Starting phenix.real_space_refine on Sat Sep 12 04:46:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zy6_11551/09_2026/6zy6_11551.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy6_11551/09_2026/6zy6_11551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zy6_11551/09_2026/6zy6_11551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy6_11551/09_2026/6zy6_11551.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zy6_11551/09_2026/6zy6_11551.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zy6_11551/09_2026/6zy6_11551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zy6_11551/09_2026/6zy6_11551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy6_11551/09_2026/6zy6_11551.map" } resolution = 4.1 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= 0.005 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 52 5.16 5 C 8418 2.51 5 N 2312 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13504 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.02, per 1000 atoms: 0.22 Number of scatterers: 13504 At special positions: 0 Unit cell: (100.969, 119.053, 122.067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 56 15.00 O 2666 8.00 N 2312 7.00 C 8418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.15 Conformation dependent library (CDL) restraints added in 576.4 milliseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 16 sheets defined 50.7% alpha, 6.7% beta 30 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.642A pdb=" N THR A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.691A pdb=" N MET A 502 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.683A pdb=" N ILE A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.612A pdb=" N LEU A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 559 removed outlier: 3.960A pdb=" N HIS A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.691A pdb=" N ARG A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.585A pdb=" N GLU A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.036A pdb=" N HIS A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.744A pdb=" N ALA A 647 " --> pdb=" O PRO A 643 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 679 Processing helix chain 'A' and resid 694 through 702 Processing helix chain 'A' and resid 702 through 715 removed outlier: 3.567A pdb=" N PHE A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.639A pdb=" N ARG A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 755 removed outlier: 3.582A pdb=" N GLY A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 750 " --> pdb=" O GLN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 773 Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 819 through 825 removed outlier: 3.891A pdb=" N HIS A 824 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 869 through 882 removed outlier: 3.906A pdb=" N VAL A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 removed outlier: 4.684A pdb=" N GLU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Proline residue: A 942 - end of helix removed outlier: 3.642A pdb=" N ASN A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 removed outlier: 3.678A pdb=" N ALA A 978 " --> pdb=" O GLU A 974 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 1014 through 1038 removed outlier: 3.811A pdb=" N ILE A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.606A pdb=" N GLU A1044 " --> pdb=" O MET A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1093 Processing helix chain 'A' and resid 1125 through 1129 Processing helix chain 'A' and resid 1132 through 1136 removed outlier: 3.696A pdb=" N TYR A1135 " --> pdb=" O PRO A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1161 removed outlier: 3.708A pdb=" N ARG A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A1149 " --> pdb=" O CYS A1145 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A1152 " --> pdb=" O ARG A1148 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1192 removed outlier: 3.917A pdb=" N GLU A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A1173 " --> pdb=" O GLU A1169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 477 removed outlier: 3.639A pdb=" N THR B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.692A pdb=" N MET B 502 " --> pdb=" O HIS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 515 removed outlier: 3.684A pdb=" N ILE B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.612A pdb=" N LEU B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.959A pdb=" N HIS B 548 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.691A pdb=" N ARG B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS B 567 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.589A pdb=" N GLU B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 4.036A pdb=" N HIS B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 652 removed outlier: 3.746A pdb=" N ALA B 647 " --> pdb=" O PRO B 643 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 679 Processing helix chain 'B' and resid 694 through 702 Processing helix chain 'B' and resid 702 through 715 removed outlier: 3.566A pdb=" N PHE B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 736 removed outlier: 3.638A pdb=" N ARG B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 755 removed outlier: 3.582A pdb=" N GLY B 749 " --> pdb=" O ALA B 745 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 750 " --> pdb=" O GLN B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 773 Processing helix chain 'B' and resid 813 through 818 Processing helix chain 'B' and resid 819 through 825 removed outlier: 3.890A pdb=" N HIS B 824 " --> pdb=" O LYS B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 869 through 882 removed outlier: 3.906A pdb=" N VAL B 873 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 945 removed outlier: 4.685A pdb=" N GLU B 941 " --> pdb=" O GLU B 937 " (cutoff:3.500A) Proline residue: B 942 - end of helix removed outlier: 3.643A pdb=" N ASN B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 984 removed outlier: 3.680A pdb=" N ALA B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 979 " --> pdb=" O GLU B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 1014 through 1038 removed outlier: 3.811A pdb=" N ILE B1018 " --> pdb=" O THR B1014 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR B1029 " --> pdb=" O LEU B1025 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B1030 " --> pdb=" O ARG B1026 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.605A pdb=" N GLU B1044 " --> pdb=" O MET B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1093 Processing helix chain 'B' and resid 1125 through 1129 Processing helix chain 'B' and resid 1132 through 1136 removed outlier: 3.695A pdb=" N TYR B1135 " --> pdb=" O PRO B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1161 removed outlier: 3.708A pdb=" N ARG B1146 " --> pdb=" O ASP B1142 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN B1149 " --> pdb=" O CYS B1145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B1151 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B1152 " --> pdb=" O ARG B1148 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B1154 " --> pdb=" O GLU B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1192 removed outlier: 3.917A pdb=" N GLU B1169 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B1173 " --> pdb=" O GLU B1169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B1174 " --> pdb=" O ASP B1170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 482 through 485 removed outlier: 6.285A pdb=" N ILE A 536 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE A 573 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 538 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 586 through 589 removed outlier: 3.713A pdb=" N VAL A 580 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 589 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 578 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 742 through 743 Processing sheet with id=AA4, first strand: chain 'A' and resid 830 through 831 removed outlier: 3.794A pdb=" N ASP A 831 " --> pdb=" O GLN A 834 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AA6, first strand: chain 'A' and resid 899 through 900 removed outlier: 3.827A pdb=" N GLU A 900 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 908 " --> pdb=" O GLU A 900 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 912 through 914 removed outlier: 6.213A pdb=" N GLU A 912 " --> pdb=" O SER A 924 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1001 through 1003 removed outlier: 3.970A pdb=" N LEU A1002 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A1010 " --> pdb=" O LEU A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 485 removed outlier: 6.286A pdb=" N ILE B 536 " --> pdb=" O GLU B 571 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE B 573 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 538 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 586 through 589 removed outlier: 3.713A pdb=" N VAL B 580 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 589 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 578 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 742 through 743 Processing sheet with id=AB3, first strand: chain 'B' and resid 830 through 831 removed outlier: 3.793A pdb=" N ASP B 831 " --> pdb=" O GLN B 834 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 854 through 856 Processing sheet with id=AB5, first strand: chain 'B' and resid 899 through 900 removed outlier: 3.825A pdb=" N GLU B 900 " --> pdb=" O VAL B 908 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 908 " --> pdb=" O GLU B 900 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 912 through 914 removed outlier: 6.213A pdb=" N GLU B 912 " --> pdb=" O SER B 924 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1001 through 1003 removed outlier: 3.967A pdb=" N LEU B1002 " --> pdb=" O LYS B1010 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B1010 " --> pdb=" O LEU B1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 494 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2441 1.32 - 1.45: 3612 1.45 - 1.57: 7651 1.57 - 1.69: 112 1.69 - 1.81: 92 Bond restraints: 13908 Sorted by residual: bond pdb=" N VAL A 939 " pdb=" CA VAL A 939 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.29e+01 bond pdb=" N VAL B 939 " pdb=" CA VAL B 939 " ideal model delta sigma weight residual 1.458 1.489 -0.032 9.00e-03 1.23e+04 1.24e+01 bond pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 1.457 1.488 -0.031 9.00e-03 1.23e+04 1.15e+01 bond pdb=" N ILE B 438 " pdb=" CA ILE B 438 " ideal model delta sigma weight residual 1.457 1.488 -0.030 9.00e-03 1.23e+04 1.14e+01 bond pdb=" N ILE B 864 " pdb=" CA ILE B 864 " ideal model delta sigma weight residual 1.456 1.485 -0.028 8.70e-03 1.32e+04 1.06e+01 ... (remaining 13903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 13148 1.08 - 2.17: 5086 2.17 - 3.25: 728 3.25 - 4.34: 62 4.34 - 5.42: 6 Bond angle restraints: 19030 Sorted by residual: angle pdb=" N ILE B1065 " pdb=" CA ILE B1065 " pdb=" C ILE B1065 " ideal model delta sigma weight residual 111.91 108.89 3.02 8.90e-01 1.26e+00 1.15e+01 angle pdb=" N ILE A1065 " pdb=" CA ILE A1065 " pdb=" C ILE A1065 " ideal model delta sigma weight residual 111.91 108.91 3.00 8.90e-01 1.26e+00 1.14e+01 angle pdb=" C GLY A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 123.33 120.41 2.92 8.70e-01 1.32e+00 1.13e+01 angle pdb=" C GLY B 437 " pdb=" N ILE B 438 " pdb=" CA ILE B 438 " ideal model delta sigma weight residual 123.33 120.41 2.92 8.70e-01 1.32e+00 1.13e+01 angle pdb=" O4' DC F 5 " pdb=" C4' DC F 5 " pdb=" C3' DC F 5 " ideal model delta sigma weight residual 106.00 104.06 1.94 6.00e-01 2.78e+00 1.05e+01 ... (remaining 19025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 8027 35.97 - 71.95: 215 71.95 - 107.92: 2 107.92 - 143.89: 0 143.89 - 179.87: 2 Dihedral angle restraints: 8246 sinusoidal: 3826 harmonic: 4420 Sorted by residual: dihedral pdb=" C ASN B 604 " pdb=" N ASN B 604 " pdb=" CA ASN B 604 " pdb=" CB ASN B 604 " ideal model delta harmonic sigma weight residual -122.60 -133.46 10.86 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" C ASN A 604 " pdb=" N ASN A 604 " pdb=" CA ASN A 604 " pdb=" CB ASN A 604 " ideal model delta harmonic sigma weight residual -122.60 -133.41 10.81 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" C4' DG D 9 " pdb=" C3' DG D 9 " pdb=" O3' DG D 9 " pdb=" P DT D 10 " ideal model delta sinusoidal sigma weight residual 220.00 40.13 179.87 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1425 0.075 - 0.149: 537 0.149 - 0.224: 122 0.224 - 0.299: 6 0.299 - 0.374: 4 Chirality restraints: 2094 Sorted by residual: chirality pdb=" CA ASN B 604 " pdb=" N ASN B 604 " pdb=" C ASN B 604 " pdb=" CB ASN B 604 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA ASN A 604 " pdb=" N ASN A 604 " pdb=" C ASN A 604 " pdb=" CB ASN A 604 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C9 EVP F 101 " pdb=" C10 EVP F 101 " pdb=" C6 EVP F 101 " pdb=" C8 EVP F 101 " both_signs ideal model delta sigma weight residual False 2.49 2.81 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 2091 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 603 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C PRO B 603 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO B 603 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN B 604 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 603 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C PRO A 603 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 603 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 604 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 617 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C GLY A 617 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY A 617 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 618 " 0.017 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3891 2.82 - 3.34: 12123 3.34 - 3.86: 21350 3.86 - 4.38: 24247 4.38 - 4.90: 39727 Nonbonded interactions: 101338 Sorted by model distance: nonbonded pdb=" OG SER A1045 " pdb=" OE2 GLU A1152 " model vdw 2.304 3.040 nonbonded pdb=" OG SER B1045 " pdb=" OE2 GLU B1152 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR A 456 " pdb=" O LYS A 480 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR B 456 " pdb=" O LYS B 480 " model vdw 2.327 3.040 nonbonded pdb=" O ASP A 524 " pdb=" OG SER A 527 " model vdw 2.349 3.040 ... (remaining 101333 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 0.010 0.040 13908 Z= 0.749 Angle : 1.067 5.421 19030 Z= 0.818 Chirality : 0.079 0.374 2094 Planarity : 0.007 0.032 2220 Dihedral : 13.243 179.868 5398 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.14 % 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 are not related in a simple way. whole: -0.70 (0.21), residues: 1512 helix: 1.33 (0.19), residues: 650 sheet: -1.64 (0.44), residues: 154 loop : -1.98 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 929 TYR 0.010 0.002 TYR B 590 PHE 0.008 0.002 PHE A1003 TRP 0.015 0.002 TRP A 664 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.01014 / 0.75 (13908) covalent geometry : angle 1.06703 / 0.82 (19030) hydrogen bonds : bond 0.12465 / 9.02 ( 572) hydrogen bonds : angle 5.28611 / 3.91 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 LEU cc_start: 0.8294 (mt) cc_final: 0.7579 (mt) REVERT: A 526 ASP cc_start: 0.9352 (m-30) cc_final: 0.8966 (t0) REVERT: A 537 MET cc_start: 0.7995 (ttp) cc_final: 0.7622 (ttt) REVERT: A 552 LEU cc_start: 0.8969 (mt) cc_final: 0.8613 (mt) REVERT: A 573 PHE cc_start: 0.9095 (t80) cc_final: 0.8758 (t80) REVERT: A 675 ARG cc_start: 0.9395 (mtt180) cc_final: 0.8940 (mtp85) REVERT: A 754 MET cc_start: 0.9090 (mtt) cc_final: 0.8795 (mpp) REVERT: A 795 HIS cc_start: 0.8240 (m90) cc_final: 0.7232 (m90) REVERT: A 809 MET cc_start: 0.8202 (ttt) cc_final: 0.7991 (tpp) REVERT: A 815 ARG cc_start: 0.8721 (mmm160) cc_final: 0.8470 (mmm160) REVERT: A 862 CYS cc_start: 0.8359 (t) cc_final: 0.7650 (p) REVERT: A 932 THR cc_start: 0.8262 (m) cc_final: 0.7653 (p) REVERT: A 956 ASP cc_start: 0.8527 (t0) cc_final: 0.8302 (t0) REVERT: A 1000 MET cc_start: 0.8338 (mtt) cc_final: 0.7810 (mmm) REVERT: A 1067 ASN cc_start: 0.7890 (m110) cc_final: 0.7684 (m-40) REVERT: A 1128 LEU cc_start: 0.9283 (mt) cc_final: 0.8964 (mt) REVERT: A 1138 LYS cc_start: 0.8332 (tttp) cc_final: 0.8131 (tmmt) REVERT: A 1171 LEU cc_start: 0.8917 (mt) cc_final: 0.8695 (mt) REVERT: B 486 LEU cc_start: 0.8293 (mt) cc_final: 0.7566 (mt) REVERT: B 526 ASP cc_start: 0.9336 (m-30) cc_final: 0.8956 (t0) REVERT: B 537 MET cc_start: 0.8025 (ttp) cc_final: 0.7613 (ttt) REVERT: B 552 LEU cc_start: 0.9017 (mt) cc_final: 0.8685 (mt) REVERT: B 573 PHE cc_start: 0.9091 (t80) cc_final: 0.8729 (t80) REVERT: B 675 ARG cc_start: 0.9395 (mtt180) cc_final: 0.8940 (mtp85) REVERT: B 702 GLU cc_start: 0.8718 (tt0) cc_final: 0.8501 (mm-30) REVERT: B 754 MET cc_start: 0.9092 (mtt) cc_final: 0.8787 (mpp) REVERT: B 795 HIS cc_start: 0.8239 (m90) cc_final: 0.7240 (m90) REVERT: B 809 MET cc_start: 0.8216 (ttt) cc_final: 0.8009 (tpp) REVERT: B 815 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8482 (mmm160) REVERT: B 862 CYS cc_start: 0.8256 (t) cc_final: 0.7571 (p) REVERT: B 932 THR cc_start: 0.8283 (m) cc_final: 0.7665 (p) REVERT: B 956 ASP cc_start: 0.8517 (t0) cc_final: 0.8301 (t0) REVERT: B 1000 MET cc_start: 0.8348 (mtt) cc_final: 0.7837 (mmm) REVERT: B 1128 LEU cc_start: 0.9266 (mt) cc_final: 0.8957 (mt) REVERT: B 1138 LYS cc_start: 0.8332 (tttp) cc_final: 0.8129 (tmmt) REVERT: B 1171 LEU cc_start: 0.8912 (mt) cc_final: 0.8692 (mt) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.1370 time to fit residues: 81.0038 Evaluate side-chains 204 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 824 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 HIS B 824 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.070493 restraints weight = 54365.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073012 restraints weight = 29684.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074800 restraints weight = 19003.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.076075 restraints weight = 13479.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.077007 restraints weight = 10308.841| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13908 Z= 0.135 Angle : 0.586 11.544 19030 Z= 0.302 Chirality : 0.041 0.188 2094 Planarity : 0.004 0.046 2220 Dihedral : 17.281 176.315 2282 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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 are not related in a simple way. whole: -0.91 (0.21), residues: 1512 helix: 1.04 (0.20), residues: 664 sheet: -1.73 (0.43), residues: 158 loop : -2.04 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 487 TYR 0.017 0.001 TYR B 686 PHE 0.010 0.001 PHE A 698 TRP 0.020 0.002 TRP B1090 HIS 0.009 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (13908) covalent geometry : angle 0.58638 / 0.30 (19030) hydrogen bonds : bond 0.04046 / 2.78 ( 572) hydrogen bonds : angle 4.35630 / 3.15 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.7261 (m-30) cc_final: 0.6836 (p0) REVERT: A 455 CYS cc_start: 0.8286 (m) cc_final: 0.7509 (m) REVERT: A 503 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7099 (mt-10) REVERT: A 526 ASP cc_start: 0.9327 (m-30) cc_final: 0.9039 (t0) REVERT: A 552 LEU cc_start: 0.9017 (mt) cc_final: 0.8638 (mt) REVERT: A 589 PHE cc_start: 0.7857 (m-10) cc_final: 0.7458 (m-10) REVERT: A 675 ARG cc_start: 0.9183 (mtt180) cc_final: 0.8580 (mtm110) REVERT: A 701 LYS cc_start: 0.8732 (mmtp) cc_final: 0.8431 (ttmt) REVERT: A 712 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7902 (mt-10) REVERT: A 728 LYS cc_start: 0.9064 (mttt) cc_final: 0.8805 (mtmt) REVERT: A 738 ASP cc_start: 0.7539 (m-30) cc_final: 0.7286 (m-30) REVERT: A 815 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8475 (mmm160) REVERT: A 862 CYS cc_start: 0.7878 (t) cc_final: 0.7478 (p) REVERT: A 923 ILE cc_start: 0.9155 (mm) cc_final: 0.8925 (mm) REVERT: A 959 GLU cc_start: 0.7620 (mp0) cc_final: 0.7387 (mp0) REVERT: A 1000 MET cc_start: 0.8426 (mtt) cc_final: 0.7831 (mmm) REVERT: A 1024 GLU cc_start: 0.8679 (tt0) cc_final: 0.8110 (tm-30) REVERT: A 1128 LEU cc_start: 0.9170 (mt) cc_final: 0.8935 (mt) REVERT: A 1155 LEU cc_start: 0.8401 (tp) cc_final: 0.8196 (tp) REVERT: A 1169 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8630 (tm-30) REVERT: B 446 ASP cc_start: 0.7285 (m-30) cc_final: 0.6933 (p0) REVERT: B 455 CYS cc_start: 0.8316 (m) cc_final: 0.7446 (m) REVERT: B 526 ASP cc_start: 0.9334 (m-30) cc_final: 0.9044 (t0) REVERT: B 552 LEU cc_start: 0.9100 (mt) cc_final: 0.8726 (mt) REVERT: B 675 ARG cc_start: 0.9198 (mtt180) cc_final: 0.8595 (mtm110) REVERT: B 712 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 728 LYS cc_start: 0.9050 (mttt) cc_final: 0.8804 (mtmt) REVERT: B 738 ASP cc_start: 0.7547 (m-30) cc_final: 0.7283 (m-30) REVERT: B 768 ILE cc_start: 0.9418 (mm) cc_final: 0.9177 (mm) REVERT: B 815 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8484 (mmm160) REVERT: B 862 CYS cc_start: 0.8039 (t) cc_final: 0.7446 (p) REVERT: B 923 ILE cc_start: 0.9166 (mm) cc_final: 0.8934 (mm) REVERT: B 1000 MET cc_start: 0.8419 (mtt) cc_final: 0.7857 (mmm) REVERT: B 1128 LEU cc_start: 0.9172 (mt) cc_final: 0.8939 (mt) REVERT: B 1155 LEU cc_start: 0.8396 (tp) cc_final: 0.8186 (tp) REVERT: B 1169 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8620 (tm-30) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1188 time to fit residues: 45.6721 Evaluate side-chains 168 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 105 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 151 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 116 optimal weight: 0.4980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.080050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.066374 restraints weight = 55971.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068782 restraints weight = 29961.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070494 restraints weight = 19096.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071685 restraints weight = 13532.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.072488 restraints weight = 10411.807| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13908 Z= 0.162 Angle : 0.595 11.736 19030 Z= 0.309 Chirality : 0.041 0.234 2094 Planarity : 0.004 0.058 2220 Dihedral : 17.541 178.969 2282 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.08 % Allowed : 1.58 % Favored : 98.34 % 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 are not related in a simple way. whole: -0.81 (0.21), residues: 1512 helix: 1.22 (0.20), residues: 674 sheet: -1.88 (0.43), residues: 156 loop : -2.09 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 450 TYR 0.046 0.002 TYR B1135 PHE 0.012 0.001 PHE B 653 TRP 0.020 0.002 TRP B1090 HIS 0.007 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (13908) covalent geometry : angle 0.59546 / 0.31 (19030) hydrogen bonds : bond 0.03799 / 2.66 ( 572) hydrogen bonds : angle 3.86968 / 2.81 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.481 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: A 455 CYS cc_start: 0.8176 (m) cc_final: 0.7820 (m) REVERT: A 503 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7249 (mt-10) REVERT: A 587 MET cc_start: 0.8277 (tpp) cc_final: 0.7816 (tpp) REVERT: A 589 PHE cc_start: 0.7919 (m-10) cc_final: 0.7538 (m-10) REVERT: A 712 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7958 (mt-10) REVERT: A 726 GLN cc_start: 0.9014 (mp10) cc_final: 0.8766 (mp10) REVERT: A 728 LYS cc_start: 0.9340 (mttt) cc_final: 0.9045 (mtmt) REVERT: A 738 ASP cc_start: 0.7584 (m-30) cc_final: 0.7316 (m-30) REVERT: A 815 ARG cc_start: 0.8792 (mmm160) cc_final: 0.8559 (mmm160) REVERT: A 856 ILE cc_start: 0.9084 (mt) cc_final: 0.8745 (tp) REVERT: A 862 CYS cc_start: 0.7968 (t) cc_final: 0.7567 (p) REVERT: A 959 GLU cc_start: 0.7745 (mp0) cc_final: 0.7512 (mp0) REVERT: A 1000 MET cc_start: 0.8376 (mtt) cc_final: 0.7729 (mpp) REVERT: A 1035 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8719 (tm-30) REVERT: A 1131 MET cc_start: 0.8923 (ttt) cc_final: 0.8705 (tpp) REVERT: A 1169 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8736 (tm-30) REVERT: B 455 CYS cc_start: 0.8170 (m) cc_final: 0.7828 (m) REVERT: B 537 MET cc_start: 0.7344 (mtm) cc_final: 0.6828 (mtt) REVERT: B 587 MET cc_start: 0.8421 (tpp) cc_final: 0.8132 (tpp) REVERT: B 712 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 726 GLN cc_start: 0.8933 (mp10) cc_final: 0.8675 (mp10) REVERT: B 728 LYS cc_start: 0.9338 (mttt) cc_final: 0.8890 (mtpt) REVERT: B 738 ASP cc_start: 0.7578 (m-30) cc_final: 0.7316 (m-30) REVERT: B 815 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8557 (mmm160) REVERT: B 862 CYS cc_start: 0.7975 (t) cc_final: 0.7591 (p) REVERT: B 1000 MET cc_start: 0.8359 (mtt) cc_final: 0.7923 (mmm) REVERT: B 1035 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8643 (tm-30) REVERT: B 1131 MET cc_start: 0.8916 (ttt) cc_final: 0.8700 (tpp) REVERT: B 1169 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8733 (tm-30) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.1112 time to fit residues: 34.9004 Evaluate side-chains 131 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065721 restraints weight = 56045.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068123 restraints weight = 29919.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.069809 restraints weight = 19033.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.071038 restraints weight = 13504.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.071924 restraints weight = 10319.961| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13908 Z= 0.125 Angle : 0.543 10.365 19030 Z= 0.282 Chirality : 0.041 0.186 2094 Planarity : 0.004 0.047 2220 Dihedral : 17.715 179.451 2282 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.08 % Allowed : 1.51 % Favored : 98.42 % 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 are not related in a simple way. whole: -0.68 (0.21), residues: 1512 helix: 1.37 (0.20), residues: 678 sheet: -1.94 (0.43), residues: 156 loop : -2.05 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 635 TYR 0.011 0.001 TYR A 686 PHE 0.007 0.001 PHE B 573 TRP 0.020 0.002 TRP A1090 HIS 0.004 0.001 HIS B 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (13908) covalent geometry : angle 0.54283 / 0.28 (19030) hydrogen bonds : bond 0.03230 / 2.24 ( 572) hydrogen bonds : angle 3.70974 / 2.72 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7626 (mt-10) REVERT: A 587 MET cc_start: 0.8295 (tpp) cc_final: 0.7897 (tpp) REVERT: A 589 PHE cc_start: 0.7983 (m-10) cc_final: 0.7643 (m-10) REVERT: A 712 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7944 (mt-10) REVERT: A 728 LYS cc_start: 0.9287 (mttt) cc_final: 0.9001 (mtmt) REVERT: A 768 ILE cc_start: 0.9452 (mm) cc_final: 0.9226 (mt) REVERT: A 815 ARG cc_start: 0.8699 (mmm160) cc_final: 0.8497 (mmm160) REVERT: A 862 CYS cc_start: 0.7985 (t) cc_final: 0.7616 (p) REVERT: A 959 GLU cc_start: 0.7885 (mp0) cc_final: 0.7626 (mp0) REVERT: A 972 MET cc_start: 0.7483 (tpt) cc_final: 0.7244 (tpt) REVERT: A 1000 MET cc_start: 0.8423 (mtt) cc_final: 0.7748 (mpp) REVERT: A 1035 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8600 (tm-30) REVERT: A 1169 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8778 (tm-30) REVERT: A 1178 LEU cc_start: 0.9036 (tt) cc_final: 0.8720 (pp) REVERT: B 587 MET cc_start: 0.8466 (tpp) cc_final: 0.8216 (tpp) REVERT: B 712 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7930 (mt-10) REVERT: B 728 LYS cc_start: 0.9288 (mttt) cc_final: 0.8845 (mtpt) REVERT: B 768 ILE cc_start: 0.9449 (mm) cc_final: 0.9244 (mt) REVERT: B 862 CYS cc_start: 0.8052 (t) cc_final: 0.7708 (p) REVERT: B 972 MET cc_start: 0.7484 (tpt) cc_final: 0.7254 (tpt) REVERT: B 1000 MET cc_start: 0.8402 (mtt) cc_final: 0.7759 (mpp) REVERT: B 1035 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8509 (tm-30) REVERT: B 1169 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8779 (tm-30) REVERT: B 1178 LEU cc_start: 0.8935 (tt) cc_final: 0.8612 (pp) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1089 time to fit residues: 30.9067 Evaluate side-chains 129 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN A 795 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 ASN B 795 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.078720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.065422 restraints weight = 55526.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067807 restraints weight = 29596.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069470 restraints weight = 18770.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070597 restraints weight = 13251.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071439 restraints weight = 10191.995| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13908 Z= 0.123 Angle : 0.540 9.471 19030 Z= 0.283 Chirality : 0.040 0.202 2094 Planarity : 0.004 0.044 2220 Dihedral : 17.856 179.476 2282 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.08 % Allowed : 1.66 % Favored : 98.27 % 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 are not related in a simple way. whole: -0.52 (0.22), residues: 1512 helix: 1.54 (0.20), residues: 676 sheet: -1.93 (0.42), residues: 156 loop : -1.98 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 815 TYR 0.020 0.001 TYR B1135 PHE 0.017 0.001 PHE B1054 TRP 0.015 0.002 TRP A1090 HIS 0.006 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (13908) covalent geometry : angle 0.53951 / 0.28 (19030) hydrogen bonds : bond 0.03259 / 2.28 ( 572) hydrogen bonds : angle 3.61342 / 2.64 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.8318 (tpp) cc_final: 0.7958 (tpp) REVERT: A 589 PHE cc_start: 0.7881 (m-10) cc_final: 0.7403 (m-10) REVERT: A 728 LYS cc_start: 0.9266 (mttt) cc_final: 0.8886 (mtmt) REVERT: A 738 ASP cc_start: 0.7317 (m-30) cc_final: 0.7075 (m-30) REVERT: A 768 ILE cc_start: 0.9456 (mm) cc_final: 0.9234 (mt) REVERT: A 815 ARG cc_start: 0.8743 (mmm160) cc_final: 0.8499 (mmm160) REVERT: A 830 TYR cc_start: 0.6470 (t80) cc_final: 0.5949 (t80) REVERT: A 856 ILE cc_start: 0.8835 (mm) cc_final: 0.8422 (tp) REVERT: A 862 CYS cc_start: 0.8096 (t) cc_final: 0.7698 (p) REVERT: A 930 THR cc_start: 0.7592 (m) cc_final: 0.7388 (p) REVERT: A 959 GLU cc_start: 0.7955 (mp0) cc_final: 0.7699 (mp0) REVERT: A 972 MET cc_start: 0.7414 (tpt) cc_final: 0.7125 (tpt) REVERT: A 1000 MET cc_start: 0.8534 (mtt) cc_final: 0.7838 (mpp) REVERT: A 1169 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8809 (tm-30) REVERT: A 1178 LEU cc_start: 0.8880 (tt) cc_final: 0.8552 (pp) REVERT: B 537 MET cc_start: 0.7572 (mtm) cc_final: 0.7318 (mtt) REVERT: B 712 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7931 (mt-10) REVERT: B 728 LYS cc_start: 0.9319 (mttt) cc_final: 0.8917 (mtmt) REVERT: B 738 ASP cc_start: 0.7320 (m-30) cc_final: 0.7079 (m-30) REVERT: B 815 ARG cc_start: 0.8842 (mmm160) cc_final: 0.8626 (mmm160) REVERT: B 830 TYR cc_start: 0.6494 (t80) cc_final: 0.5937 (t80) REVERT: B 862 CYS cc_start: 0.8176 (t) cc_final: 0.7822 (p) REVERT: B 930 THR cc_start: 0.7593 (m) cc_final: 0.7379 (p) REVERT: B 972 MET cc_start: 0.7426 (tpt) cc_final: 0.7134 (tpt) REVERT: B 1000 MET cc_start: 0.8506 (mtt) cc_final: 0.7845 (mpp) REVERT: B 1169 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8827 (tm-30) REVERT: B 1178 LEU cc_start: 0.8892 (tt) cc_final: 0.8561 (pp) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1160 time to fit residues: 33.3534 Evaluate side-chains 121 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 0.0040 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 116 optimal weight: 0.0170 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.3430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 ASN ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.079182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.065459 restraints weight = 55670.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067878 restraints weight = 29777.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.069537 restraints weight = 18882.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070669 restraints weight = 13396.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071555 restraints weight = 10393.244| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13908 Z= 0.098 Angle : 0.529 9.485 19030 Z= 0.273 Chirality : 0.040 0.211 2094 Planarity : 0.004 0.039 2220 Dihedral : 17.881 179.702 2282 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.08 % Allowed : 0.75 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1512 helix: 1.71 (0.20), residues: 666 sheet: -1.85 (0.42), residues: 156 loop : -1.81 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 434 TYR 0.030 0.001 TYR A1030 PHE 0.006 0.001 PHE B 573 TRP 0.012 0.001 TRP A1090 HIS 0.004 0.001 HIS B 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.10 (13908) covalent geometry : angle 0.52917 / 0.27 (19030) hydrogen bonds : bond 0.02985 / 2.05 ( 572) hydrogen bonds : angle 3.54613 / 2.62 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.8344 (tpp) cc_final: 0.8079 (tpp) REVERT: A 675 ARG cc_start: 0.9161 (mtt180) cc_final: 0.8578 (mtm110) REVERT: A 712 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7922 (mt-10) REVERT: A 728 LYS cc_start: 0.9287 (mttt) cc_final: 0.8892 (mtmt) REVERT: A 815 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8500 (mmm160) REVERT: A 862 CYS cc_start: 0.8065 (t) cc_final: 0.7620 (p) REVERT: A 959 GLU cc_start: 0.7953 (mp0) cc_final: 0.7628 (mp0) REVERT: A 972 MET cc_start: 0.7332 (tpt) cc_final: 0.7041 (tpt) REVERT: A 1000 MET cc_start: 0.8463 (mtt) cc_final: 0.7811 (mpp) REVERT: A 1035 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8512 (tm-30) REVERT: A 1169 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8745 (tm-30) REVERT: A 1178 LEU cc_start: 0.9058 (tt) cc_final: 0.8735 (pp) REVERT: B 712 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7923 (mt-10) REVERT: B 728 LYS cc_start: 0.9298 (mttt) cc_final: 0.8878 (mtmt) REVERT: B 809 MET cc_start: 0.8208 (tmm) cc_final: 0.7937 (tmm) REVERT: B 815 ARG cc_start: 0.8840 (mmm160) cc_final: 0.8573 (mmm160) REVERT: B 830 TYR cc_start: 0.6455 (t80) cc_final: 0.5868 (t80) REVERT: B 847 MET cc_start: 0.8884 (mmm) cc_final: 0.8680 (mmm) REVERT: B 862 CYS cc_start: 0.8135 (t) cc_final: 0.7766 (p) REVERT: B 972 MET cc_start: 0.7323 (tpt) cc_final: 0.7044 (tpt) REVERT: B 1000 MET cc_start: 0.8426 (mtt) cc_final: 0.7801 (mpp) REVERT: B 1035 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8503 (tm-30) REVERT: B 1169 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8764 (tm-30) REVERT: B 1178 LEU cc_start: 0.9063 (tt) cc_final: 0.8738 (pp) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1074 time to fit residues: 29.7253 Evaluate side-chains 115 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.078009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.064615 restraints weight = 57069.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067024 restraints weight = 30465.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068670 restraints weight = 19373.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069814 restraints weight = 13730.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.070641 restraints weight = 10561.910| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13908 Z= 0.129 Angle : 0.556 11.004 19030 Z= 0.290 Chirality : 0.040 0.215 2094 Planarity : 0.004 0.040 2220 Dihedral : 17.954 179.490 2282 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.22), residues: 1512 helix: 1.90 (0.21), residues: 664 sheet: -1.78 (0.43), residues: 152 loop : -1.73 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 635 TYR 0.013 0.001 TYR A 805 PHE 0.015 0.001 PHE A1054 TRP 0.011 0.002 TRP A1090 HIS 0.005 0.001 HIS B 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (13908) covalent geometry : angle 0.55607 / 0.29 (19030) hydrogen bonds : bond 0.03209 / 2.23 ( 572) hydrogen bonds : angle 3.58238 / 2.65 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7573 (mt-10) REVERT: A 728 LYS cc_start: 0.9254 (mttt) cc_final: 0.9026 (mtmt) REVERT: A 738 ASP cc_start: 0.7551 (m-30) cc_final: 0.7141 (m-30) REVERT: A 815 ARG cc_start: 0.8742 (mmm160) cc_final: 0.8503 (mmm160) REVERT: A 830 TYR cc_start: 0.6546 (t80) cc_final: 0.5992 (t80) REVERT: A 847 MET cc_start: 0.8923 (mmm) cc_final: 0.8701 (mmm) REVERT: A 862 CYS cc_start: 0.8181 (t) cc_final: 0.7768 (p) REVERT: A 959 GLU cc_start: 0.8095 (mp0) cc_final: 0.7822 (mp0) REVERT: A 972 MET cc_start: 0.7451 (tpt) cc_final: 0.7147 (tpt) REVERT: A 1000 MET cc_start: 0.8503 (mtt) cc_final: 0.7869 (mpp) REVERT: A 1030 TYR cc_start: 0.6271 (m-10) cc_final: 0.5910 (m-80) REVERT: A 1169 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8788 (tm-30) REVERT: A 1178 LEU cc_start: 0.8843 (tt) cc_final: 0.8629 (pp) REVERT: B 571 GLU cc_start: 0.6026 (tt0) cc_final: 0.5137 (tm-30) REVERT: B 587 MET cc_start: 0.8134 (tpp) cc_final: 0.7910 (tpp) REVERT: B 712 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 728 LYS cc_start: 0.9270 (mttt) cc_final: 0.9025 (mtmt) REVERT: B 738 ASP cc_start: 0.7559 (m-30) cc_final: 0.7170 (m-30) REVERT: B 815 ARG cc_start: 0.8856 (mmm160) cc_final: 0.8591 (mmm160) REVERT: B 830 TYR cc_start: 0.6519 (t80) cc_final: 0.5919 (t80) REVERT: B 847 MET cc_start: 0.8944 (mmm) cc_final: 0.8726 (mmm) REVERT: B 862 CYS cc_start: 0.8298 (t) cc_final: 0.7895 (p) REVERT: B 972 MET cc_start: 0.7459 (tpt) cc_final: 0.7161 (tpt) REVERT: B 1000 MET cc_start: 0.8418 (mtt) cc_final: 0.7893 (mpp) REVERT: B 1030 TYR cc_start: 0.6254 (m-10) cc_final: 0.5935 (m-80) REVERT: B 1169 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8803 (tm-30) REVERT: B 1178 LEU cc_start: 0.8849 (tt) cc_final: 0.8637 (pp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1052 time to fit residues: 27.3352 Evaluate side-chains 115 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 555 ASN ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.063796 restraints weight = 56546.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066165 restraints weight = 30416.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.067773 restraints weight = 19422.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068967 restraints weight = 13825.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069759 restraints weight = 10587.304| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13908 Z= 0.124 Angle : 0.557 8.415 19030 Z= 0.290 Chirality : 0.040 0.225 2094 Planarity : 0.004 0.039 2220 Dihedral : 18.083 179.793 2282 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.08 % Allowed : 0.60 % 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 are not related in a simple way. whole: -0.03 (0.22), residues: 1512 helix: 1.95 (0.21), residues: 664 sheet: -1.55 (0.44), residues: 148 loop : -1.69 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1033 TYR 0.013 0.001 TYR B1135 PHE 0.007 0.001 PHE A 589 TRP 0.013 0.002 TRP A1090 HIS 0.004 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (13908) covalent geometry : angle 0.55741 / 0.29 (19030) hydrogen bonds : bond 0.03100 / 2.15 ( 572) hydrogen bonds : angle 3.57606 / 2.65 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.8572 (tpp) cc_final: 0.8367 (tpp) REVERT: A 675 ARG cc_start: 0.9170 (mtt180) cc_final: 0.8735 (ptp-110) REVERT: A 728 LYS cc_start: 0.9286 (mttt) cc_final: 0.9017 (mtmt) REVERT: A 738 ASP cc_start: 0.7585 (m-30) cc_final: 0.7359 (m-30) REVERT: A 754 MET cc_start: 0.8167 (mpp) cc_final: 0.7913 (mpp) REVERT: A 815 ARG cc_start: 0.8791 (mmm160) cc_final: 0.8516 (mmm160) REVERT: A 830 TYR cc_start: 0.6515 (t80) cc_final: 0.5861 (t80) REVERT: A 847 MET cc_start: 0.8938 (mmm) cc_final: 0.8677 (mmm) REVERT: A 862 CYS cc_start: 0.8293 (t) cc_final: 0.7865 (p) REVERT: A 959 GLU cc_start: 0.8210 (mp0) cc_final: 0.7925 (mp0) REVERT: A 972 MET cc_start: 0.7422 (tpt) cc_final: 0.7109 (tpt) REVERT: A 1000 MET cc_start: 0.8430 (mtt) cc_final: 0.7968 (mpp) REVERT: A 1030 TYR cc_start: 0.6148 (m-10) cc_final: 0.5790 (m-80) REVERT: A 1131 MET cc_start: 0.8820 (tpp) cc_final: 0.8599 (tpp) REVERT: A 1169 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8883 (tm-30) REVERT: A 1178 LEU cc_start: 0.8848 (tt) cc_final: 0.8623 (pp) REVERT: B 571 GLU cc_start: 0.5322 (tt0) cc_final: 0.4626 (tm-30) REVERT: B 587 MET cc_start: 0.8176 (tpp) cc_final: 0.7939 (tpp) REVERT: B 712 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8003 (mt-10) REVERT: B 728 LYS cc_start: 0.9369 (mttt) cc_final: 0.9108 (mtmt) REVERT: B 738 ASP cc_start: 0.7718 (m-30) cc_final: 0.7317 (m-30) REVERT: B 754 MET cc_start: 0.8234 (mpp) cc_final: 0.7977 (mpp) REVERT: B 809 MET cc_start: 0.8299 (tmm) cc_final: 0.8058 (tmm) REVERT: B 815 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8533 (mmm160) REVERT: B 830 TYR cc_start: 0.6651 (t80) cc_final: 0.5987 (t80) REVERT: B 847 MET cc_start: 0.8923 (mmm) cc_final: 0.8671 (mmm) REVERT: B 862 CYS cc_start: 0.8399 (t) cc_final: 0.7979 (p) REVERT: B 972 MET cc_start: 0.7368 (tpt) cc_final: 0.7056 (tpt) REVERT: B 1000 MET cc_start: 0.8437 (mtt) cc_final: 0.7942 (mpp) REVERT: B 1030 TYR cc_start: 0.6109 (m-10) cc_final: 0.5799 (m-80) REVERT: B 1131 MET cc_start: 0.8700 (tpp) cc_final: 0.8454 (tpp) REVERT: B 1169 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8897 (tm-30) REVERT: B 1178 LEU cc_start: 0.8854 (tt) cc_final: 0.8632 (pp) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1164 time to fit residues: 28.7359 Evaluate side-chains 114 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 93 optimal weight: 0.0570 chunk 62 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 795 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.063861 restraints weight = 57322.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066276 restraints weight = 30643.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.067870 restraints weight = 19504.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069086 restraints weight = 13943.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069915 restraints weight = 10633.139| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13908 Z= 0.106 Angle : 0.534 7.676 19030 Z= 0.279 Chirality : 0.040 0.229 2094 Planarity : 0.004 0.038 2220 Dihedral : 18.097 178.962 2282 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 are not related in a simple way. whole: 0.01 (0.22), residues: 1512 helix: 1.94 (0.20), residues: 664 sheet: -1.61 (0.43), residues: 150 loop : -1.61 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 804 TYR 0.011 0.001 TYR A 805 PHE 0.016 0.001 PHE A1054 TRP 0.011 0.002 TRP B1090 HIS 0.005 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (13908) covalent geometry : angle 0.53364 / 0.28 (19030) hydrogen bonds : bond 0.03013 / 2.04 ( 572) hydrogen bonds : angle 3.55176 / 2.64 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.8596 (tpp) cc_final: 0.8386 (tpp) REVERT: A 675 ARG cc_start: 0.9168 (mtt180) cc_final: 0.8734 (ptp-110) REVERT: A 726 GLN cc_start: 0.8813 (mp10) cc_final: 0.8587 (mp10) REVERT: A 728 LYS cc_start: 0.9240 (mttt) cc_final: 0.9036 (mtmt) REVERT: A 738 ASP cc_start: 0.7709 (m-30) cc_final: 0.7496 (m-30) REVERT: A 815 ARG cc_start: 0.8799 (mmm160) cc_final: 0.8518 (mmm160) REVERT: A 830 TYR cc_start: 0.6529 (t80) cc_final: 0.5865 (t80) REVERT: A 847 MET cc_start: 0.8934 (mmm) cc_final: 0.8673 (mmm) REVERT: A 862 CYS cc_start: 0.8261 (t) cc_final: 0.7851 (p) REVERT: A 959 GLU cc_start: 0.8255 (mp0) cc_final: 0.8019 (mp0) REVERT: A 972 MET cc_start: 0.7333 (tpt) cc_final: 0.7012 (tpt) REVERT: A 1000 MET cc_start: 0.8433 (mtt) cc_final: 0.7955 (mpp) REVERT: A 1030 TYR cc_start: 0.6190 (m-10) cc_final: 0.5908 (m-80) REVERT: A 1169 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8848 (tm-30) REVERT: A 1178 LEU cc_start: 0.8852 (tt) cc_final: 0.8623 (pp) REVERT: B 571 GLU cc_start: 0.5182 (tt0) cc_final: 0.4527 (tm-30) REVERT: B 587 MET cc_start: 0.8179 (tpp) cc_final: 0.7951 (tpp) REVERT: B 712 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 728 LYS cc_start: 0.9294 (mttt) cc_final: 0.9069 (mtmt) REVERT: B 738 ASP cc_start: 0.7705 (m-30) cc_final: 0.7503 (m-30) REVERT: B 815 ARG cc_start: 0.8797 (mmm160) cc_final: 0.8560 (mmm160) REVERT: B 830 TYR cc_start: 0.6676 (t80) cc_final: 0.6008 (t80) REVERT: B 847 MET cc_start: 0.8901 (mmm) cc_final: 0.8642 (mmm) REVERT: B 862 CYS cc_start: 0.8358 (t) cc_final: 0.7967 (p) REVERT: B 972 MET cc_start: 0.7350 (tpt) cc_final: 0.7028 (tpt) REVERT: B 1000 MET cc_start: 0.8440 (mtt) cc_final: 0.7945 (mpp) REVERT: B 1030 TYR cc_start: 0.6150 (m-10) cc_final: 0.5924 (m-80) REVERT: B 1169 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8843 (tm-30) REVERT: B 1178 LEU cc_start: 0.8859 (tt) cc_final: 0.8633 (pp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1104 time to fit residues: 27.9389 Evaluate side-chains 116 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 35 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 555 ASN A 559 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 ASN B 559 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.074557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061068 restraints weight = 59878.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.063320 restraints weight = 33204.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064907 restraints weight = 21711.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065966 restraints weight = 15684.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066814 restraints weight = 12329.815| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13908 Z= 0.183 Angle : 0.627 9.071 19030 Z= 0.327 Chirality : 0.042 0.237 2094 Planarity : 0.004 0.046 2220 Dihedral : 18.266 179.377 2282 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.15 % Allowed : 0.08 % Favored : 99.77 % 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 are not related in a simple way. whole: -0.09 (0.22), residues: 1512 helix: 1.95 (0.21), residues: 664 sheet: -1.84 (0.44), residues: 132 loop : -1.74 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 804 TYR 0.017 0.002 TYR B 892 PHE 0.016 0.002 PHE A1023 TRP 0.012 0.002 TRP A1090 HIS 0.005 0.001 HIS B 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (13908) covalent geometry : angle 0.62723 / 0.33 (19030) hydrogen bonds : bond 0.03732 / 2.57 ( 572) hydrogen bonds : angle 3.77558 / 2.78 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.8665 (tpp) cc_final: 0.8380 (tpp) REVERT: A 675 ARG cc_start: 0.9198 (mtt180) cc_final: 0.8851 (mtp-110) REVERT: A 712 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8110 (mt-10) REVERT: A 754 MET cc_start: 0.8235 (mpp) cc_final: 0.7934 (mpp) REVERT: A 815 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8586 (mmm160) REVERT: A 847 MET cc_start: 0.9042 (mmm) cc_final: 0.8712 (mmm) REVERT: A 867 PHE cc_start: 0.6839 (m-10) cc_final: 0.6016 (m-10) REVERT: A 959 GLU cc_start: 0.8476 (mp0) cc_final: 0.8182 (mp0) REVERT: A 972 MET cc_start: 0.7436 (tpt) cc_final: 0.7078 (tpt) REVERT: A 1000 MET cc_start: 0.8491 (mtt) cc_final: 0.8159 (mpp) REVERT: A 1030 TYR cc_start: 0.6296 (m-10) cc_final: 0.6082 (m-80) REVERT: A 1178 LEU cc_start: 0.8836 (tt) cc_final: 0.8601 (pp) REVERT: B 587 MET cc_start: 0.8208 (tpp) cc_final: 0.7877 (tpp) REVERT: B 675 ARG cc_start: 0.9189 (mtt180) cc_final: 0.8849 (mtp-110) REVERT: B 712 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 728 LYS cc_start: 0.9375 (mttt) cc_final: 0.9171 (mtmt) REVERT: B 847 MET cc_start: 0.9018 (mmm) cc_final: 0.8720 (mmm) REVERT: B 867 PHE cc_start: 0.6895 (m-10) cc_final: 0.6014 (m-10) REVERT: B 972 MET cc_start: 0.7445 (tpt) cc_final: 0.7096 (tpt) REVERT: B 1000 MET cc_start: 0.8445 (mtt) cc_final: 0.8132 (mpp) REVERT: B 1030 TYR cc_start: 0.6211 (m-10) cc_final: 0.5952 (m-80) REVERT: B 1178 LEU cc_start: 0.8841 (tt) cc_final: 0.8608 (pp) outliers start: 2 outliers final: 0 residues processed: 156 average time/residue: 0.1092 time to fit residues: 26.0810 Evaluate side-chains 112 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 93 optimal weight: 0.9980 chunk 131 optimal weight: 0.0020 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.075263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061741 restraints weight = 58769.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064099 restraints weight = 32094.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065684 restraints weight = 20655.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066840 restraints weight = 14853.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.067606 restraints weight = 11472.116| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13908 Z= 0.117 Angle : 0.563 7.498 19030 Z= 0.294 Chirality : 0.041 0.236 2094 Planarity : 0.004 0.038 2220 Dihedral : 18.328 179.557 2282 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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 are not related in a simple way. whole: -0.06 (0.22), residues: 1512 helix: 1.84 (0.21), residues: 666 sheet: -1.89 (0.43), residues: 136 loop : -1.57 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 804 TYR 0.014 0.001 TYR A 805 PHE 0.019 0.001 PHE A1054 TRP 0.030 0.002 TRP A1090 HIS 0.003 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (13908) covalent geometry : angle 0.56305 / 0.29 (19030) hydrogen bonds : bond 0.03192 / 2.15 ( 572) hydrogen bonds : angle 3.68577 / 2.74 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.85 seconds wall clock time: 36 minutes 57.71 seconds (2217.71 seconds total)