: 0.8538 (mmt) REVERT: D 2033 PHE cc_start: 0.8880 (t80) cc_final: 0.8416 (t80) REVERT: D 2037 LEU cc_start: 0.9547 (mt) cc_final: 0.9049 (mt) REVERT: D 2047 PHE cc_start: 0.8716 (t80) cc_final: 0.8308 (t80) REVERT: D 2076 LEU cc_start: 0.9523 (mt) cc_final: 0.9306 (mt) REVERT: D 2117 GLU cc_start: 0.9164 (mp0) cc_final: 0.8697 (mm-30) REVERT: D 2137 MET cc_start: 0.9152 (mtm) cc_final: 0.8501 (ttt) REVERT: D 2140 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8779 (mm-30) REVERT: D 2149 ILE cc_start: 0.9794 (mt) cc_final: 0.9557 (tp) REVERT: D 2466 ILE cc_start: 0.9413 (pt) cc_final: 0.8991 (pt) REVERT: D 2467 MET cc_start: 0.7086 (pmm) cc_final: 0.6808 (pmm) REVERT: D 2496 GLU cc_start: 0.9277 (pt0) cc_final: 0.8986 (pt0) REVERT: D 2499 LEU cc_start: 0.9675 (tt) cc_final: 0.9369 (tp) outliers start: 6 outliers final: 1 residues processed: 449 average time/residue: 0.1669 time to fit residues: 126.0917 Evaluate side-chains 342 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 341 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 344 optimal weight: 0.5980 chunk 272 optimal weight: 3.9990 chunk 356 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 361 optimal weight: 0.7980 chunk 5 optimal weight: 40.0000 chunk 83 optimal weight: 0.7980 chunk 187 optimal weight: 9.9990 chunk 280 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN A 932 HIS ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 GLN ** A1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 GLN ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** 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 ** B1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 HIS B2042 HIS B2100 HIS ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN D 932 HIS ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1789 GLN ** D2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2100 HIS ** D2102 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.088681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.074277 restraints weight = 339966.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.074304 restraints weight = 208521.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.075159 restraints weight = 136185.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.075193 restraints weight = 94873.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.075347 restraints weight = 98591.893| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.9370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 32357 Z= 0.148 Angle : 0.732 8.407 43878 Z= 0.372 Chirality : 0.043 0.251 5043 Planarity : 0.006 0.117 5381 Dihedral : 5.053 26.741 4251 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.16 % Favored : 92.29 % Rotamer: Outliers : 0.15 % Allowed : 2.40 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.14), residues: 3801 helix: 0.73 (0.10), residues: 2610 sheet: -3.96 (0.31), residues: 153 loop : -3.49 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 703 TYR 0.029 0.001 TYR B1307 PHE 0.035 0.002 PHE A2356 TRP 0.037 0.002 TRP D2066 HIS 0.021 0.002 HIS B1535 Details of bonding type rmsd covalent geometry : bond 0.00335 (32354) covalent geometry : angle 0.73173 (43872) SS BOND : bond 0.00086 ( 3) SS BOND : angle 0.86746 ( 6) hydrogen bonds : bond 0.03839 ( 1952) hydrogen bonds : angle 4.56943 ( 5745) *********************** 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 438 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 433 time to evaluate : 1.140 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 1694 ILE cc_start: 0.9253 (mm) cc_final: 0.9037 (mm) REVERT: A 1696 ILE cc_start: 0.9228 (mm) cc_final: 0.8677 (mm) REVERT: A 1719 MET cc_start: 0.8608 (ttt) cc_final: 0.7902 (ttt) REVERT: A 1724 ARG cc_start: 0.9098 (pmt-80) cc_final: 0.8409 (mmm160) REVERT: A 1964 MET cc_start: 0.9064 (mtp) cc_final: 0.8734 (mmm) REVERT: A 2007 MET cc_start: 0.9247 (mmp) cc_final: 0.9004 (mmm) REVERT: A 2015 MET cc_start: 0.9056 (mmt) cc_final: 0.8552 (mmt) REVERT: A 2033 PHE cc_start: 0.8821 (t80) cc_final: 0.8329 (t80) REVERT: A 2037 LEU cc_start: 0.9473 (mt) cc_final: 0.8986 (mp) REVERT: A 2047 PHE cc_start: 0.8804 (t80) cc_final: 0.8345 (t80) REVERT: A 2076 LEU cc_start: 0.9548 (mt) cc_final: 0.9333 (mt) REVERT: A 2117 GLU cc_start: 0.9249 (mp0) cc_final: 0.8729 (mp0) REVERT: A 2118 LEU cc_start: 0.9528 (mt) cc_final: 0.9238 (mt) REVERT: A 2123 ASP cc_start: 0.9350 (m-30) cc_final: 0.8629 (m-30) REVERT: A 2175 MET cc_start: 0.8659 (mtm) cc_final: 0.8399 (mmp) REVERT: A 2181 LEU cc_start: 0.9386 (mm) cc_final: 0.9161 (pp) REVERT: A 2182 PHE cc_start: 0.9550 (t80) cc_final: 0.9314 (t80) REVERT: A 2288 MET cc_start: 0.1360 (mtt) cc_final: 0.0796 (ptt) REVERT: A 2420 MET cc_start: 0.5255 (mmt) cc_final: 0.4308 (mmt) REVERT: A 2467 MET cc_start: 0.8601 (ttp) cc_final: 0.8275 (ttm) REVERT: A 2468 PHE cc_start: 0.8128 (m-80) cc_final: 0.7906 (m-10) REVERT: A 2496 GLU cc_start: 0.9310 (tt0) cc_final: 0.8941 (mt-10) REVERT: A 2499 LEU cc_start: 0.9781 (tt) cc_final: 0.9549 (tp) REVERT: B 1694 ILE cc_start: 0.9195 (mm) cc_final: 0.8943 (mm) REVERT: B 1710 LEU cc_start: 0.9658 (mt) cc_final: 0.9406 (mt) REVERT: B 1719 MET cc_start: 0.8584 (ttt) cc_final: 0.8042 (ttt) REVERT: B 1736 PHE cc_start: 0.9241 (t80) cc_final: 0.8772 (t80) REVERT: B 1791 MET cc_start: 0.8687 (ppp) cc_final: 0.8482 (ppp) REVERT: B 1964 MET cc_start: 0.8996 (mtp) cc_final: 0.8606 (mmm) REVERT: B 2012 PHE cc_start: 0.9195 (t80) cc_final: 0.8885 (t80) REVERT: B 2033 PHE cc_start: 0.8996 (t80) cc_final: 0.8465 (t80) REVERT: B 2037 LEU cc_start: 0.9520 (mt) cc_final: 0.8981 (mt) REVERT: B 2047 PHE cc_start: 0.8808 (t80) cc_final: 0.8368 (t80) REVERT: B 2070 LYS cc_start: 0.9236 (ptpp) cc_final: 0.8826 (pttm) REVERT: B 2076 LEU cc_start: 0.9470 (mt) cc_final: 0.9228 (mt) REVERT: B 2118 LEU cc_start: 0.9448 (mt) cc_final: 0.9114 (mt) REVERT: B 2123 ASP cc_start: 0.9426 (m-30) cc_final: 0.8608 (m-30) REVERT: B 2496 GLU cc_start: 0.9414 (pt0) cc_final: 0.8971 (pt0) REVERT: B 2506 LEU cc_start: 0.9656 (mm) cc_final: 0.9139 (mm) REVERT: B 2513 MET cc_start: 0.9407 (mmm) cc_final: 0.8817 (mmm) REVERT: C 240 CYS cc_start: 0.6286 (t) cc_final: 0.5317 (p) REVERT: C 243 ILE cc_start: 0.7181 (tp) cc_final: 0.6979 (mt) REVERT: D 706 MET cc_start: -0.1187 (mmp) cc_final: -0.1448 (tpt) REVERT: D 1694 ILE cc_start: 0.9218 (mm) cc_final: 0.8994 (mm) REVERT: D 1696 ILE cc_start: 0.9197 (mm) cc_final: 0.8598 (mm) REVERT: D 1716 LEU cc_start: 0.8966 (mp) cc_final: 0.8709 (mm) REVERT: D 1719 MET cc_start: 0.8549 (ttt) cc_final: 0.7788 (ttt) REVERT: D 1724 ARG cc_start: 0.9181 (pmt-80) cc_final: 0.8512 (mmm160) REVERT: D 1964 MET cc_start: 0.8980 (mtp) cc_final: 0.8731 (mmm) REVERT: D 2007 MET cc_start: 0.9225 (mmp) cc_final: 0.9003 (mmm) REVERT: D 2015 MET cc_start: 0.9115 (mmt) cc_final: 0.8627 (mmt) REVERT: D 2033 PHE cc_start: 0.8930 (t80) cc_final: 0.8210 (t80) REVERT: D 2037 LEU cc_start: 0.9549 (mt) cc_final: 0.8813 (mt) REVERT: D 2047 PHE cc_start: 0.8752 (t80) cc_final: 0.8303 (t80) REVERT: D 2070 LYS cc_start: 0.9372 (ptpp) cc_final: 0.8794 (pttm) REVERT: D 2117 GLU cc_start: 0.9146 (mp0) cc_final: 0.8796 (mp0) REVERT: D 2137 MET cc_start: 0.9187 (mtm) cc_final: 0.8495 (ttt) REVERT: D 2140 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8748 (mm-30) REVERT: D 2149 ILE cc_start: 0.9832 (mt) cc_final: 0.9548 (tp) REVERT: D 2478 LEU cc_start: 0.9729 (tt) cc_final: 0.9465 (pp) REVERT: D 2496 GLU cc_start: 0.9361 (pt0) cc_final: 0.8945 (pt0) REVERT: D 2506 LEU cc_start: 0.9429 (mm) cc_final: 0.8875 (mm) outliers start: 5 outliers final: 0 residues processed: 438 average time/residue: 0.1766 time to fit residues: 129.0288 Evaluate side-chains 340 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 370 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 303 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 333 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 GLN A2042 HIS ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 ASN ** B1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1112 GLN D1114 GLN D1222 ASN ** D1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1789 GLN D2042 HIS ** D2102 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.087273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.069774 restraints weight = 342106.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.071808 restraints weight = 174804.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.072986 restraints weight = 109417.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.073724 restraints weight = 79528.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.073981 restraints weight = 64935.828| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.9757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 32357 Z= 0.168 Angle : 0.736 8.803 43878 Z= 0.378 Chirality : 0.043 0.212 5043 Planarity : 0.006 0.117 5381 Dihedral : 5.068 28.391 4251 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.45 % Favored : 91.95 % Rotamer: Outliers : 0.12 % Allowed : 1.90 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.14), residues: 3801 helix: 0.72 (0.10), residues: 2598 sheet: -4.09 (0.29), residues: 174 loop : -3.31 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D2082 TYR 0.034 0.002 TYR B2067 PHE 0.038 0.002 PHE D1302 TRP 0.023 0.002 TRP D1113 HIS 0.032 0.002 HIS A 702 Details of bonding type rmsd covalent geometry : bond 0.00367 (32354) covalent geometry : angle 0.73587 (43872) SS BOND : bond 0.00112 ( 3) SS BOND : angle 0.69740 ( 6) hydrogen bonds : bond 0.03831 ( 1952) hydrogen bonds : angle 4.61456 ( 5745) *********************** 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 422 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 418 time to evaluate : 1.237 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: A 605 MET cc_start: 0.1536 (tpt) cc_final: 0.1189 (mtm) REVERT: A 1694 ILE cc_start: 0.9217 (mm) cc_final: 0.8994 (mm) REVERT: A 1719 MET cc_start: 0.8560 (ttt) cc_final: 0.8093 (ttt) REVERT: A 1724 ARG cc_start: 0.9042 (pmt-80) cc_final: 0.8424 (mmm160) REVERT: A 1964 MET cc_start: 0.9003 (mtp) cc_final: 0.8508 (mmm) REVERT: A 2007 MET cc_start: 0.9215 (mmp) cc_final: 0.8958 (mmm) REVERT: A 2033 PHE cc_start: 0.8740 (t80) cc_final: 0.8535 (t80) REVERT: A 2047 PHE cc_start: 0.8785 (t80) cc_final: 0.8361 (t80) REVERT: A 2070 LYS cc_start: 0.9129 (ptpp) cc_final: 0.8690 (pttm) REVERT: A 2076 LEU cc_start: 0.9557 (mt) cc_final: 0.9227 (mt) REVERT: A 2117 GLU cc_start: 0.9254 (mp0) cc_final: 0.8793 (mp0) REVERT: A 2181 LEU cc_start: 0.9356 (mm) cc_final: 0.9107 (pp) REVERT: A 2182 PHE cc_start: 0.9478 (t80) cc_final: 0.9221 (t80) REVERT: A 2288 MET cc_start: 0.1311 (mtt) cc_final: 0.0890 (ptt) REVERT: A 2420 MET cc_start: 0.5415 (mmt) cc_final: 0.4448 (mmt) REVERT: A 2496 GLU cc_start: 0.9256 (tt0) cc_final: 0.8917 (mt-10) REVERT: A 2506 LEU cc_start: 0.9616 (mm) cc_final: 0.9256 (mm) REVERT: A 2513 MET cc_start: 0.9306 (mmt) cc_final: 0.9069 (mmt) REVERT: B 1420 LEU cc_start: 0.8540 (mt) cc_final: 0.8239 (mt) REVERT: B 1694 ILE cc_start: 0.9164 (mm) cc_final: 0.8915 (mm) REVERT: B 1710 LEU cc_start: 0.9620 (mt) cc_final: 0.9339 (mt) REVERT: B 1736 PHE cc_start: 0.9196 (t80) cc_final: 0.8730 (t80) REVERT: B 1791 MET cc_start: 0.8657 (ppp) cc_final: 0.8454 (ppp) REVERT: B 1964 MET cc_start: 0.9006 (mtp) cc_final: 0.8616 (mmm) REVERT: B 1968 ASP cc_start: 0.9039 (t0) cc_final: 0.8806 (t0) REVERT: B 2007 MET cc_start: 0.9277 (mmp) cc_final: 0.9059 (mmm) REVERT: B 2012 PHE cc_start: 0.9197 (t80) cc_final: 0.8909 (t80) REVERT: B 2033 PHE cc_start: 0.8892 (t80) cc_final: 0.8499 (t80) REVERT: B 2037 LEU cc_start: 0.9567 (mt) cc_final: 0.9278 (mt) REVERT: B 2047 PHE cc_start: 0.8736 (t80) cc_final: 0.8344 (t80) REVERT: B 2070 LYS cc_start: 0.9172 (ptpp) cc_final: 0.8855 (pttm) REVERT: B 2214 LEU cc_start: 0.9482 (mp) cc_final: 0.9245 (mp) REVERT: B 2225 MET cc_start: 0.7078 (tpp) cc_final: 0.6554 (tpp) REVERT: B 2479 LYS cc_start: 0.9596 (pptt) cc_final: 0.9361 (pptt) REVERT: B 2496 GLU cc_start: 0.9439 (pt0) cc_final: 0.9057 (pt0) REVERT: B 2506 LEU cc_start: 0.9636 (mm) cc_final: 0.8900 (mm) REVERT: B 2513 MET cc_start: 0.9403 (mmm) cc_final: 0.8848 (mmm) REVERT: C 240 CYS cc_start: 0.6298 (t) cc_final: 0.5264 (p) REVERT: D 605 MET cc_start: 0.1814 (tpt) cc_final: 0.1494 (mtm) REVERT: D 706 MET cc_start: -0.0769 (mmp) cc_final: -0.1037 (tpt) REVERT: D 848 MET cc_start: -0.3339 (mmp) cc_final: -0.3724 (mmp) REVERT: D 1175 PHE cc_start: 0.9448 (t80) cc_final: 0.9227 (t80) REVERT: D 1694 ILE cc_start: 0.9218 (mm) cc_final: 0.8989 (mm) REVERT: D 1719 MET cc_start: 0.8424 (ttt) cc_final: 0.8053 (ttt) REVERT: D 1724 ARG cc_start: 0.9082 (pmt-80) cc_final: 0.8444 (mmm160) REVERT: D 2007 MET cc_start: 0.9198 (mmp) cc_final: 0.8982 (mmm) REVERT: D 2033 PHE cc_start: 0.8845 (t80) cc_final: 0.8168 (t80) REVERT: D 2037 LEU cc_start: 0.9520 (mt) cc_final: 0.8820 (mt) REVERT: D 2117 GLU cc_start: 0.9138 (mp0) cc_final: 0.8683 (mp0) REVERT: D 2118 LEU cc_start: 0.9641 (pp) cc_final: 0.9406 (pp) REVERT: D 2123 ASP cc_start: 0.9361 (m-30) cc_final: 0.8781 (m-30) REVERT: D 2137 MET cc_start: 0.9091 (mtm) cc_final: 0.8472 (ttt) REVERT: D 2140 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8568 (mm-30) REVERT: D 2149 ILE cc_start: 0.9831 (mt) cc_final: 0.9588 (tp) REVERT: D 2496 GLU cc_start: 0.9314 (pt0) cc_final: 0.8997 (pt0) REVERT: D 2506 LEU cc_start: 0.9389 (mm) cc_final: 0.9069 (mm) outliers start: 4 outliers final: 0 residues processed: 422 average time/residue: 0.1721 time to fit residues: 123.1332 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 : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 221 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 311 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 347 optimal weight: 0.9990 chunk 385 optimal weight: 7.9990 chunk 387 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 GLN A2042 HIS ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 ASN ** B1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1789 GLN D2042 HIS ** D2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.087867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.072150 restraints weight = 340097.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.072985 restraints weight = 185330.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.074038 restraints weight = 119419.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.074289 restraints weight = 80612.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.074321 restraints weight = 82792.356| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.9981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 32357 Z= 0.143 Angle : 0.732 10.866 43878 Z= 0.371 Chirality : 0.043 0.204 5043 Planarity : 0.006 0.118 5381 Dihedral : 5.021 27.298 4251 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.37 % Favored : 92.03 % Rotamer: Outliers : 0.09 % Allowed : 0.92 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.14), residues: 3801 helix: 0.80 (0.10), residues: 2568 sheet: -3.88 (0.31), residues: 171 loop : -3.20 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D2508 TYR 0.040 0.001 TYR D2067 PHE 0.034 0.002 PHE A2356 TRP 0.024 0.001 TRP B 802 HIS 0.019 0.001 HIS A 702 Details of bonding type rmsd covalent geometry : bond 0.00323 (32354) covalent geometry : angle 0.73167 (43872) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.75156 ( 6) hydrogen bonds : bond 0.03790 ( 1952) hydrogen bonds : angle 4.54725 ( 5745) *********************** 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: 3 poor density : 419 time to evaluate : 0.894 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: A 605 MET cc_start: 0.1446 (tpt) cc_final: 0.1147 (mtm) REVERT: A 1412 VAL cc_start: 0.8334 (p) cc_final: 0.8065 (m) REVERT: A 1719 MET cc_start: 0.8475 (ttt) cc_final: 0.7925 (ttt) REVERT: A 1964 MET cc_start: 0.9018 (mtp) cc_final: 0.8716 (mmm) REVERT: A 2007 MET cc_start: 0.9252 (mmp) cc_final: 0.8957 (mmm) REVERT: A 2015 MET cc_start: 0.9105 (mmp) cc_final: 0.8869 (mmm) REVERT: A 2033 PHE cc_start: 0.8865 (t80) cc_final: 0.8523 (t80) REVERT: A 2037 LEU cc_start: 0.9569 (mt) cc_final: 0.9319 (mt) REVERT: A 2047 PHE cc_start: 0.8765 (t80) cc_final: 0.8343 (t80) REVERT: A 2070 LYS cc_start: 0.9140 (ptpp) cc_final: 0.8773 (pttm) REVERT: A 2076 LEU cc_start: 0.9560 (mt) cc_final: 0.9348 (mt) REVERT: A 2117 GLU cc_start: 0.9263 (mp0) cc_final: 0.8779 (mp0) REVERT: A 2181 LEU cc_start: 0.9400 (mm) cc_final: 0.9184 (pp) REVERT: A 2182 PHE cc_start: 0.9558 (t80) cc_final: 0.9307 (t80) REVERT: A 2288 MET cc_start: 0.1048 (mtt) cc_final: 0.0713 (ptt) REVERT: A 2420 MET cc_start: 0.5303 (mmt) cc_final: 0.4406 (mmt) REVERT: A 2466 ILE cc_start: 0.9581 (pt) cc_final: 0.9333 (pt) REVERT: A 2506 LEU cc_start: 0.9610 (mm) cc_final: 0.9172 (mm) REVERT: B 605 MET cc_start: 0.1755 (tpt) cc_final: 0.1498 (ptm) REVERT: B 1420 LEU cc_start: 0.8584 (mt) cc_final: 0.8282 (mt) REVERT: B 1694 ILE cc_start: 0.9136 (mm) cc_final: 0.8881 (mm) REVERT: B 1710 LEU cc_start: 0.9643 (mt) cc_final: 0.9389 (mt) REVERT: B 1719 MET cc_start: 0.8556 (ttt) cc_final: 0.7772 (ttt) REVERT: B 1736 PHE cc_start: 0.9245 (t80) cc_final: 0.8781 (t80) REVERT: B 1964 MET cc_start: 0.8965 (mtp) cc_final: 0.8614 (mmm) REVERT: B 2007 MET cc_start: 0.9273 (mmp) cc_final: 0.9038 (mmm) REVERT: B 2012 PHE cc_start: 0.9246 (t80) cc_final: 0.8922 (t80) REVERT: B 2033 PHE cc_start: 0.8927 (t80) cc_final: 0.8557 (t80) REVERT: B 2037 LEU cc_start: 0.9562 (mt) cc_final: 0.9278 (mt) REVERT: B 2070 LYS cc_start: 0.9152 (ptpp) cc_final: 0.8823 (pttm) REVERT: B 2225 MET cc_start: 0.7141 (tpp) cc_final: 0.6617 (tpp) REVERT: B 2325 MET cc_start: 0.9163 (pmm) cc_final: 0.8264 (tpt) REVERT: B 2479 LYS cc_start: 0.9595 (pptt) cc_final: 0.9320 (pptt) REVERT: B 2496 GLU cc_start: 0.9431 (pt0) cc_final: 0.9089 (pt0) REVERT: B 2506 LEU cc_start: 0.9690 (mm) cc_final: 0.9156 (mm) REVERT: B 2513 MET cc_start: 0.9200 (mmm) cc_final: 0.8971 (mmm) REVERT: C 240 CYS cc_start: 0.5836 (t) cc_final: 0.5249 (p) REVERT: D 605 MET cc_start: 0.1658 (tpt) cc_final: 0.1418 (ptm) REVERT: D 1290 VAL cc_start: 0.7542 (t) cc_final: 0.7311 (t) REVERT: D 1690 LEU cc_start: 0.9110 (tt) cc_final: 0.8849 (pp) REVERT: D 1719 MET cc_start: 0.8527 (ttt) cc_final: 0.7981 (ttt) REVERT: D 1964 MET cc_start: 0.9019 (mtp) cc_final: 0.8769 (mmm) REVERT: D 2007 MET cc_start: 0.9257 (mmp) cc_final: 0.9002 (mmm) REVERT: D 2033 PHE cc_start: 0.8849 (t80) cc_final: 0.8163 (t80) REVERT: D 2037 LEU cc_start: 0.9493 (mt) cc_final: 0.8797 (mt) REVERT: D 2047 PHE cc_start: 0.8756 (t80) cc_final: 0.8353 (t80) REVERT: D 2070 LYS cc_start: 0.9154 (ptpp) cc_final: 0.8876 (ptpp) REVERT: D 2076 LEU cc_start: 0.9553 (mt) cc_final: 0.9337 (mt) REVERT: D 2117 GLU cc_start: 0.9177 (mp0) cc_final: 0.8666 (mp0) REVERT: D 2137 MET cc_start: 0.9090 (mtm) cc_final: 0.8401 (ttt) REVERT: D 2149 ILE cc_start: 0.9823 (mt) cc_final: 0.9581 (tp) REVERT: D 2479 LYS cc_start: 0.9591 (pptt) cc_final: 0.9324 (pptt) REVERT: D 2496 GLU cc_start: 0.9316 (pt0) cc_final: 0.8992 (pt0) REVERT: D 2506 LEU cc_start: 0.9636 (mm) cc_final: 0.9308 (mm) outliers start: 3 outliers final: 1 residues processed: 422 average time/residue: 0.1671 time to fit residues: 119.3079 Evaluate side-chains 325 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 187 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 40.0000 chunk 264 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 40.0000 chunk 126 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** ** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN ** A1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 GLN A1951 HIS ** A2042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2464 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** ** 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 ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2409 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1222 ASN ** D1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1951 HIS D1999 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.084255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.068173 restraints weight = 344798.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.068593 restraints weight = 195815.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.069747 restraints weight = 127963.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.069640 restraints weight = 93386.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.069642 restraints weight = 87671.518| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 1.0496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 32357 Z= 0.233 Angle : 0.822 10.334 43878 Z= 0.425 Chirality : 0.046 0.334 5043 Planarity : 0.007 0.123 5381 Dihedral : 5.366 33.499 4251 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 25.99 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.79 % Favored : 90.61 % Rotamer: Outliers : 0.09 % Allowed : 0.65 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.13), residues: 3801 helix: 0.46 (0.10), residues: 2568 sheet: -3.85 (0.28), residues: 198 loop : -3.25 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B2082 TYR 0.042 0.002 TYR A2067 PHE 0.038 0.002 PHE A2356 TRP 0.032 0.002 TRP D2066 HIS 0.017 0.002 HIS A 702 Details of bonding type rmsd covalent geometry : bond 0.00486 (32354) covalent geometry : angle 0.82157 (43872) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.70261 ( 6) hydrogen bonds : bond 0.04257 ( 1952) hydrogen bonds : angle 4.88560 ( 5745) ********************** 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 405 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 402 time to evaluate : 1.108 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: A 605 MET cc_start: 0.1326 (tpt) cc_final: 0.1045 (ptm) REVERT: A 1694 ILE cc_start: 0.9294 (mm) cc_final: 0.9081 (mm) REVERT: A 1719 MET cc_start: 0.8657 (ttt) cc_final: 0.8083 (ttt) REVERT: A 1964 MET cc_start: 0.9139 (mtp) cc_final: 0.8731 (mmm) REVERT: A 2007 MET cc_start: 0.9391 (mmp) cc_final: 0.9048 (mmm) REVERT: A 2033 PHE cc_start: 0.8901 (t80) cc_final: 0.8647 (t80) REVERT: A 2037 LEU cc_start: 0.9632 (mt) cc_final: 0.9410 (mt) REVERT: A 2117 GLU cc_start: 0.9327 (mp0) cc_final: 0.8939 (mp0) REVERT: A 2181 LEU cc_start: 0.9437 (mm) cc_final: 0.9212 (pp) REVERT: A 2182 PHE cc_start: 0.9569 (t80) cc_final: 0.9312 (t80) REVERT: A 2288 MET cc_start: 0.1369 (mtt) cc_final: 0.0936 (ptm) REVERT: A 2420 MET cc_start: 0.5700 (mmt) cc_final: 0.4840 (mmt) REVERT: B 605 MET cc_start: 0.1643 (tpt) cc_final: 0.1353 (mtm) REVERT: B 848 MET cc_start: -0.1695 (mmp) cc_final: -0.2063 (mmp) REVERT: B 1420 LEU cc_start: 0.8725 (mt) cc_final: 0.8435 (mt) REVERT: B 1694 ILE cc_start: 0.9231 (mm) cc_final: 0.9007 (mm) REVERT: B 1719 MET cc_start: 0.8537 (ttt) cc_final: 0.8136 (ttt) REVERT: B 1791 MET cc_start: 0.8674 (ppp) cc_final: 0.8426 (ppp) REVERT: B 2007 MET cc_start: 0.9414 (mmp) cc_final: 0.9129 (mmm) REVERT: B 2012 PHE cc_start: 0.9304 (t80) cc_final: 0.8985 (t80) REVERT: B 2033 PHE cc_start: 0.8986 (t80) cc_final: 0.8636 (t80) REVERT: B 2037 LEU cc_start: 0.9607 (mt) cc_final: 0.9342 (mt) REVERT: B 2496 GLU cc_start: 0.9401 (pt0) cc_final: 0.9150 (pt0) REVERT: B 2506 LEU cc_start: 0.9764 (mm) cc_final: 0.8985 (mm) REVERT: B 2513 MET cc_start: 0.9429 (mmm) cc_final: 0.8900 (mmm) REVERT: D 605 MET cc_start: 0.1587 (tpt) cc_final: 0.1296 (mtm) REVERT: D 1719 MET cc_start: 0.8581 (ttt) cc_final: 0.7953 (ttt) REVERT: D 1964 MET cc_start: 0.9148 (mtp) cc_final: 0.8753 (mmm) REVERT: D 2007 MET cc_start: 0.9418 (mmp) cc_final: 0.9084 (mmm) REVERT: D 2018 ASP cc_start: 0.9086 (m-30) cc_final: 0.8808 (m-30) REVERT: D 2033 PHE cc_start: 0.8917 (t80) cc_final: 0.8347 (t80) REVERT: D 2037 LEU cc_start: 0.9599 (mt) cc_final: 0.8881 (mt) REVERT: D 2117 GLU cc_start: 0.9251 (mp0) cc_final: 0.8900 (mm-30) REVERT: D 2123 ASP cc_start: 0.9325 (m-30) cc_final: 0.8902 (m-30) REVERT: D 2137 MET cc_start: 0.9192 (mtm) cc_final: 0.8459 (ttt) REVERT: D 2506 LEU cc_start: 0.9635 (mm) cc_final: 0.9129 (mm) REVERT: D 2513 MET cc_start: 0.9580 (mmp) cc_final: 0.9111 (mmm) outliers start: 3 outliers final: 1 residues processed: 405 average time/residue: 0.1647 time to fit residues: 113.4595 Evaluate side-chains 313 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 165 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 319 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 296 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- 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** ** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1699 HIS A1789 GLN A2042 HIS ** A2375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 ASN ** B1535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1699 HIS B2042 HIS ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1222 ASN D1699 HIS D1789 GLN D1999 GLN ** D2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2042 HIS ** D2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2375 GLN ** 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 = 0.4101 r_free = 0.4101 target = 0.085877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.068139 restraints weight = 343897.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.070018 restraints weight = 175152.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.071150 restraints weight = 107729.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.071706 restraints weight = 77770.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.071908 restraints weight = 65006.872| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 1.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 32357 Z= 0.165 Angle : 0.772 12.671 43878 Z= 0.392 Chirality : 0.044 0.313 5043 Planarity : 0.006 0.120 5381 Dihedral : 5.205 30.716 4251 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.79 % Favored : 91.61 % Rotamer: Outliers : 0.09 % Allowed : 0.59 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.14), residues: 3801 helix: 0.59 (0.10), residues: 2580 sheet: -3.81 (0.31), residues: 174 loop : -3.24 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 703 TYR 0.049 0.002 TYR B2067 PHE 0.036 0.002 PHE A2356 TRP 0.075 0.002 TRP A2066 HIS 0.025 0.002 HIS D 702 Details of bonding type rmsd covalent geometry : bond 0.00372 (32354) covalent geometry : angle 0.77222 (43872) SS BOND : bond 0.00094 ( 3) SS BOND : angle 0.66853 ( 6) hydrogen bonds : bond 0.03990 ( 1952) hydrogen bonds : angle 4.66828 ( 5745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10140.49 seconds wall clock time: 174 minutes 13.50 seconds (10453.50 seconds total)