Starting phenix.real_space_refine on Thu Jul 31 20:21:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy6_11551/07_2025/6zy6_11551.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy6_11551/07_2025/6zy6_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_2025/6zy6_11551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy6_11551/07_2025/6zy6_11551.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy6_11551/07_2025/6zy6_11551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy6_11551/07_2025/6zy6_11551.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.29, per 1000 atoms: 0.54 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: 3.49 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.53 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: 4.90 Time building geometry restraints manager: 4.19 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: 13176 1.08 - 2.17: 5044 2.17 - 3.25: 744 3.25 - 4.34: 60 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=" CA GLU B1066 " pdb=" C GLU B1066 " pdb=" O GLU B1066 " ideal model delta sigma weight residual 122.64 118.66 3.98 1.25e+00 6.40e-01 1.02e+01 ... (remaining 19025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 8145 35.97 - 71.95: 231 71.95 - 107.92: 2 107.92 - 143.89: 4 143.89 - 179.87: 2 Dihedral angle restraints: 8384 sinusoidal: 3964 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 8381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1440 0.075 - 0.149: 523 0.149 - 0.224: 121 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: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.470 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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= 0.747 Angle : 1.070 5.421 19030 Z= 0.811 Chirality : 0.079 0.374 2094 Planarity : 0.007 0.032 2220 Dihedral : 13.750 179.868 5536 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (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 TRP 0.015 0.002 TRP A 664 HIS 0.006 0.001 HIS A 634 PHE 0.008 0.002 PHE A1003 TYR 0.010 0.002 TYR B 590 ARG 0.007 0.001 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.12465 ( 572) hydrogen bonds : angle 5.28611 ( 1554) covalent geometry : bond 0.01019 (13908) covalent geometry : angle 1.06956 (19030) *********************** 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 : 1.489 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: 0.8130 (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: 0.8009 (tpp) REVERT: B 815 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8482 (mmm160) REVERT: B 862 CYS cc_start: 0.8256 (t) cc_final: 0.7571 (p) REVERT: B 932 THR cc_start: 0.8283 (m) cc_final: 0.7666 (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: 0.7838 (mmm) REVERT: B 1128 LEU cc_start: 0.9266 (mt) cc_final: 0.8957 (mt) REVERT: B 1138 LYS cc_start: 0.8333 (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: 0.2990 time to fit residues: 173.3997 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 : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN A 795 HIS A 824 HIS ** A 961 HIS ** 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 = 0.3550 r_free = 0.3550 target = 0.080157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066255 restraints weight = 54090.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.068666 restraints weight = 29318.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.070399 restraints weight = 18742.114| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13908 Z= 0.162 Angle : 0.585 9.561 19030 Z= 0.297 Chirality : 0.040 0.181 2094 Planarity : 0.004 0.034 2220 Dihedral : 17.554 178.909 2420 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1512 helix: 1.34 (0.20), residues: 674 sheet: -1.72 (0.44), residues: 160 loop : -1.94 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1090 HIS 0.005 0.001 HIS A 634 PHE 0.012 0.001 PHE A 653 TYR 0.016 0.001 TYR B 686 ARG 0.006 0.001 ARG B1160 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 572) hydrogen bonds : angle 3.95958 ( 1554) covalent geometry : bond 0.00355 (13908) covalent geometry : angle 0.58479 (19030) *********************** 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 239 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.8411 (m) cc_final: 0.7943 (m) REVERT: A 503 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7596 (pt0) REVERT: A 526 ASP cc_start: 0.9360 (m-30) cc_final: 0.9118 (t0) REVERT: A 537 MET cc_start: 0.8431 (ttp) cc_final: 0.7872 (ttt) REVERT: A 539 MET cc_start: 0.7383 (ppp) cc_final: 0.7070 (ppp) REVERT: A 701 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8487 (tttt) REVERT: A 712 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7958 (mt-10) REVERT: A 728 LYS cc_start: 0.9254 (mttt) cc_final: 0.8880 (mtpt) REVERT: A 738 ASP cc_start: 0.7457 (m-30) cc_final: 0.7156 (m-30) REVERT: A 754 MET cc_start: 0.9279 (mtt) cc_final: 0.9035 (mpp) REVERT: A 815 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8491 (mmm160) REVERT: A 839 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7875 (mm-30) REVERT: A 856 ILE cc_start: 0.9058 (mt) cc_final: 0.8663 (tt) REVERT: A 862 CYS cc_start: 0.8149 (t) cc_final: 0.7672 (p) REVERT: A 959 GLU cc_start: 0.8022 (mp0) cc_final: 0.7775 (mp0) REVERT: A 1000 MET cc_start: 0.8585 (mtt) cc_final: 0.7855 (mpp) REVERT: A 1128 LEU cc_start: 0.9195 (mt) cc_final: 0.8960 (mt) REVERT: A 1169 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8845 (tm-30) REVERT: A 1178 LEU cc_start: 0.9075 (tt) cc_final: 0.8705 (pp) REVERT: B 455 CYS cc_start: 0.8431 (m) cc_final: 0.7961 (m) REVERT: B 526 ASP cc_start: 0.9357 (m-30) cc_final: 0.9092 (t0) REVERT: B 537 MET cc_start: 0.8449 (ttp) cc_final: 0.7853 (ttt) REVERT: B 539 MET cc_start: 0.7363 (ppp) cc_final: 0.7042 (ppp) REVERT: B 712 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7925 (mt-10) REVERT: B 728 LYS cc_start: 0.9250 (mttt) cc_final: 0.8871 (mtpt) REVERT: B 738 ASP cc_start: 0.7456 (m-30) cc_final: 0.7154 (m-30) REVERT: B 754 MET cc_start: 0.9287 (mtt) cc_final: 0.9033 (mpp) REVERT: B 815 ARG cc_start: 0.8733 (mmm160) cc_final: 0.8500 (mmm160) REVERT: B 839 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7860 (mm-30) REVERT: B 862 CYS cc_start: 0.8082 (t) cc_final: 0.7378 (p) REVERT: B 912 GLU cc_start: 0.8374 (tt0) cc_final: 0.8172 (pt0) REVERT: B 959 GLU cc_start: 0.8001 (mp0) cc_final: 0.7755 (mp0) REVERT: B 1000 MET cc_start: 0.8588 (mtt) cc_final: 0.7877 (mpp) REVERT: B 1036 TRP cc_start: 0.9027 (t-100) cc_final: 0.8706 (t-100) REVERT: B 1128 LEU cc_start: 0.9185 (mt) cc_final: 0.8940 (mt) REVERT: B 1169 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8836 (tm-30) REVERT: B 1178 LEU cc_start: 0.9074 (tt) cc_final: 0.8709 (pp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2569 time to fit residues: 89.3899 Evaluate side-chains 149 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 65 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.0370 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3521 r_free = 0.3521 target = 0.078384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.064631 restraints weight = 54312.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067006 restraints weight = 29247.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068679 restraints weight = 18679.004| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13908 Z= 0.118 Angle : 0.514 8.823 19030 Z= 0.266 Chirality : 0.038 0.138 2094 Planarity : 0.004 0.046 2220 Dihedral : 17.378 179.646 2420 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1512 helix: 1.56 (0.20), residues: 666 sheet: -1.78 (0.43), residues: 152 loop : -1.81 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1090 HIS 0.003 0.001 HIS A 605 PHE 0.008 0.001 PHE A 589 TYR 0.011 0.001 TYR B1030 ARG 0.004 0.000 ARG B 804 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 572) hydrogen bonds : angle 3.73521 ( 1554) covalent geometry : bond 0.00262 (13908) covalent geometry : angle 0.51448 (19030) *********************** 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 215 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 MET cc_start: 0.8430 (ttp) cc_final: 0.7850 (ttt) REVERT: A 539 MET cc_start: 0.7350 (ppp) cc_final: 0.7123 (ppp) REVERT: A 726 GLN cc_start: 0.8805 (mp10) cc_final: 0.8555 (mp10) REVERT: A 728 LYS cc_start: 0.9306 (mttt) cc_final: 0.9019 (mtmt) REVERT: A 767 THR cc_start: 0.9237 (m) cc_final: 0.8976 (m) REVERT: A 782 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8537 (p0) REVERT: A 815 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8530 (mmm160) REVERT: A 839 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7866 (mm-30) REVERT: A 856 ILE cc_start: 0.9023 (mt) cc_final: 0.8685 (tp) REVERT: A 862 CYS cc_start: 0.8144 (t) cc_final: 0.7718 (p) REVERT: A 924 SER cc_start: 0.7116 (m) cc_final: 0.6446 (t) REVERT: A 930 THR cc_start: 0.7800 (m) cc_final: 0.7598 (p) REVERT: A 959 GLU cc_start: 0.8098 (mp0) cc_final: 0.7778 (mp0) REVERT: A 977 LEU cc_start: 0.8945 (mt) cc_final: 0.8735 (mt) REVERT: A 1000 MET cc_start: 0.8536 (mtt) cc_final: 0.7923 (mpp) REVERT: A 1131 MET cc_start: 0.9035 (ttt) cc_final: 0.8779 (tpp) REVERT: A 1169 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8851 (tm-30) REVERT: A 1178 LEU cc_start: 0.9056 (tt) cc_final: 0.8687 (pp) REVERT: B 539 MET cc_start: 0.7316 (ppp) cc_final: 0.7062 (ppp) REVERT: B 570 LEU cc_start: 0.8505 (mt) cc_final: 0.8160 (tp) REVERT: B 712 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 726 GLN cc_start: 0.8841 (mp10) cc_final: 0.8609 (mp10) REVERT: B 728 LYS cc_start: 0.9296 (mttt) cc_final: 0.9013 (mtmt) REVERT: B 754 MET cc_start: 0.9234 (mtt) cc_final: 0.9026 (mpp) REVERT: B 767 THR cc_start: 0.9231 (m) cc_final: 0.8968 (m) REVERT: B 782 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8555 (p0) REVERT: B 815 ARG cc_start: 0.8781 (mmm160) cc_final: 0.8537 (mmm160) REVERT: B 839 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7844 (mm-30) REVERT: B 862 CYS cc_start: 0.8177 (t) cc_final: 0.7688 (p) REVERT: B 959 GLU cc_start: 0.8087 (mp0) cc_final: 0.7760 (mp0) REVERT: B 977 LEU cc_start: 0.8961 (mt) cc_final: 0.8750 (mt) REVERT: B 1000 MET cc_start: 0.8520 (mtt) cc_final: 0.7922 (mpp) REVERT: B 1035 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8863 (tm-30) REVERT: B 1131 MET cc_start: 0.9041 (ttt) cc_final: 0.8784 (tpp) REVERT: B 1169 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8863 (tm-30) REVERT: B 1178 LEU cc_start: 0.9058 (tt) cc_final: 0.8694 (pp) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.2560 time to fit residues: 79.9682 Evaluate side-chains 137 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 50 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN A 559 HIS A 711 ASN A 795 HIS B 555 ASN B 559 HIS B 711 ASN B 795 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.056656 restraints weight = 58971.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.058849 restraints weight = 32505.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060375 restraints weight = 21166.390| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 13908 Z= 0.263 Angle : 0.721 9.621 19030 Z= 0.373 Chirality : 0.043 0.177 2094 Planarity : 0.005 0.047 2220 Dihedral : 18.092 173.610 2420 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.15 % Allowed : 2.11 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1512 helix: 1.33 (0.20), residues: 672 sheet: -1.38 (0.44), residues: 148 loop : -1.94 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1090 HIS 0.005 0.001 HIS B 759 PHE 0.015 0.002 PHE A1125 TYR 0.017 0.002 TYR A 907 ARG 0.004 0.001 ARG A1033 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 572) hydrogen bonds : angle 4.20029 ( 1554) covalent geometry : bond 0.00562 (13908) covalent geometry : angle 0.72143 (19030) *********************** 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 153 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 MET cc_start: 0.8243 (ttp) cc_final: 0.7594 (ttt) REVERT: A 539 MET cc_start: 0.7617 (ppp) cc_final: 0.7273 (ppp) REVERT: A 561 TRP cc_start: 0.8511 (m-90) cc_final: 0.8183 (m-90) REVERT: A 712 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7953 (mp0) REVERT: A 726 GLN cc_start: 0.8846 (mp10) cc_final: 0.8497 (mp10) REVERT: A 754 MET cc_start: 0.8229 (mpp) cc_final: 0.7971 (mpp) REVERT: A 768 ILE cc_start: 0.9533 (mm) cc_final: 0.9318 (mm) REVERT: A 847 MET cc_start: 0.9169 (mmm) cc_final: 0.8749 (mmm) REVERT: A 862 CYS cc_start: 0.8827 (t) cc_final: 0.8341 (p) REVERT: A 1000 MET cc_start: 0.8592 (mtt) cc_final: 0.8335 (mpp) REVERT: A 1030 TYR cc_start: 0.5867 (m-80) cc_final: 0.5591 (m-80) REVERT: A 1131 MET cc_start: 0.9142 (ttt) cc_final: 0.8840 (tpp) REVERT: B 539 MET cc_start: 0.7660 (ppp) cc_final: 0.7367 (ppp) REVERT: B 561 TRP cc_start: 0.8508 (m-90) cc_final: 0.8194 (m-90) REVERT: B 570 LEU cc_start: 0.8430 (mt) cc_final: 0.7490 (mt) REVERT: B 726 GLN cc_start: 0.8957 (mp10) cc_final: 0.8596 (mp10) REVERT: B 768 ILE cc_start: 0.9537 (mm) cc_final: 0.9323 (mm) REVERT: B 805 TYR cc_start: 0.8412 (m-80) cc_final: 0.8070 (m-80) REVERT: B 847 MET cc_start: 0.9152 (mmm) cc_final: 0.8718 (mmm) REVERT: B 862 CYS cc_start: 0.8551 (t) cc_final: 0.8260 (p) REVERT: B 1000 MET cc_start: 0.8598 (mtt) cc_final: 0.8349 (mpp) REVERT: B 1030 TYR cc_start: 0.5893 (m-80) cc_final: 0.5653 (m-80) REVERT: B 1131 MET cc_start: 0.9135 (ttt) cc_final: 0.8821 (tpp) outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 0.2418 time to fit residues: 55.1537 Evaluate side-chains 99 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 128 optimal weight: 0.0470 chunk 21 optimal weight: 0.0980 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 0.0470 chunk 16 optimal weight: 3.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN B 711 ASN ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062605 restraints weight = 57291.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.064926 restraints weight = 31465.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.066584 restraints weight = 20362.721| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13908 Z= 0.103 Angle : 0.516 6.164 19030 Z= 0.270 Chirality : 0.038 0.160 2094 Planarity : 0.003 0.040 2220 Dihedral : 17.852 177.960 2420 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1512 helix: 1.76 (0.21), residues: 668 sheet: -1.59 (0.46), residues: 134 loop : -1.51 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B1090 HIS 0.003 0.001 HIS B 548 PHE 0.006 0.001 PHE B 595 TYR 0.015 0.001 TYR B1030 ARG 0.003 0.000 ARG B 740 Details of bonding type rmsd hydrogen bonds : bond 0.02807 ( 572) hydrogen bonds : angle 3.58168 ( 1554) covalent geometry : bond 0.00220 (13908) covalent geometry : angle 0.51607 (19030) *********************** 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 177 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 MET cc_start: 0.8207 (ttp) cc_final: 0.7463 (ttt) REVERT: A 675 ARG cc_start: 0.9206 (mtt180) cc_final: 0.8856 (mtp-110) REVERT: A 712 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8063 (mt-10) REVERT: A 726 GLN cc_start: 0.8793 (mp10) cc_final: 0.8580 (mp10) REVERT: A 754 MET cc_start: 0.8308 (mpp) cc_final: 0.7998 (mpp) REVERT: A 768 ILE cc_start: 0.9468 (mm) cc_final: 0.9251 (mt) REVERT: A 815 ARG cc_start: 0.8747 (mmm160) cc_final: 0.8544 (mmm160) REVERT: A 847 MET cc_start: 0.9097 (mmm) cc_final: 0.8648 (mmm) REVERT: A 862 CYS cc_start: 0.8484 (t) cc_final: 0.8101 (p) REVERT: A 972 MET cc_start: 0.7936 (tpp) cc_final: 0.7213 (tpp) REVERT: A 1000 MET cc_start: 0.8697 (mtt) cc_final: 0.8274 (mpp) REVERT: A 1131 MET cc_start: 0.8985 (ttt) cc_final: 0.8711 (tpp) REVERT: A 1169 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 1178 LEU cc_start: 0.9142 (tt) cc_final: 0.8704 (pp) REVERT: B 570 LEU cc_start: 0.7793 (mt) cc_final: 0.7375 (tp) REVERT: B 675 ARG cc_start: 0.9200 (mtt180) cc_final: 0.8922 (mtp-110) REVERT: B 712 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 726 GLN cc_start: 0.8893 (mp10) cc_final: 0.8608 (mp10) REVERT: B 754 MET cc_start: 0.8517 (mpp) cc_final: 0.8185 (mpp) REVERT: B 768 ILE cc_start: 0.9483 (mm) cc_final: 0.9276 (mt) REVERT: B 847 MET cc_start: 0.9024 (mmm) cc_final: 0.8639 (mmm) REVERT: B 862 CYS cc_start: 0.8492 (t) cc_final: 0.8164 (p) REVERT: B 923 ILE cc_start: 0.9196 (mm) cc_final: 0.8637 (mm) REVERT: B 972 MET cc_start: 0.7934 (tpp) cc_final: 0.7210 (tpp) REVERT: B 1000 MET cc_start: 0.8655 (mtt) cc_final: 0.8274 (mpp) REVERT: B 1128 LEU cc_start: 0.9078 (mt) cc_final: 0.8874 (mt) REVERT: B 1131 MET cc_start: 0.9092 (ttt) cc_final: 0.8745 (tpp) REVERT: B 1169 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8667 (tm-30) REVERT: B 1178 LEU cc_start: 0.9138 (tt) cc_final: 0.8703 (pp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2329 time to fit residues: 61.6037 Evaluate side-chains 130 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 70 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 ASN A 961 HIS A1067 ASN B 961 HIS B1067 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059788 restraints weight = 59300.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.062058 restraints weight = 32260.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063632 restraints weight = 20799.691| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13908 Z= 0.128 Angle : 0.526 6.106 19030 Z= 0.275 Chirality : 0.039 0.127 2094 Planarity : 0.004 0.037 2220 Dihedral : 17.848 176.185 2420 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1512 helix: 1.83 (0.21), residues: 668 sheet: -1.67 (0.45), residues: 138 loop : -1.39 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1090 HIS 0.003 0.001 HIS A 559 PHE 0.015 0.001 PHE B1054 TYR 0.009 0.001 TYR A 907 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 572) hydrogen bonds : angle 3.59492 ( 1554) covalent geometry : bond 0.00281 (13908) covalent geometry : angle 0.52596 (19030) *********************** 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 157 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 LYS cc_start: 0.8133 (mmpt) cc_final: 0.7822 (mmmm) REVERT: A 537 MET cc_start: 0.8273 (ttp) cc_final: 0.7624 (ttt) REVERT: A 675 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8807 (mtp-110) REVERT: A 712 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 754 MET cc_start: 0.8245 (mpp) cc_final: 0.7852 (mpp) REVERT: A 815 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8563 (mmm160) REVERT: A 847 MET cc_start: 0.9171 (mmm) cc_final: 0.8685 (mmm) REVERT: A 862 CYS cc_start: 0.8560 (t) cc_final: 0.8163 (p) REVERT: A 954 ILE cc_start: 0.9009 (mm) cc_final: 0.8747 (mm) REVERT: A 972 MET cc_start: 0.7672 (tpp) cc_final: 0.7450 (tpp) REVERT: A 1000 MET cc_start: 0.8557 (mtt) cc_final: 0.8330 (mpp) REVERT: A 1131 MET cc_start: 0.9074 (ttt) cc_final: 0.8764 (tpp) REVERT: A 1178 LEU cc_start: 0.9100 (tt) cc_final: 0.8776 (pp) REVERT: B 542 GLN cc_start: 0.7471 (mm110) cc_final: 0.7114 (mm110) REVERT: B 675 ARG cc_start: 0.9129 (mtt180) cc_final: 0.8792 (mtp-110) REVERT: B 712 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8119 (mt-10) REVERT: B 726 GLN cc_start: 0.8904 (mp10) cc_final: 0.8676 (mp10) REVERT: B 768 ILE cc_start: 0.9503 (mm) cc_final: 0.9294 (mt) REVERT: B 847 MET cc_start: 0.9158 (mmm) cc_final: 0.8693 (mmm) REVERT: B 862 CYS cc_start: 0.8597 (t) cc_final: 0.8122 (p) REVERT: B 867 PHE cc_start: 0.7005 (m-10) cc_final: 0.6636 (m-10) REVERT: B 954 ILE cc_start: 0.9005 (mm) cc_final: 0.8748 (mm) REVERT: B 1000 MET cc_start: 0.8592 (mtt) cc_final: 0.8338 (mpp) REVERT: B 1131 MET cc_start: 0.9056 (ttt) cc_final: 0.8764 (tpp) REVERT: B 1178 LEU cc_start: 0.9104 (tt) cc_final: 0.8781 (pp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2355 time to fit residues: 55.7502 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 : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 4.9990 chunk 151 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.0070 chunk 133 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 ASN A1051 GLN A1067 ASN B 509 ASN ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.071033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.057918 restraints weight = 60238.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060084 restraints weight = 33080.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061615 restraints weight = 21512.367| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13908 Z= 0.157 Angle : 0.571 6.977 19030 Z= 0.299 Chirality : 0.040 0.226 2094 Planarity : 0.004 0.036 2220 Dihedral : 17.963 175.971 2420 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1512 helix: 1.67 (0.21), residues: 682 sheet: -1.43 (0.45), residues: 148 loop : -1.37 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B1090 HIS 0.004 0.001 HIS A 559 PHE 0.016 0.001 PHE A 867 TYR 0.014 0.002 TYR A1029 ARG 0.004 0.000 ARG A 804 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 572) hydrogen bonds : angle 3.74044 ( 1554) covalent geometry : bond 0.00343 (13908) covalent geometry : angle 0.57056 (19030) *********************** 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 : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 LEU cc_start: 0.9249 (tp) cc_final: 0.9042 (tp) REVERT: A 537 MET cc_start: 0.8057 (ttp) cc_final: 0.7562 (ttt) REVERT: A 675 ARG cc_start: 0.9191 (mtt180) cc_final: 0.8857 (mtp-110) REVERT: A 712 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8041 (mt-10) REVERT: A 805 TYR cc_start: 0.8185 (m-80) cc_final: 0.7984 (m-10) REVERT: A 847 MET cc_start: 0.9278 (mmm) cc_final: 0.8544 (mmm) REVERT: A 862 CYS cc_start: 0.8735 (t) cc_final: 0.8332 (p) REVERT: A 867 PHE cc_start: 0.7533 (m-80) cc_final: 0.6684 (m-10) REVERT: A 954 ILE cc_start: 0.8955 (mm) cc_final: 0.8700 (mm) REVERT: A 1054 PHE cc_start: 0.9259 (t80) cc_final: 0.9026 (t80) REVERT: A 1131 MET cc_start: 0.9045 (ttt) cc_final: 0.8810 (tpp) REVERT: A 1178 LEU cc_start: 0.9212 (tt) cc_final: 0.8893 (pp) REVERT: B 675 ARG cc_start: 0.9163 (mtt180) cc_final: 0.8847 (mtp-110) REVERT: B 712 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7953 (mp0) REVERT: B 754 MET cc_start: 0.8128 (mpp) cc_final: 0.7717 (mpp) REVERT: B 847 MET cc_start: 0.9213 (mmm) cc_final: 0.8634 (mmm) REVERT: B 862 CYS cc_start: 0.8745 (t) cc_final: 0.8267 (p) REVERT: B 867 PHE cc_start: 0.6992 (m-10) cc_final: 0.6584 (m-10) REVERT: B 954 ILE cc_start: 0.8949 (mm) cc_final: 0.8677 (mm) REVERT: B 1128 LEU cc_start: 0.9262 (mt) cc_final: 0.9060 (mt) REVERT: B 1131 MET cc_start: 0.9034 (ttt) cc_final: 0.8779 (tpp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2216 time to fit residues: 51.9997 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 : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 19 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.059737 restraints weight = 58561.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.061955 restraints weight = 31780.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.063494 restraints weight = 20565.011| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.6889 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= 0.105 Angle : 0.520 6.527 19030 Z= 0.270 Chirality : 0.039 0.187 2094 Planarity : 0.003 0.037 2220 Dihedral : 17.947 179.418 2420 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1512 helix: 1.82 (0.21), residues: 680 sheet: -1.47 (0.47), residues: 136 loop : -1.28 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B1090 HIS 0.004 0.001 HIS B 548 PHE 0.017 0.001 PHE B1054 TYR 0.007 0.001 TYR A1029 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.02829 ( 572) hydrogen bonds : angle 3.57487 ( 1554) covalent geometry : bond 0.00228 (13908) covalent geometry : angle 0.52019 (19030) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.653 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 489 LYS cc_start: 0.8301 (mmpt) cc_final: 0.8067 (mmmm) REVERT: A 537 MET cc_start: 0.8112 (ttp) cc_final: 0.7598 (ttt) REVERT: A 545 ASP cc_start: 0.8772 (m-30) cc_final: 0.8477 (m-30) REVERT: A 663 GLU cc_start: 0.9023 (pp20) cc_final: 0.8751 (pp20) REVERT: A 675 ARG cc_start: 0.9196 (mtt180) cc_final: 0.8817 (mtp-110) REVERT: A 712 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7940 (mp0) REVERT: A 805 TYR cc_start: 0.8191 (m-80) cc_final: 0.7902 (m-10) REVERT: A 847 MET cc_start: 0.9198 (mmm) cc_final: 0.8685 (mmm) REVERT: A 862 CYS cc_start: 0.8618 (t) cc_final: 0.8208 (p) REVERT: A 867 PHE cc_start: 0.7901 (m-80) cc_final: 0.6782 (m-10) REVERT: A 1131 MET cc_start: 0.9064 (ttt) cc_final: 0.8751 (tpp) REVERT: A 1178 LEU cc_start: 0.9207 (tt) cc_final: 0.8895 (pp) REVERT: B 542 GLN cc_start: 0.7511 (mm110) cc_final: 0.7181 (mm110) REVERT: B 570 LEU cc_start: 0.8055 (mt) cc_final: 0.7468 (mp) REVERT: B 663 GLU cc_start: 0.8961 (pp20) cc_final: 0.8674 (pp20) REVERT: B 675 ARG cc_start: 0.9180 (mtt180) cc_final: 0.8865 (mtp-110) REVERT: B 712 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 726 GLN cc_start: 0.8620 (mp10) cc_final: 0.8196 (pm20) REVERT: B 754 MET cc_start: 0.8213 (mpp) cc_final: 0.7763 (mpp) REVERT: B 847 MET cc_start: 0.9159 (mmm) cc_final: 0.8629 (mmm) REVERT: B 867 PHE cc_start: 0.6990 (m-10) cc_final: 0.6647 (m-10) REVERT: B 954 ILE cc_start: 0.8955 (mm) cc_final: 0.8658 (mm) REVERT: B 972 MET cc_start: 0.7852 (tpp) cc_final: 0.6928 (tpp) REVERT: B 1131 MET cc_start: 0.9028 (ttt) cc_final: 0.8768 (tpp) REVERT: B 1178 LEU cc_start: 0.9127 (tt) cc_final: 0.8693 (pp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2209 time to fit residues: 56.0012 Evaluate side-chains 110 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 130 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN B1067 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.072873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059651 restraints weight = 58178.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061861 restraints weight = 31790.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063402 restraints weight = 20602.293| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.7024 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= 0.109 Angle : 0.528 6.809 19030 Z= 0.273 Chirality : 0.039 0.182 2094 Planarity : 0.003 0.037 2220 Dihedral : 17.970 179.686 2420 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.08 % Allowed : 0.15 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1512 helix: 1.82 (0.21), residues: 680 sheet: -1.24 (0.47), residues: 146 loop : -1.24 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1090 HIS 0.003 0.001 HIS A 759 PHE 0.016 0.001 PHE A1054 TYR 0.008 0.001 TYR A 805 ARG 0.003 0.000 ARG B 804 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 572) hydrogen bonds : angle 3.57904 ( 1554) covalent geometry : bond 0.00240 (13908) covalent geometry : angle 0.52814 (19030) *********************** 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 160 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.521 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 489 LYS cc_start: 0.8285 (mmpt) cc_final: 0.7933 (mmmm) REVERT: A 537 MET cc_start: 0.8070 (ttp) cc_final: 0.7610 (ttt) REVERT: A 555 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.9061 (t0) REVERT: A 663 GLU cc_start: 0.8984 (pp20) cc_final: 0.8695 (pp20) REVERT: A 675 ARG cc_start: 0.9183 (mtt180) cc_final: 0.8812 (mtp-110) REVERT: A 712 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7933 (mp0) REVERT: A 805 TYR cc_start: 0.8130 (m-80) cc_final: 0.7881 (m-10) REVERT: A 847 MET cc_start: 0.9237 (mmm) cc_final: 0.8698 (mmm) REVERT: A 862 CYS cc_start: 0.8583 (t) cc_final: 0.8181 (p) REVERT: A 867 PHE cc_start: 0.7854 (m-80) cc_final: 0.6339 (m-10) REVERT: A 1131 MET cc_start: 0.9037 (ttt) cc_final: 0.8755 (tpp) REVERT: A 1178 LEU cc_start: 0.9185 (tt) cc_final: 0.8877 (pp) REVERT: B 542 GLN cc_start: 0.7531 (mm110) cc_final: 0.7182 (mm110) REVERT: B 545 ASP cc_start: 0.8961 (m-30) cc_final: 0.8698 (m-30) REVERT: B 570 LEU cc_start: 0.8117 (mt) cc_final: 0.7520 (mp) REVERT: B 635 ARG cc_start: 0.7040 (ttt-90) cc_final: 0.6176 (ttp80) REVERT: B 675 ARG cc_start: 0.9173 (mtt180) cc_final: 0.8866 (mtp-110) REVERT: B 712 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 754 MET cc_start: 0.8177 (mpp) cc_final: 0.7751 (mpp) REVERT: B 847 MET cc_start: 0.9177 (mmm) cc_final: 0.8642 (mmm) REVERT: B 867 PHE cc_start: 0.7255 (m-10) cc_final: 0.6900 (m-10) REVERT: B 1131 MET cc_start: 0.9053 (ttt) cc_final: 0.8760 (tpp) REVERT: B 1178 LEU cc_start: 0.9038 (tt) cc_final: 0.8635 (pp) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2252 time to fit residues: 55.4740 Evaluate side-chains 113 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN B 555 ASN B1067 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058798 restraints weight = 58922.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060990 restraints weight = 32104.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.062524 restraints weight = 20720.912| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13908 Z= 0.122 Angle : 0.540 7.032 19030 Z= 0.279 Chirality : 0.039 0.173 2094 Planarity : 0.004 0.037 2220 Dihedral : 18.084 179.756 2420 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1512 helix: 1.85 (0.21), residues: 678 sheet: -1.15 (0.47), residues: 146 loop : -1.22 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1090 HIS 0.003 0.001 HIS A 559 PHE 0.016 0.001 PHE B1054 TYR 0.011 0.001 TYR A1030 ARG 0.003 0.000 ARG B 804 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 572) hydrogen bonds : angle 3.57873 ( 1554) covalent geometry : bond 0.00269 (13908) covalent geometry : angle 0.53980 (19030) ********************** 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 151 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 LEU cc_start: 0.9232 (tp) cc_final: 0.9025 (tp) REVERT: A 489 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7960 (mmmm) REVERT: A 537 MET cc_start: 0.8026 (ttp) cc_final: 0.7591 (ttt) REVERT: A 675 ARG cc_start: 0.9201 (mtt180) cc_final: 0.8828 (mtp-110) REVERT: A 712 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7938 (mp0) REVERT: A 847 MET cc_start: 0.9250 (mmm) cc_final: 0.8703 (mmm) REVERT: A 862 CYS cc_start: 0.8603 (t) cc_final: 0.8189 (p) REVERT: A 1054 PHE cc_start: 0.9311 (t80) cc_final: 0.9070 (t80) REVERT: A 1131 MET cc_start: 0.9046 (ttt) cc_final: 0.8790 (tpp) REVERT: A 1178 LEU cc_start: 0.9184 (tt) cc_final: 0.8874 (pp) REVERT: B 570 LEU cc_start: 0.7933 (mt) cc_final: 0.7430 (mp) REVERT: B 675 ARG cc_start: 0.9175 (mtt180) cc_final: 0.8868 (mtp-110) REVERT: B 712 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7969 (mp0) REVERT: B 754 MET cc_start: 0.8170 (mpp) cc_final: 0.7731 (mpp) REVERT: B 847 MET cc_start: 0.9199 (mmm) cc_final: 0.8683 (mmm) REVERT: B 1054 PHE cc_start: 0.9310 (t80) cc_final: 0.9059 (t80) REVERT: B 1128 LEU cc_start: 0.9178 (mt) cc_final: 0.8956 (mt) REVERT: B 1131 MET cc_start: 0.9049 (ttt) cc_final: 0.8800 (tpp) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.2218 time to fit residues: 52.3231 Evaluate side-chains 101 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN B1067 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059597 restraints weight = 58417.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061801 restraints weight = 31950.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.063364 restraints weight = 20740.150| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13908 Z= 0.106 Angle : 0.524 6.736 19030 Z= 0.270 Chirality : 0.039 0.162 2094 Planarity : 0.004 0.042 2220 Dihedral : 18.053 179.928 2420 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1512 helix: 1.91 (0.21), residues: 678 sheet: -1.15 (0.47), residues: 146 loop : -1.22 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1090 HIS 0.002 0.001 HIS A 548 PHE 0.016 0.001 PHE B1054 TYR 0.009 0.001 TYR B1030 ARG 0.004 0.000 ARG B 804 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 572) hydrogen bonds : angle 3.51555 ( 1554) covalent geometry : bond 0.00235 (13908) covalent geometry : angle 0.52381 (19030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4001.15 seconds wall clock time: 70 minutes 19.96 seconds (4219.96 seconds total)