Starting phenix.real_space_refine on Fri Jul 3 11:01:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zy6_11551/07_2026/6zy6_11551.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy6_11551/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zy6_11551/07_2026/6zy6_11551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy6_11551/07_2026/6zy6_11551.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy6_11551/07_2026/6zy6_11551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy6_11551/07_2026/6zy6_11551.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zy6_11551/07_2026/6zy6_11551.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zy6_11551/07_2026/6zy6_11551.cif" } 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-dev-6108/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: 3.24, per 1000 atoms: 0.24 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: 1.13 Conformation dependent library (CDL) restraints added in 487.1 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: 1.47 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: 2.16 Time building geometry restraints manager: 1.45 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: 13151 1.08 - 2.17: 5084 2.17 - 3.25: 727 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.040 Find NCS groups from input model: 0.110 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.330 ------------------------------------------------------------------------------- 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= 0.817 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 1.06653 / 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 : 0.402 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 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: 0.7567 (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: 0.8730 (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: 0.8786 (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: 0.8008 (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: 0.7666 (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: 0.1291 time to fit residues: 75.6312 Evaluate side-chains 203 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.084242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070336 restraints weight = 53448.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072846 restraints weight = 28886.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074638 restraints weight = 18391.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075923 restraints weight = 12962.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076851 restraints weight = 9888.837| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13908 Z= 0.136 Angle : 0.584 11.849 19030 Z= 0.301 Chirality : 0.042 0.217 2094 Planarity : 0.004 0.046 2220 Dihedral : 17.299 176.101 2282 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -0.90 (0.21), residues: 1512 helix: 1.05 (0.20), residues: 664 sheet: -1.72 (0.43), residues: 158 loop : -2.02 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 487 TYR 0.016 0.001 TYR B 686 PHE 0.010 0.001 PHE A 698 TRP 0.021 0.002 TRP A1090 HIS 0.007 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (13908) covalent geometry : angle 0.58412 / 0.30 (19030) hydrogen bonds : bond 0.04059 / 2.80 ( 572) hydrogen bonds : angle 4.32942 / 3.14 ( 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 : 0.491 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 446 ASP cc_start: 0.7181 (m-30) cc_final: 0.6841 (p0) REVERT: A 455 CYS cc_start: 0.8228 (m) cc_final: 0.7498 (m) REVERT: A 503 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7125 (mt-10) REVERT: A 526 ASP cc_start: 0.9317 (m-30) cc_final: 0.9030 (t0) REVERT: A 552 LEU cc_start: 0.9021 (mt) cc_final: 0.8639 (mt) REVERT: A 589 PHE cc_start: 0.7844 (m-10) cc_final: 0.7443 (m-10) REVERT: A 675 ARG cc_start: 0.9166 (mtt180) cc_final: 0.8568 (mtm110) REVERT: A 701 LYS cc_start: 0.8717 (mmtp) cc_final: 0.8430 (ttmt) REVERT: A 712 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 728 LYS cc_start: 0.9088 (mttt) cc_final: 0.8823 (mtmt) REVERT: A 738 ASP cc_start: 0.7542 (m-30) cc_final: 0.7294 (m-30) REVERT: A 815 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8480 (mmm160) REVERT: A 862 CYS cc_start: 0.7838 (t) cc_final: 0.7472 (p) REVERT: A 923 ILE cc_start: 0.9136 (mm) cc_final: 0.8916 (mm) REVERT: A 1000 MET cc_start: 0.8429 (mtt) cc_final: 0.7821 (mmm) REVERT: A 1024 GLU cc_start: 0.8678 (tt0) cc_final: 0.8112 (tm-30) REVERT: A 1128 LEU cc_start: 0.9163 (mt) cc_final: 0.8931 (mt) REVERT: A 1155 LEU cc_start: 0.8417 (tp) cc_final: 0.8206 (tp) REVERT: A 1169 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8607 (tm-30) REVERT: B 446 ASP cc_start: 0.7218 (m-30) cc_final: 0.6926 (p0) REVERT: B 455 CYS cc_start: 0.8257 (m) cc_final: 0.7437 (m) REVERT: B 526 ASP cc_start: 0.9321 (m-30) cc_final: 0.9032 (t0) REVERT: B 552 LEU cc_start: 0.9099 (mt) cc_final: 0.8721 (mt) REVERT: B 675 ARG cc_start: 0.9175 (mtt180) cc_final: 0.8590 (mtm110) REVERT: B 712 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7897 (mt-10) REVERT: B 728 LYS cc_start: 0.9078 (mttt) cc_final: 0.8816 (mtmt) REVERT: B 738 ASP cc_start: 0.7549 (m-30) cc_final: 0.7288 (m-30) REVERT: B 815 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8490 (mmm160) REVERT: B 862 CYS cc_start: 0.8008 (t) cc_final: 0.7443 (p) REVERT: B 923 ILE cc_start: 0.9151 (mm) cc_final: 0.8927 (mm) REVERT: B 1000 MET cc_start: 0.8415 (mtt) cc_final: 0.7847 (mmm) REVERT: B 1128 LEU cc_start: 0.9167 (mt) cc_final: 0.8935 (mt) REVERT: B 1155 LEU cc_start: 0.8413 (tp) cc_final: 0.8196 (tp) REVERT: B 1169 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8600 (tm-30) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1110 time to fit residues: 42.8537 Evaluate side-chains 166 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 4.9990 chunk 131 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS A 795 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS B 711 ASN B 795 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 = 0.3434 r_free = 0.3434 target = 0.074045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060617 restraints weight = 58850.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.062840 restraints weight = 32295.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.064406 restraints weight = 21094.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065529 restraints weight = 15257.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066324 restraints weight = 11907.608| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 13908 Z= 0.336 Angle : 0.892 11.832 19030 Z= 0.454 Chirality : 0.047 0.191 2094 Planarity : 0.007 0.075 2220 Dihedral : 17.866 179.597 2282 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.15 % Allowed : 2.71 % Favored : 97.14 % 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: -1.16 (0.21), residues: 1512 helix: 0.93 (0.20), residues: 678 sheet: -1.92 (0.44), residues: 154 loop : -2.33 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 450 TYR 0.023 0.003 TYR B1030 PHE 0.020 0.002 PHE B 653 TRP 0.026 0.003 TRP B1090 HIS 0.011 0.003 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.34 (13908) covalent geometry : angle 0.89205 / 0.45 (19030) hydrogen bonds : bond 0.05853 / 4.01 ( 572) hydrogen bonds : angle 4.40394 / 3.11 ( 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 169 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 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: symmetry clash revert: symmetry clash REVERT: A 539 MET cc_start: 0.7580 (ppp) cc_final: 0.7333 (ppp) REVERT: A 587 MET cc_start: 0.8306 (tpp) cc_final: 0.7730 (tpp) REVERT: A 712 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 726 GLN cc_start: 0.9077 (mp10) cc_final: 0.8835 (mp10) REVERT: A 738 ASP cc_start: 0.7842 (m-30) cc_final: 0.7613 (m-30) REVERT: A 754 MET cc_start: 0.8311 (mpp) cc_final: 0.8086 (mpp) REVERT: A 766 MET cc_start: 0.9243 (mmp) cc_final: 0.8990 (mmp) REVERT: A 815 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8559 (mmm160) REVERT: A 839 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8028 (mm-30) REVERT: A 856 ILE cc_start: 0.9265 (mt) cc_final: 0.8814 (tt) REVERT: A 862 CYS cc_start: 0.8472 (t) cc_final: 0.7963 (p) REVERT: A 1000 MET cc_start: 0.8468 (mtt) cc_final: 0.7991 (mpp) REVERT: B 537 MET cc_start: 0.7513 (mtm) cc_final: 0.7276 (mtt) REVERT: B 539 MET cc_start: 0.7568 (ppp) cc_final: 0.7352 (ppp) REVERT: B 587 MET cc_start: 0.8448 (tpp) cc_final: 0.7879 (tpp) REVERT: B 712 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 726 GLN cc_start: 0.8996 (mp10) cc_final: 0.8703 (mp10) REVERT: B 738 ASP cc_start: 0.7845 (m-30) cc_final: 0.7626 (m-30) REVERT: B 754 MET cc_start: 0.8306 (mpp) cc_final: 0.8084 (mpp) REVERT: B 762 MET cc_start: 0.8304 (mmm) cc_final: 0.7926 (mmp) REVERT: B 766 MET cc_start: 0.9196 (mmp) cc_final: 0.8990 (mmp) REVERT: B 767 THR cc_start: 0.9327 (m) cc_final: 0.9120 (p) REVERT: B 768 ILE cc_start: 0.9428 (mm) cc_final: 0.9225 (mm) REVERT: B 815 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8565 (mmm160) REVERT: B 839 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8013 (mm-30) REVERT: B 862 CYS cc_start: 0.8511 (t) cc_final: 0.7819 (p) REVERT: B 1000 MET cc_start: 0.8471 (mtt) cc_final: 0.8011 (mpp) outliers start: 2 outliers final: 0 residues processed: 169 average time/residue: 0.1087 time to fit residues: 27.8014 Evaluate side-chains 111 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 782 ASN ** 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 = 0.3489 r_free = 0.3489 target = 0.077041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.063358 restraints weight = 57082.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065680 restraints weight = 31092.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067329 restraints weight = 20143.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.068537 restraints weight = 14420.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069320 restraints weight = 11109.328| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13908 Z= 0.127 Angle : 0.571 10.429 19030 Z= 0.299 Chirality : 0.042 0.183 2094 Planarity : 0.004 0.048 2220 Dihedral : 18.034 179.772 2282 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.15 % Allowed : 1.51 % 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: -0.74 (0.21), residues: 1512 helix: 1.39 (0.20), residues: 664 sheet: -1.83 (0.44), residues: 150 loop : -2.14 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 487 TYR 0.013 0.001 TYR A 590 PHE 0.007 0.001 PHE B 668 TRP 0.015 0.002 TRP A1090 HIS 0.005 0.001 HIS B 961 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (13908) covalent geometry : angle 0.57056 / 0.30 (19030) hydrogen bonds : bond 0.03559 / 2.43 ( 572) hydrogen bonds : angle 3.89498 / 2.83 ( 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 185 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.8252 (m) cc_final: 0.7809 (m) REVERT: A 712 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7961 (mp0) REVERT: A 768 ILE cc_start: 0.9439 (mm) cc_final: 0.9218 (mt) REVERT: A 782 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8773 (p0) REVERT: A 815 ARG cc_start: 0.8738 (mmm160) cc_final: 0.8505 (mmm160) REVERT: A 839 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7949 (mm-30) REVERT: A 856 ILE cc_start: 0.9020 (mt) cc_final: 0.8559 (tt) REVERT: A 862 CYS cc_start: 0.8267 (t) cc_final: 0.7801 (p) REVERT: A 930 THR cc_start: 0.7725 (m) cc_final: 0.7487 (p) REVERT: A 1000 MET cc_start: 0.8483 (mtt) cc_final: 0.7895 (mpp) REVERT: A 1030 TYR cc_start: 0.6011 (m-80) cc_final: 0.4546 (m-80) REVERT: A 1178 LEU cc_start: 0.9232 (tp) cc_final: 0.9008 (tt) REVERT: B 455 CYS cc_start: 0.8279 (m) cc_final: 0.7814 (m) REVERT: B 537 MET cc_start: 0.7501 (mtm) cc_final: 0.7232 (mtt) REVERT: B 539 MET cc_start: 0.7398 (ppp) cc_final: 0.7198 (ppp) REVERT: B 587 MET cc_start: 0.8416 (tpp) cc_final: 0.8055 (tpp) REVERT: B 726 GLN cc_start: 0.8908 (mp10) cc_final: 0.8640 (mp10) REVERT: B 767 THR cc_start: 0.9270 (m) cc_final: 0.8992 (m) REVERT: B 782 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8799 (p0) REVERT: B 815 ARG cc_start: 0.8742 (mmm160) cc_final: 0.8512 (mmm160) REVERT: B 839 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7973 (mm-30) REVERT: B 862 CYS cc_start: 0.8288 (t) cc_final: 0.7771 (p) REVERT: B 1000 MET cc_start: 0.8497 (mtt) cc_final: 0.7916 (mpp) REVERT: B 1030 TYR cc_start: 0.5999 (m-80) cc_final: 0.4540 (m-80) REVERT: B 1178 LEU cc_start: 0.9229 (tp) cc_final: 0.9006 (tt) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.1087 time to fit residues: 30.4844 Evaluate side-chains 120 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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: 0.6980 chunk 51 optimal weight: 0.0870 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 555 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.063236 restraints weight = 56910.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065591 restraints weight = 30781.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067237 restraints weight = 19745.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068409 restraints weight = 14087.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069284 restraints weight = 10875.240| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4731 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= 0.110 Angle : 0.549 9.936 19030 Z= 0.287 Chirality : 0.041 0.193 2094 Planarity : 0.004 0.039 2220 Dihedral : 18.098 179.528 2282 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.08 % Allowed : 1.88 % Favored : 98.04 % 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: -0.48 (0.22), residues: 1512 helix: 1.57 (0.20), residues: 666 sheet: -1.65 (0.45), residues: 146 loop : -1.99 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 635 TYR 0.013 0.001 TYR B 805 PHE 0.014 0.001 PHE A1054 TRP 0.009 0.001 TRP A1036 HIS 0.006 0.001 HIS B 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (13908) covalent geometry : angle 0.54883 / 0.29 (19030) hydrogen bonds : bond 0.03279 / 2.26 ( 572) hydrogen bonds : angle 3.73337 / 2.73 ( 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 175 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.8065 (tpp) cc_final: 0.7857 (tpp) REVERT: A 738 ASP cc_start: 0.7637 (m-30) cc_final: 0.7254 (m-30) REVERT: A 754 MET cc_start: 0.8510 (mpp) cc_final: 0.8219 (mpp) REVERT: A 768 ILE cc_start: 0.9452 (mm) cc_final: 0.9250 (mt) REVERT: A 815 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8509 (mmm160) REVERT: A 856 ILE cc_start: 0.8944 (mt) cc_final: 0.8603 (tt) REVERT: A 862 CYS cc_start: 0.8207 (t) cc_final: 0.7797 (p) REVERT: A 930 THR cc_start: 0.7772 (m) cc_final: 0.7552 (p) REVERT: A 1000 MET cc_start: 0.8531 (mtt) cc_final: 0.7922 (mpp) REVERT: A 1030 TYR cc_start: 0.5669 (m-80) cc_final: 0.4396 (m-80) REVERT: B 537 MET cc_start: 0.7488 (mtm) cc_final: 0.7189 (mtt) REVERT: B 712 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7982 (mt-10) REVERT: B 726 GLN cc_start: 0.8892 (mp10) cc_final: 0.8634 (mp10) REVERT: B 728 LYS cc_start: 0.9270 (mttt) cc_final: 0.8849 (mtpt) REVERT: B 738 ASP cc_start: 0.7626 (m-30) cc_final: 0.7252 (m-30) REVERT: B 754 MET cc_start: 0.8519 (mpp) cc_final: 0.8243 (mpp) REVERT: B 762 MET cc_start: 0.8302 (mmp) cc_final: 0.8082 (mmm) REVERT: B 767 THR cc_start: 0.9243 (m) cc_final: 0.8916 (m) REVERT: B 768 ILE cc_start: 0.9422 (mm) cc_final: 0.9219 (mt) REVERT: B 815 ARG cc_start: 0.8755 (mmm160) cc_final: 0.8514 (mmm160) REVERT: B 847 MET cc_start: 0.8881 (mmm) cc_final: 0.8681 (mmm) REVERT: B 862 CYS cc_start: 0.8253 (t) cc_final: 0.7711 (p) REVERT: B 1000 MET cc_start: 0.8545 (mtt) cc_final: 0.7947 (mpp) REVERT: B 1030 TYR cc_start: 0.5657 (m-80) cc_final: 0.4387 (m-80) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1059 time to fit residues: 28.3556 Evaluate side-chains 119 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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: 3.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 102 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.0570 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 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 = 0.3499 r_free = 0.3499 target = 0.077340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.063635 restraints weight = 56019.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066011 restraints weight = 30297.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.067676 restraints weight = 19408.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068865 restraints weight = 13829.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069691 restraints weight = 10641.994| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4832 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= 0.104 Angle : 0.530 8.119 19030 Z= 0.279 Chirality : 0.040 0.197 2094 Planarity : 0.004 0.038 2220 Dihedral : 18.097 179.380 2282 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: 1.68 (0.21), residues: 666 sheet: -1.61 (0.44), residues: 146 loop : -1.85 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 804 TYR 0.009 0.001 TYR A 907 PHE 0.006 0.001 PHE B 573 TRP 0.010 0.001 TRP B1090 HIS 0.003 0.001 HIS B 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (13908) covalent geometry : angle 0.53043 / 0.28 (19030) hydrogen bonds : bond 0.03150 / 2.16 ( 572) hydrogen bonds : angle 3.67255 / 2.69 ( 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 177 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 ASP cc_start: 0.7646 (m-30) cc_final: 0.7426 (m-30) REVERT: A 815 ARG cc_start: 0.8766 (mmm160) cc_final: 0.8511 (mmm160) REVERT: A 847 MET cc_start: 0.8901 (mmm) cc_final: 0.8694 (mmm) REVERT: A 862 CYS cc_start: 0.8213 (t) cc_final: 0.7824 (p) REVERT: A 925 GLU cc_start: 0.7667 (tt0) cc_final: 0.7221 (tt0) REVERT: A 952 PRO cc_start: 0.8583 (Cg_endo) cc_final: 0.8356 (Cg_exo) REVERT: A 1000 MET cc_start: 0.8454 (mtt) cc_final: 0.7962 (mpp) REVERT: A 1030 TYR cc_start: 0.5828 (m-80) cc_final: 0.4718 (m-80) REVERT: A 1169 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8832 (tm-30) REVERT: A 1178 LEU cc_start: 0.8991 (tt) cc_final: 0.8659 (pp) REVERT: B 537 MET cc_start: 0.7472 (mtm) cc_final: 0.7172 (mtt) REVERT: B 587 MET cc_start: 0.8602 (tpp) cc_final: 0.8398 (tpp) REVERT: B 726 GLN cc_start: 0.8858 (mp10) cc_final: 0.8555 (mp10) REVERT: B 738 ASP cc_start: 0.7626 (m-30) cc_final: 0.7416 (m-30) REVERT: B 767 THR cc_start: 0.9283 (m) cc_final: 0.9055 (m) REVERT: B 815 ARG cc_start: 0.8767 (mmm160) cc_final: 0.8514 (mmm160) REVERT: B 847 MET cc_start: 0.8887 (mmm) cc_final: 0.8674 (mmm) REVERT: B 862 CYS cc_start: 0.8221 (t) cc_final: 0.7778 (p) REVERT: B 925 GLU cc_start: 0.7754 (tt0) cc_final: 0.7239 (tt0) REVERT: B 952 PRO cc_start: 0.8568 (Cg_endo) cc_final: 0.8344 (Cg_exo) REVERT: B 1000 MET cc_start: 0.8440 (mtt) cc_final: 0.7972 (mpp) REVERT: B 1030 TYR cc_start: 0.5806 (m-80) cc_final: 0.4727 (m-80) REVERT: B 1169 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8829 (tm-30) REVERT: B 1178 LEU cc_start: 0.8987 (tt) cc_final: 0.8659 (pp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1052 time to fit residues: 28.3827 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 : 0.512 ------------------------------------------------------------------------------- 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: 0.9980 chunk 59 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 146 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 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 = 0.3422 r_free = 0.3422 target = 0.073859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060336 restraints weight = 57918.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062598 restraints weight = 31702.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064185 restraints weight = 20599.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.065307 restraints weight = 14797.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066086 restraints weight = 11527.013| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13908 Z= 0.183 Angle : 0.625 8.087 19030 Z= 0.327 Chirality : 0.042 0.204 2094 Planarity : 0.005 0.043 2220 Dihedral : 18.241 179.144 2282 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -0.24 (0.22), residues: 1512 helix: 1.80 (0.21), residues: 666 sheet: -1.84 (0.44), residues: 132 loop : -1.82 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 804 TYR 0.016 0.002 TYR B 907 PHE 0.021 0.002 PHE A 867 TRP 0.014 0.002 TRP B 860 HIS 0.005 0.001 HIS B 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (13908) covalent geometry : angle 0.62546 / 0.33 (19030) hydrogen bonds : bond 0.03905 / 2.69 ( 572) hydrogen bonds : angle 3.79575 / 2.76 ( 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 151 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 LEU cc_start: 0.9304 (tp) cc_final: 0.8875 (tp) REVERT: A 587 MET cc_start: 0.8577 (tpp) cc_final: 0.8273 (tpp) REVERT: A 675 ARG cc_start: 0.9159 (mtt180) cc_final: 0.8841 (mtp-110) REVERT: A 712 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8039 (mt-10) REVERT: A 809 MET cc_start: 0.8352 (tmm) cc_final: 0.8088 (tmm) REVERT: A 815 ARG cc_start: 0.8833 (mmm160) cc_final: 0.8573 (mmm160) REVERT: A 847 MET cc_start: 0.9069 (mmm) cc_final: 0.8781 (mmm) REVERT: A 862 CYS cc_start: 0.8189 (t) cc_final: 0.7968 (p) REVERT: A 867 PHE cc_start: 0.6774 (m-10) cc_final: 0.6298 (m-10) REVERT: A 925 GLU cc_start: 0.7687 (tt0) cc_final: 0.7303 (tt0) REVERT: A 952 PRO cc_start: 0.8649 (Cg_endo) cc_final: 0.8446 (Cg_exo) REVERT: A 1000 MET cc_start: 0.8468 (mtt) cc_final: 0.8137 (mpp) REVERT: A 1131 MET cc_start: 0.8762 (tpp) cc_final: 0.8531 (tpp) REVERT: A 1178 LEU cc_start: 0.9006 (tt) cc_final: 0.8622 (pp) REVERT: B 537 MET cc_start: 0.7490 (mtm) cc_final: 0.7176 (mtt) REVERT: B 587 MET cc_start: 0.8541 (tpp) cc_final: 0.8232 (tpp) REVERT: B 675 ARG cc_start: 0.9171 (mtt180) cc_final: 0.8835 (mtp-110) REVERT: B 726 GLN cc_start: 0.8941 (mp10) cc_final: 0.8684 (mp10) REVERT: B 767 THR cc_start: 0.9342 (m) cc_final: 0.9131 (p) REVERT: B 768 ILE cc_start: 0.9478 (mm) cc_final: 0.9243 (mt) REVERT: B 809 MET cc_start: 0.8399 (tmm) cc_final: 0.8164 (tmm) REVERT: B 815 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8574 (mmm160) REVERT: B 847 MET cc_start: 0.8973 (mmm) cc_final: 0.8691 (mmm) REVERT: B 925 GLU cc_start: 0.7709 (tt0) cc_final: 0.7327 (tt0) REVERT: B 930 THR cc_start: 0.8359 (m) cc_final: 0.8082 (p) REVERT: B 952 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8433 (Cg_exo) REVERT: B 1000 MET cc_start: 0.8509 (mtt) cc_final: 0.8158 (mpp) REVERT: B 1131 MET cc_start: 0.8755 (tpp) cc_final: 0.8524 (tpp) REVERT: B 1178 LEU cc_start: 0.9008 (tt) cc_final: 0.8630 (pp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1066 time to fit residues: 24.9622 Evaluate side-chains 107 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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: 5.9990 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 509 ASN B 795 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.059005 restraints weight = 59170.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.061173 restraints weight = 32659.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062691 restraints weight = 21330.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.063793 restraints weight = 15467.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.064510 restraints weight = 12086.556| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13908 Z= 0.187 Angle : 0.619 7.405 19030 Z= 0.331 Chirality : 0.042 0.219 2094 Planarity : 0.004 0.036 2220 Dihedral : 18.451 178.463 2282 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -0.36 (0.22), residues: 1512 helix: 1.66 (0.20), residues: 666 sheet: -1.72 (0.45), residues: 132 loop : -1.88 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 635 TYR 0.015 0.001 TYR A1029 PHE 0.016 0.001 PHE A1023 TRP 0.027 0.003 TRP A1090 HIS 0.005 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (13908) covalent geometry : angle 0.61928 / 0.33 (19030) hydrogen bonds : bond 0.03897 / 2.63 ( 572) hydrogen bonds : angle 3.85212 / 2.81 ( 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 152 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 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: A 587 MET cc_start: 0.8804 (tpp) cc_final: 0.8487 (tpp) REVERT: A 675 ARG cc_start: 0.9184 (mtt180) cc_final: 0.8879 (mtp-110) REVERT: A 712 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8093 (mt-10) REVERT: A 847 MET cc_start: 0.9191 (mmm) cc_final: 0.8851 (mmm) REVERT: A 862 CYS cc_start: 0.8375 (t) cc_final: 0.8156 (p) REVERT: A 867 PHE cc_start: 0.7058 (m-10) cc_final: 0.6582 (m-10) REVERT: A 925 GLU cc_start: 0.7814 (tt0) cc_final: 0.7377 (tt0) REVERT: A 1000 MET cc_start: 0.8503 (mtt) cc_final: 0.8228 (mpp) REVERT: A 1128 LEU cc_start: 0.9181 (mt) cc_final: 0.8981 (mt) REVERT: A 1178 LEU cc_start: 0.8979 (tt) cc_final: 0.8662 (pp) REVERT: B 538 ILE cc_start: 0.8999 (mt) cc_final: 0.8768 (mt) REVERT: B 675 ARG cc_start: 0.9179 (mtt180) cc_final: 0.8874 (mtp-110) REVERT: B 712 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8092 (mt-10) REVERT: B 726 GLN cc_start: 0.8980 (mp10) cc_final: 0.8674 (mp10) REVERT: B 768 ILE cc_start: 0.9515 (mm) cc_final: 0.9301 (mt) REVERT: B 847 MET cc_start: 0.9107 (mmm) cc_final: 0.8772 (mmm) REVERT: B 925 GLU cc_start: 0.7811 (tt0) cc_final: 0.7574 (tt0) REVERT: B 1000 MET cc_start: 0.8490 (mtt) cc_final: 0.8226 (mpp) REVERT: B 1128 LEU cc_start: 0.9196 (mt) cc_final: 0.8979 (mt) REVERT: B 1178 LEU cc_start: 0.8998 (tt) cc_final: 0.8566 (pp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1113 time to fit residues: 25.3992 Evaluate side-chains 108 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 0.7980 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 37 optimal weight: 0.1980 chunk 77 optimal weight: 7.9990 chunk 97 optimal weight: 0.0980 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 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 = 0.3428 r_free = 0.3428 target = 0.074371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060826 restraints weight = 59105.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.063167 restraints weight = 32087.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.064773 restraints weight = 20654.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065906 restraints weight = 14792.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.066765 restraints weight = 11470.590| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13908 Z= 0.113 Angle : 0.574 6.410 19030 Z= 0.303 Chirality : 0.041 0.221 2094 Planarity : 0.004 0.034 2220 Dihedral : 18.468 179.496 2282 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % 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: -0.24 (0.22), residues: 1512 helix: 1.66 (0.21), residues: 666 sheet: -1.74 (0.45), residues: 132 loop : -1.68 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 727 TYR 0.009 0.001 TYR B 907 PHE 0.019 0.001 PHE B1054 TRP 0.014 0.002 TRP A 931 HIS 0.003 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (13908) covalent geometry : angle 0.57371 / 0.30 (19030) hydrogen bonds : bond 0.03290 / 2.21 ( 572) hydrogen bonds : angle 3.73270 / 2.75 ( 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 155 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 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 457 LEU cc_start: 0.9390 (tp) cc_final: 0.9036 (tp) REVERT: A 499 LYS cc_start: 0.9487 (tttp) cc_final: 0.9197 (ttmm) REVERT: A 545 ASP cc_start: 0.8792 (m-30) cc_final: 0.8400 (t0) REVERT: A 587 MET cc_start: 0.8584 (tpp) cc_final: 0.8303 (tpp) REVERT: A 675 ARG cc_start: 0.9183 (mtt180) cc_final: 0.8848 (mtp-110) REVERT: A 754 MET cc_start: 0.8245 (mpp) cc_final: 0.7914 (mpp) REVERT: A 847 MET cc_start: 0.9129 (mmm) cc_final: 0.8799 (mmm) REVERT: A 862 CYS cc_start: 0.8164 (t) cc_final: 0.7957 (p) REVERT: A 867 PHE cc_start: 0.6754 (m-10) cc_final: 0.6190 (m-10) REVERT: A 925 GLU cc_start: 0.7727 (tt0) cc_final: 0.6765 (pt0) REVERT: A 1000 MET cc_start: 0.8515 (mtt) cc_final: 0.8213 (mpp) REVERT: A 1128 LEU cc_start: 0.9141 (mt) cc_final: 0.8900 (mt) REVERT: A 1178 LEU cc_start: 0.9045 (tt) cc_final: 0.8622 (pp) REVERT: B 499 LYS cc_start: 0.9491 (tttp) cc_final: 0.9229 (ttmm) REVERT: B 675 ARG cc_start: 0.9181 (mtt180) cc_final: 0.8859 (mtp-110) REVERT: B 754 MET cc_start: 0.8251 (mpp) cc_final: 0.7886 (mpp) REVERT: B 768 ILE cc_start: 0.9447 (mm) cc_final: 0.9246 (mt) REVERT: B 847 MET cc_start: 0.9031 (mmm) cc_final: 0.8696 (mmm) REVERT: B 867 PHE cc_start: 0.8315 (m-80) cc_final: 0.7081 (m-80) REVERT: B 925 GLU cc_start: 0.7743 (tt0) cc_final: 0.6761 (pt0) REVERT: B 1000 MET cc_start: 0.8469 (mtt) cc_final: 0.8201 (mpp) REVERT: B 1128 LEU cc_start: 0.9104 (mt) cc_final: 0.8899 (mt) REVERT: B 1178 LEU cc_start: 0.9045 (tt) cc_final: 0.8623 (pp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1071 time to fit residues: 25.2022 Evaluate side-chains 109 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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: 8.9990 chunk 141 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 116 optimal weight: 0.0770 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.073440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060136 restraints weight = 58308.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.062428 restraints weight = 31789.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.064014 restraints weight = 20470.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.065087 restraints weight = 14619.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065970 restraints weight = 11390.423| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13908 Z= 0.131 Angle : 0.585 8.686 19030 Z= 0.305 Chirality : 0.041 0.215 2094 Planarity : 0.004 0.042 2220 Dihedral : 18.528 179.858 2282 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.14 (0.23), residues: 1512 helix: 1.72 (0.21), residues: 666 sheet: -1.89 (0.44), residues: 136 loop : -1.56 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 815 TYR 0.015 0.001 TYR B 805 PHE 0.009 0.001 PHE A 573 TRP 0.024 0.002 TRP B1134 HIS 0.005 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (13908) covalent geometry : angle 0.58458 / 0.30 (19030) hydrogen bonds : bond 0.03387 / 2.30 ( 572) hydrogen bonds : angle 3.73771 / 2.77 ( 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 147 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 ASP cc_start: 0.8740 (m-30) cc_final: 0.8338 (t0) REVERT: A 587 MET cc_start: 0.8598 (tpp) cc_final: 0.8266 (tpp) REVERT: A 675 ARG cc_start: 0.9196 (mtt180) cc_final: 0.8861 (mtp-110) REVERT: A 754 MET cc_start: 0.8269 (mpp) cc_final: 0.7972 (mpp) REVERT: A 815 ARG cc_start: 0.8798 (mmm160) cc_final: 0.7922 (mmm160) REVERT: A 847 MET cc_start: 0.9107 (mmm) cc_final: 0.8747 (mmm) REVERT: A 867 PHE cc_start: 0.6828 (m-10) cc_final: 0.6388 (m-10) REVERT: A 925 GLU cc_start: 0.7788 (tt0) cc_final: 0.6847 (pt0) REVERT: A 1000 MET cc_start: 0.8529 (mtt) cc_final: 0.8238 (mpp) REVERT: A 1128 LEU cc_start: 0.9417 (mt) cc_final: 0.9180 (mt) REVERT: A 1178 LEU cc_start: 0.9031 (tt) cc_final: 0.8725 (pp) REVERT: B 537 MET cc_start: 0.7608 (tpp) cc_final: 0.7209 (tpt) REVERT: B 542 GLN cc_start: 0.7381 (mm110) cc_final: 0.7125 (mm110) REVERT: B 675 ARG cc_start: 0.9189 (mtt180) cc_final: 0.8851 (mtp-110) REVERT: B 754 MET cc_start: 0.8168 (mpp) cc_final: 0.7818 (mpp) REVERT: B 768 ILE cc_start: 0.9460 (mm) cc_final: 0.9252 (mt) REVERT: B 847 MET cc_start: 0.9131 (mmm) cc_final: 0.8650 (mmm) REVERT: B 867 PHE cc_start: 0.8378 (m-80) cc_final: 0.7118 (m-80) REVERT: B 925 GLU cc_start: 0.7796 (tt0) cc_final: 0.6925 (pt0) REVERT: B 1000 MET cc_start: 0.8482 (mtt) cc_final: 0.8221 (mpp) REVERT: B 1128 LEU cc_start: 0.9416 (mt) cc_final: 0.9176 (mt) REVERT: B 1178 LEU cc_start: 0.9030 (tt) cc_final: 0.8722 (pp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1164 time to fit residues: 25.8526 Evaluate side-chains 106 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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: 0.0670 chunk 131 optimal weight: 0.0670 chunk 72 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.075621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.062407 restraints weight = 56700.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.064696 restraints weight = 31068.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066240 restraints weight = 20061.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.067405 restraints weight = 14455.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068150 restraints weight = 11157.431| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13908 Z= 0.111 Angle : 0.565 8.716 19030 Z= 0.297 Chirality : 0.040 0.213 2094 Planarity : 0.004 0.039 2220 Dihedral : 18.550 179.813 2282 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: -0.14 (0.23), residues: 1512 helix: 1.69 (0.21), residues: 662 sheet: -1.86 (0.44), residues: 136 loop : -1.51 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1026 TYR 0.040 0.001 TYR A1030 PHE 0.017 0.001 PHE B1054 TRP 0.054 0.003 TRP A1167 HIS 0.003 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (13908) covalent geometry : angle 0.56531 / 0.30 (19030) hydrogen bonds : bond 0.03165 / 2.12 ( 572) hydrogen bonds : angle 3.68950 / 2.75 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2077.03 seconds wall clock time: 36 minutes 53.31 seconds (2213.31 seconds total)