Starting phenix.real_space_refine on Wed Mar 4 13:00:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy6_11551/03_2026/6zy6_11551.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy6_11551/03_2026/6zy6_11551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zy6_11551/03_2026/6zy6_11551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy6_11551/03_2026/6zy6_11551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zy6_11551/03_2026/6zy6_11551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy6_11551/03_2026/6zy6_11551.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 52 5.16 5 C 8418 2.51 5 N 2312 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13504 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.07, per 1000 atoms: 0.23 Number of scatterers: 13504 At special positions: 0 Unit cell: (100.969, 119.053, 122.067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 56 15.00 O 2666 8.00 N 2312 7.00 C 8418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 552.9 milliseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 16 sheets defined 50.7% alpha, 6.7% beta 30 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.642A pdb=" N THR A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.691A pdb=" N MET A 502 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.683A pdb=" N ILE A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.612A pdb=" N LEU A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 559 removed outlier: 3.960A pdb=" N HIS A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.691A pdb=" N ARG A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.585A pdb=" N GLU A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.036A pdb=" N HIS A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.744A pdb=" N ALA A 647 " --> pdb=" O PRO A 643 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 679 Processing helix chain 'A' and resid 694 through 702 Processing helix chain 'A' and resid 702 through 715 removed outlier: 3.567A pdb=" N PHE A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.639A pdb=" N ARG A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 755 removed outlier: 3.582A pdb=" N GLY A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 750 " --> pdb=" O GLN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 773 Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 819 through 825 removed outlier: 3.891A pdb=" N HIS A 824 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 869 through 882 removed outlier: 3.906A pdb=" N VAL A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 removed outlier: 4.684A pdb=" N GLU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Proline residue: A 942 - end of helix removed outlier: 3.642A pdb=" N ASN A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 removed outlier: 3.678A pdb=" N ALA A 978 " --> pdb=" O GLU A 974 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 1014 through 1038 removed outlier: 3.811A pdb=" N ILE A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.606A pdb=" N GLU A1044 " --> pdb=" O MET A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1093 Processing helix chain 'A' and resid 1125 through 1129 Processing helix chain 'A' and resid 1132 through 1136 removed outlier: 3.696A pdb=" N TYR A1135 " --> pdb=" O PRO A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1161 removed outlier: 3.708A pdb=" N ARG A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A1149 " --> pdb=" O CYS A1145 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A1152 " --> pdb=" O ARG A1148 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1192 removed outlier: 3.917A pdb=" N GLU A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A1173 " --> pdb=" O GLU A1169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 477 removed outlier: 3.639A pdb=" N THR B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.692A pdb=" N MET B 502 " --> pdb=" O HIS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 515 removed outlier: 3.684A pdb=" N ILE B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.612A pdb=" N LEU B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.959A pdb=" N HIS B 548 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.691A pdb=" N ARG B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS B 567 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.589A pdb=" N GLU B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 4.036A pdb=" N HIS B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 652 removed outlier: 3.746A pdb=" N ALA B 647 " --> pdb=" O PRO B 643 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 679 Processing helix chain 'B' and resid 694 through 702 Processing helix chain 'B' and resid 702 through 715 removed outlier: 3.566A pdb=" N PHE B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 736 removed outlier: 3.638A pdb=" N ARG B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 755 removed outlier: 3.582A pdb=" N GLY B 749 " --> pdb=" O ALA B 745 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 750 " --> pdb=" O GLN B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 773 Processing helix chain 'B' and resid 813 through 818 Processing helix chain 'B' and resid 819 through 825 removed outlier: 3.890A pdb=" N HIS B 824 " --> pdb=" O LYS B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 869 through 882 removed outlier: 3.906A pdb=" N VAL B 873 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 945 removed outlier: 4.685A pdb=" N GLU B 941 " --> pdb=" O GLU B 937 " (cutoff:3.500A) Proline residue: B 942 - end of helix removed outlier: 3.643A pdb=" N ASN B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 984 removed outlier: 3.680A pdb=" N ALA B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 979 " --> pdb=" O GLU B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 1014 through 1038 removed outlier: 3.811A pdb=" N ILE B1018 " --> pdb=" O THR B1014 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR B1029 " --> pdb=" O LEU B1025 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B1030 " --> pdb=" O ARG B1026 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.605A pdb=" N GLU B1044 " --> pdb=" O MET B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1093 Processing helix chain 'B' and resid 1125 through 1129 Processing helix chain 'B' and resid 1132 through 1136 removed outlier: 3.695A pdb=" N TYR B1135 " --> pdb=" O PRO B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1161 removed outlier: 3.708A pdb=" N ARG B1146 " --> pdb=" O ASP B1142 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN B1149 " --> pdb=" O CYS B1145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B1151 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B1152 " --> pdb=" O ARG B1148 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B1154 " --> pdb=" O GLU B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1192 removed outlier: 3.917A pdb=" N GLU B1169 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B1173 " --> pdb=" O GLU B1169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B1174 " --> pdb=" O ASP B1170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 482 through 485 removed outlier: 6.285A pdb=" N ILE A 536 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE A 573 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 538 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 586 through 589 removed outlier: 3.713A pdb=" N VAL A 580 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 589 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 578 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 742 through 743 Processing sheet with id=AA4, first strand: chain 'A' and resid 830 through 831 removed outlier: 3.794A pdb=" N ASP A 831 " --> pdb=" O GLN A 834 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AA6, first strand: chain 'A' and resid 899 through 900 removed outlier: 3.827A pdb=" N GLU A 900 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 908 " --> pdb=" O GLU A 900 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 912 through 914 removed outlier: 6.213A pdb=" N GLU A 912 " --> pdb=" O SER A 924 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1001 through 1003 removed outlier: 3.970A pdb=" N LEU A1002 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A1010 " --> pdb=" O LEU A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 485 removed outlier: 6.286A pdb=" N ILE B 536 " --> pdb=" O GLU B 571 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE B 573 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 538 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 586 through 589 removed outlier: 3.713A pdb=" N VAL B 580 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 589 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 578 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 742 through 743 Processing sheet with id=AB3, first strand: chain 'B' and resid 830 through 831 removed outlier: 3.793A pdb=" N ASP B 831 " --> pdb=" O GLN B 834 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 854 through 856 Processing sheet with id=AB5, first strand: chain 'B' and resid 899 through 900 removed outlier: 3.825A pdb=" N GLU B 900 " --> pdb=" O VAL B 908 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 908 " --> pdb=" O GLU B 900 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 912 through 914 removed outlier: 6.213A pdb=" N GLU B 912 " --> pdb=" O SER B 924 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1001 through 1003 removed outlier: 3.967A pdb=" N LEU B1002 " --> pdb=" O LYS B1010 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B1010 " --> pdb=" O LEU B1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 494 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.55 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1512 helix: 1.33 (0.19), residues: 650 sheet: -1.64 (0.44), residues: 154 loop : -1.98 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 929 TYR 0.010 0.002 TYR B 590 PHE 0.008 0.002 PHE A1003 TRP 0.015 0.002 TRP A 664 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.01019 (13908) covalent geometry : angle 1.06956 (19030) hydrogen bonds : bond 0.12465 ( 572) hydrogen bonds : angle 5.28611 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 LEU cc_start: 0.8294 (mt) cc_final: 0.7579 (mt) REVERT: A 526 ASP cc_start: 0.9352 (m-30) cc_final: 0.8966 (t0) REVERT: A 537 MET cc_start: 0.7995 (ttp) cc_final: 0.7622 (ttt) REVERT: A 552 LEU cc_start: 0.8969 (mt) cc_final: 0.8613 (mt) REVERT: A 573 PHE cc_start: 0.9095 (t80) cc_final: 0.8758 (t80) REVERT: A 675 ARG cc_start: 0.9395 (mtt180) cc_final: 0.8940 (mtp85) REVERT: A 754 MET cc_start: 0.9090 (mtt) cc_final: 0.8795 (mpp) REVERT: A 795 HIS cc_start: 0.8240 (m90) cc_final: 0.7232 (m90) REVERT: A 809 MET cc_start: 0.8202 (ttt) cc_final: 0.7991 (tpp) REVERT: A 815 ARG cc_start: 0.8721 (mmm160) cc_final: 0.8470 (mmm160) REVERT: A 862 CYS cc_start: 0.8359 (t) cc_final: 0.7650 (p) REVERT: A 932 THR cc_start: 0.8262 (m) cc_final: 0.7653 (p) REVERT: A 956 ASP cc_start: 0.8527 (t0) cc_final: 0.8302 (t0) REVERT: A 1000 MET cc_start: 0.8338 (mtt) cc_final: 0.7810 (mmm) REVERT: A 1067 ASN cc_start: 0.7890 (m110) cc_final: 0.7684 (m-40) REVERT: A 1128 LEU cc_start: 0.9283 (mt) cc_final: 0.8964 (mt) REVERT: A 1138 LYS cc_start: 0.8332 (tttp) cc_final: 0.8131 (tmmt) REVERT: A 1171 LEU cc_start: 0.8917 (mt) cc_final: 0.8695 (mt) REVERT: B 486 LEU cc_start: 0.8293 (mt) cc_final: 0.7567 (mt) REVERT: B 526 ASP cc_start: 0.9336 (m-30) cc_final: 0.8956 (t0) REVERT: B 537 MET cc_start: 0.8025 (ttp) cc_final: 0.7613 (ttt) REVERT: B 552 LEU cc_start: 0.9017 (mt) cc_final: 0.8685 (mt) REVERT: B 573 PHE cc_start: 0.9091 (t80) cc_final: 0.8730 (t80) REVERT: B 675 ARG cc_start: 0.9395 (mtt180) cc_final: 0.8940 (mtp85) REVERT: B 702 GLU cc_start: 0.8718 (tt0) cc_final: 0.8501 (mm-30) REVERT: B 754 MET cc_start: 0.9092 (mtt) cc_final: 0.8786 (mpp) REVERT: B 795 HIS cc_start: 0.8239 (m90) cc_final: 0.7240 (m90) REVERT: B 809 MET cc_start: 0.8216 (ttt) cc_final: 0.8008 (tpp) REVERT: B 815 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8482 (mmm160) REVERT: B 862 CYS cc_start: 0.8256 (t) cc_final: 0.7571 (p) REVERT: B 932 THR cc_start: 0.8283 (m) cc_final: 0.7666 (p) REVERT: B 956 ASP cc_start: 0.8517 (t0) cc_final: 0.8301 (t0) REVERT: B 1000 MET cc_start: 0.8348 (mtt) cc_final: 0.7837 (mmm) REVERT: B 1128 LEU cc_start: 0.9266 (mt) cc_final: 0.8957 (mt) REVERT: B 1138 LYS cc_start: 0.8332 (tttp) cc_final: 0.8129 (tmmt) REVERT: B 1171 LEU cc_start: 0.8912 (mt) cc_final: 0.8692 (mt) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.1263 time to fit residues: 74.1382 Evaluate side-chains 203 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 824 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 HIS B 824 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.082842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068866 restraints weight = 53415.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071350 restraints weight = 28793.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073130 restraints weight = 18394.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074332 restraints weight = 12972.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.075301 restraints weight = 9977.796| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13908 Z= 0.121 Angle : 0.547 9.598 19030 Z= 0.275 Chirality : 0.039 0.177 2094 Planarity : 0.004 0.035 2220 Dihedral : 17.436 179.886 2420 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1512 helix: 1.36 (0.20), residues: 670 sheet: -1.73 (0.43), residues: 160 loop : -1.90 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1160 TYR 0.016 0.001 TYR B 686 PHE 0.009 0.001 PHE A 653 TRP 0.018 0.002 TRP B1090 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00262 (13908) covalent geometry : angle 0.54685 (19030) hydrogen bonds : bond 0.03418 ( 572) hydrogen bonds : angle 3.91615 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.7284 (m-30) cc_final: 0.6783 (p0) REVERT: A 455 CYS cc_start: 0.8253 (m) cc_final: 0.7510 (m) REVERT: A 503 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7357 (mt-10) REVERT: A 526 ASP cc_start: 0.9329 (m-30) cc_final: 0.9077 (t0) REVERT: A 539 MET cc_start: 0.7346 (ppp) cc_final: 0.7000 (ppp) REVERT: A 701 LYS cc_start: 0.8763 (mmtp) cc_final: 0.8453 (ttmt) REVERT: A 712 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 728 LYS cc_start: 0.9241 (mttt) cc_final: 0.8991 (mtmt) REVERT: A 738 ASP cc_start: 0.7323 (m-30) cc_final: 0.7035 (m-30) REVERT: A 768 ILE cc_start: 0.9360 (mm) cc_final: 0.9122 (mm) REVERT: A 815 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8500 (mmm160) REVERT: A 856 ILE cc_start: 0.8936 (mt) cc_final: 0.8394 (tt) REVERT: A 862 CYS cc_start: 0.7791 (t) cc_final: 0.7421 (p) REVERT: A 923 ILE cc_start: 0.9151 (mm) cc_final: 0.8624 (mm) REVERT: A 959 GLU cc_start: 0.7801 (mp0) cc_final: 0.7575 (mp0) REVERT: A 1000 MET cc_start: 0.8500 (mtt) cc_final: 0.7731 (mpp) REVERT: A 1169 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8751 (tm-30) REVERT: A 1178 LEU cc_start: 0.9044 (tt) cc_final: 0.8699 (pp) REVERT: B 446 ASP cc_start: 0.7313 (m-30) cc_final: 0.6784 (p0) REVERT: B 455 CYS cc_start: 0.8276 (m) cc_final: 0.7539 (m) REVERT: B 526 ASP cc_start: 0.9333 (m-30) cc_final: 0.9075 (t0) REVERT: B 539 MET cc_start: 0.7363 (ppp) cc_final: 0.6999 (ppp) REVERT: B 712 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 728 LYS cc_start: 0.9239 (mttt) cc_final: 0.8994 (mtmt) REVERT: B 738 ASP cc_start: 0.7314 (m-30) cc_final: 0.7020 (m-30) REVERT: B 754 MET cc_start: 0.9211 (mtt) cc_final: 0.9007 (mpp) REVERT: B 768 ILE cc_start: 0.9361 (mm) cc_final: 0.9124 (mm) REVERT: B 815 ARG cc_start: 0.8791 (mmm160) cc_final: 0.8503 (mmm160) REVERT: B 839 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 862 CYS cc_start: 0.7956 (t) cc_final: 0.7462 (p) REVERT: B 923 ILE cc_start: 0.9165 (mm) cc_final: 0.8639 (mm) REVERT: B 959 GLU cc_start: 0.7783 (mp0) cc_final: 0.7556 (mp0) REVERT: B 1000 MET cc_start: 0.8483 (mtt) cc_final: 0.7735 (mpp) REVERT: B 1169 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8744 (tm-30) REVERT: B 1178 LEU cc_start: 0.9045 (tt) cc_final: 0.8701 (pp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1037 time to fit residues: 40.1657 Evaluate side-chains 161 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 105 optimal weight: 0.0020 chunk 131 optimal weight: 0.0470 chunk 151 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 overall best weight: 1.1088 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.079294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.065534 restraints weight = 55286.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.067928 restraints weight = 29417.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.069551 restraints weight = 18665.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.070764 restraints weight = 13343.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071619 restraints weight = 10243.597| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13908 Z= 0.134 Angle : 0.522 8.952 19030 Z= 0.272 Chirality : 0.039 0.143 2094 Planarity : 0.004 0.034 2220 Dihedral : 17.280 179.462 2420 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.15 % Allowed : 1.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.22), residues: 1512 helix: 1.42 (0.20), residues: 674 sheet: -1.78 (0.43), residues: 156 loop : -1.90 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.020 0.001 TYR B 686 PHE 0.009 0.001 PHE B 573 TRP 0.020 0.002 TRP A 840 HIS 0.003 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00292 (13908) covalent geometry : angle 0.52205 (19030) hydrogen bonds : bond 0.03160 ( 572) hydrogen bonds : angle 3.75084 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 0.506 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: A 455 CYS cc_start: 0.8221 (m) cc_final: 0.7859 (m) REVERT: A 503 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7639 (mt-10) REVERT: A 539 MET cc_start: 0.7491 (ppp) cc_final: 0.7254 (ppp) REVERT: A 561 TRP cc_start: 0.8887 (m-90) cc_final: 0.8148 (m-90) REVERT: A 701 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8451 (tttt) REVERT: A 712 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 726 GLN cc_start: 0.8938 (mp10) cc_final: 0.8669 (mp10) REVERT: A 728 LYS cc_start: 0.9302 (mttt) cc_final: 0.8908 (mtmt) REVERT: A 738 ASP cc_start: 0.7430 (m-30) cc_final: 0.7097 (m-30) REVERT: A 809 MET cc_start: 0.8191 (tmm) cc_final: 0.7920 (tmm) REVERT: A 815 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8494 (mmm160) REVERT: A 830 TYR cc_start: 0.6461 (t80) cc_final: 0.5933 (t80) REVERT: A 856 ILE cc_start: 0.9068 (mt) cc_final: 0.8539 (tt) REVERT: A 862 CYS cc_start: 0.7996 (t) cc_final: 0.7610 (p) REVERT: A 930 THR cc_start: 0.7655 (m) cc_final: 0.7443 (p) REVERT: A 959 GLU cc_start: 0.7970 (mp0) cc_final: 0.7667 (mp0) REVERT: A 1000 MET cc_start: 0.8563 (mtt) cc_final: 0.7831 (mpp) REVERT: A 1169 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8827 (tm-30) REVERT: A 1178 LEU cc_start: 0.9055 (tt) cc_final: 0.8690 (pp) REVERT: B 455 CYS cc_start: 0.8211 (m) cc_final: 0.7838 (m) REVERT: B 539 MET cc_start: 0.7445 (ppp) cc_final: 0.7206 (ppp) REVERT: B 561 TRP cc_start: 0.8933 (m-90) cc_final: 0.8179 (m-90) REVERT: B 571 GLU cc_start: 0.5930 (tt0) cc_final: 0.5662 (tt0) REVERT: B 587 MET cc_start: 0.8495 (tpp) cc_final: 0.8222 (tpp) REVERT: B 712 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 726 GLN cc_start: 0.8918 (mp10) cc_final: 0.8623 (mp10) REVERT: B 728 LYS cc_start: 0.9299 (mttt) cc_final: 0.8906 (mtmt) REVERT: B 738 ASP cc_start: 0.7443 (m-30) cc_final: 0.7108 (m-30) REVERT: B 809 MET cc_start: 0.8199 (tmm) cc_final: 0.7928 (tmm) REVERT: B 815 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8500 (mmm160) REVERT: B 839 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7872 (mm-30) REVERT: B 856 ILE cc_start: 0.9067 (mm) cc_final: 0.8866 (mm) REVERT: B 862 CYS cc_start: 0.7998 (t) cc_final: 0.7597 (p) REVERT: B 930 THR cc_start: 0.7639 (m) cc_final: 0.7427 (p) REVERT: B 959 GLU cc_start: 0.7959 (mp0) cc_final: 0.7659 (mp0) REVERT: B 1000 MET cc_start: 0.8537 (mtt) cc_final: 0.7845 (mpp) REVERT: B 1169 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8817 (tm-30) REVERT: B 1178 LEU cc_start: 0.9055 (tt) cc_final: 0.8691 (pp) outliers start: 2 outliers final: 0 residues processed: 214 average time/residue: 0.1165 time to fit residues: 36.7438 Evaluate side-chains 141 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN A 795 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 ASN B 795 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.063123 restraints weight = 56030.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065597 restraints weight = 29447.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067315 restraints weight = 18548.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068537 restraints weight = 13093.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069359 restraints weight = 10033.379| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13908 Z= 0.129 Angle : 0.524 6.774 19030 Z= 0.276 Chirality : 0.038 0.136 2094 Planarity : 0.004 0.047 2220 Dihedral : 17.496 178.634 2420 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.15 % Allowed : 1.66 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.22), residues: 1512 helix: 1.77 (0.21), residues: 662 sheet: -1.87 (0.42), residues: 158 loop : -1.76 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 804 TYR 0.021 0.001 TYR A1030 PHE 0.016 0.001 PHE A1054 TRP 0.014 0.002 TRP A 840 HIS 0.003 0.001 HIS A 605 Details of bonding type rmsd covalent geometry : bond 0.00285 (13908) covalent geometry : angle 0.52426 (19030) hydrogen bonds : bond 0.03041 ( 572) hydrogen bonds : angle 3.58448 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.562 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 537 MET cc_start: 0.7814 (ttm) cc_final: 0.7166 (tpp) REVERT: A 538 ILE cc_start: 0.9089 (mt) cc_final: 0.8827 (mt) REVERT: A 561 TRP cc_start: 0.9104 (m-90) cc_final: 0.8400 (m-90) REVERT: A 670 GLU cc_start: 0.9442 (tt0) cc_final: 0.9220 (pt0) REVERT: A 726 GLN cc_start: 0.8783 (mp10) cc_final: 0.8528 (mp10) REVERT: A 728 LYS cc_start: 0.9380 (mttt) cc_final: 0.9145 (mtmt) REVERT: A 795 HIS cc_start: 0.8467 (m-70) cc_final: 0.8260 (m90) REVERT: A 815 ARG cc_start: 0.8777 (mmm160) cc_final: 0.8521 (mmm160) REVERT: A 830 TYR cc_start: 0.6609 (t80) cc_final: 0.6000 (t80) REVERT: A 856 ILE cc_start: 0.8989 (mt) cc_final: 0.8740 (tt) REVERT: A 862 CYS cc_start: 0.8265 (t) cc_final: 0.7876 (p) REVERT: A 930 THR cc_start: 0.8265 (m) cc_final: 0.8015 (p) REVERT: A 956 ASP cc_start: 0.8465 (t0) cc_final: 0.8252 (t0) REVERT: A 959 GLU cc_start: 0.8259 (mp0) cc_final: 0.7986 (mp0) REVERT: A 1000 MET cc_start: 0.8539 (mtt) cc_final: 0.7982 (mpp) REVERT: A 1131 MET cc_start: 0.9024 (ttt) cc_final: 0.8704 (tpp) REVERT: A 1178 LEU cc_start: 0.9041 (tt) cc_final: 0.8765 (pp) REVERT: B 537 MET cc_start: 0.7773 (mtt) cc_final: 0.7497 (mtt) REVERT: B 561 TRP cc_start: 0.9105 (m-90) cc_final: 0.8408 (m-90) REVERT: B 670 GLU cc_start: 0.9399 (tt0) cc_final: 0.9131 (pt0) REVERT: B 712 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 726 GLN cc_start: 0.8737 (mp10) cc_final: 0.8508 (mp10) REVERT: B 728 LYS cc_start: 0.9348 (mttt) cc_final: 0.9089 (mtmt) REVERT: B 795 HIS cc_start: 0.8469 (m-70) cc_final: 0.8260 (m90) REVERT: B 815 ARG cc_start: 0.8781 (mmm160) cc_final: 0.8524 (mmm160) REVERT: B 830 TYR cc_start: 0.6692 (t80) cc_final: 0.6120 (t80) REVERT: B 862 CYS cc_start: 0.8275 (t) cc_final: 0.7813 (p) REVERT: B 930 THR cc_start: 0.8288 (m) cc_final: 0.8040 (p) REVERT: B 956 ASP cc_start: 0.8471 (t0) cc_final: 0.8252 (t0) REVERT: B 959 GLU cc_start: 0.8264 (mp0) cc_final: 0.7986 (mp0) REVERT: B 1000 MET cc_start: 0.8548 (mtt) cc_final: 0.7986 (mpp) REVERT: B 1131 MET cc_start: 0.9026 (ttt) cc_final: 0.8675 (tpp) REVERT: B 1178 LEU cc_start: 0.9035 (tt) cc_final: 0.8764 (pp) outliers start: 2 outliers final: 0 residues processed: 203 average time/residue: 0.1147 time to fit residues: 34.7926 Evaluate side-chains 129 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.062815 restraints weight = 56354.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065223 restraints weight = 30290.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066867 restraints weight = 19266.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067977 restraints weight = 13677.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.068860 restraints weight = 10610.528| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5252 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= 0.108 Angle : 0.493 5.668 19030 Z= 0.259 Chirality : 0.038 0.142 2094 Planarity : 0.003 0.039 2220 Dihedral : 17.538 178.989 2420 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1512 helix: 1.84 (0.20), residues: 664 sheet: -1.61 (0.44), residues: 154 loop : -1.57 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.013 0.001 TYR A1030 PHE 0.007 0.001 PHE B 573 TRP 0.017 0.002 TRP B1090 HIS 0.003 0.001 HIS B 605 Details of bonding type rmsd covalent geometry : bond 0.00233 (13908) covalent geometry : angle 0.49273 (19030) hydrogen bonds : bond 0.02728 ( 572) hydrogen bonds : angle 3.49099 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.546 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: A 670 GLU cc_start: 0.9462 (tt0) cc_final: 0.9200 (pt0) REVERT: A 726 GLN cc_start: 0.8739 (mp10) cc_final: 0.8479 (mp10) REVERT: A 728 LYS cc_start: 0.9190 (mttt) cc_final: 0.8951 (mtmt) REVERT: A 738 ASP cc_start: 0.7731 (m-30) cc_final: 0.7508 (m-30) REVERT: A 815 ARG cc_start: 0.8827 (mmm160) cc_final: 0.8535 (mmm160) REVERT: A 830 TYR cc_start: 0.6714 (t80) cc_final: 0.6060 (t80) REVERT: A 847 MET cc_start: 0.8900 (mmm) cc_final: 0.8637 (mmm) REVERT: A 862 CYS cc_start: 0.8309 (t) cc_final: 0.7938 (p) REVERT: A 952 PRO cc_start: 0.8666 (Cg_endo) cc_final: 0.8446 (Cg_exo) REVERT: A 956 ASP cc_start: 0.8499 (t0) cc_final: 0.8257 (t0) REVERT: A 959 GLU cc_start: 0.8398 (mp0) cc_final: 0.8151 (mp0) REVERT: A 1000 MET cc_start: 0.8586 (mtt) cc_final: 0.8125 (mpp) REVERT: A 1035 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8602 (tm-30) REVERT: A 1128 LEU cc_start: 0.9087 (mt) cc_final: 0.8884 (mt) REVERT: A 1131 MET cc_start: 0.8998 (ttt) cc_final: 0.8702 (tpp) REVERT: A 1169 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 1178 LEU cc_start: 0.9042 (tt) cc_final: 0.8761 (pp) REVERT: B 537 MET cc_start: 0.7754 (mtt) cc_final: 0.7511 (mtt) REVERT: B 670 GLU cc_start: 0.9462 (tt0) cc_final: 0.9197 (pt0) REVERT: B 726 GLN cc_start: 0.8742 (mp10) cc_final: 0.8507 (mp10) REVERT: B 728 LYS cc_start: 0.9184 (mttt) cc_final: 0.8939 (mtmt) REVERT: B 738 ASP cc_start: 0.7753 (m-30) cc_final: 0.7524 (m-30) REVERT: B 815 ARG cc_start: 0.8829 (mmm160) cc_final: 0.8539 (mmm160) REVERT: B 830 TYR cc_start: 0.6685 (t80) cc_final: 0.6026 (t80) REVERT: B 847 MET cc_start: 0.8876 (mmm) cc_final: 0.8607 (mmm) REVERT: B 862 CYS cc_start: 0.8282 (t) cc_final: 0.7835 (p) REVERT: B 952 PRO cc_start: 0.8662 (Cg_endo) cc_final: 0.8443 (Cg_exo) REVERT: B 956 ASP cc_start: 0.8505 (t0) cc_final: 0.8254 (t0) REVERT: B 959 GLU cc_start: 0.8412 (mp0) cc_final: 0.8156 (mp0) REVERT: B 1000 MET cc_start: 0.8625 (mtt) cc_final: 0.8128 (mpp) REVERT: B 1016 LEU cc_start: 0.9502 (mt) cc_final: 0.9300 (pp) REVERT: B 1035 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8581 (tm-30) REVERT: B 1128 LEU cc_start: 0.9086 (mt) cc_final: 0.8881 (mt) REVERT: B 1131 MET cc_start: 0.8996 (ttt) cc_final: 0.8696 (tpp) REVERT: B 1169 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8721 (tm-30) REVERT: B 1178 LEU cc_start: 0.9041 (tt) cc_final: 0.8762 (pp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1182 time to fit residues: 32.1789 Evaluate side-chains 128 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.062106 restraints weight = 57317.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064481 restraints weight = 30655.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066145 restraints weight = 19603.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067354 restraints weight = 13975.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068201 restraints weight = 10733.424| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5520 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= 0.113 Angle : 0.500 6.555 19030 Z= 0.263 Chirality : 0.038 0.155 2094 Planarity : 0.003 0.036 2220 Dihedral : 17.579 178.686 2420 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.08 % Allowed : 1.36 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1512 helix: 2.01 (0.21), residues: 664 sheet: -1.49 (0.44), residues: 152 loop : -1.46 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.011 0.001 TYR A1030 PHE 0.016 0.001 PHE B1054 TRP 0.018 0.002 TRP A1090 HIS 0.002 0.001 HIS B 605 Details of bonding type rmsd covalent geometry : bond 0.00245 (13908) covalent geometry : angle 0.50011 (19030) hydrogen bonds : bond 0.02774 ( 572) hydrogen bonds : angle 3.45824 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.511 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: A 670 GLU cc_start: 0.9502 (tt0) cc_final: 0.9216 (pt0) REVERT: A 712 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8006 (mt-10) REVERT: A 726 GLN cc_start: 0.8833 (mp10) cc_final: 0.8533 (mp10) REVERT: A 728 LYS cc_start: 0.9163 (mttt) cc_final: 0.8904 (mtmt) REVERT: A 815 ARG cc_start: 0.8859 (mmm160) cc_final: 0.8534 (mmm160) REVERT: A 847 MET cc_start: 0.8946 (mmm) cc_final: 0.8596 (mmm) REVERT: A 862 CYS cc_start: 0.8452 (t) cc_final: 0.8047 (p) REVERT: A 952 PRO cc_start: 0.8714 (Cg_endo) cc_final: 0.8497 (Cg_exo) REVERT: A 956 ASP cc_start: 0.8544 (t0) cc_final: 0.8282 (t0) REVERT: A 1000 MET cc_start: 0.8504 (mtt) cc_final: 0.8121 (mpp) REVERT: A 1030 TYR cc_start: 0.5713 (m-80) cc_final: 0.4687 (m-80) REVERT: A 1131 MET cc_start: 0.8957 (ttt) cc_final: 0.8680 (tpp) REVERT: A 1169 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 1178 LEU cc_start: 0.9052 (tt) cc_final: 0.8759 (pp) REVERT: B 670 GLU cc_start: 0.9505 (tt0) cc_final: 0.9217 (pt0) REVERT: B 726 GLN cc_start: 0.8707 (mp10) cc_final: 0.8473 (mp10) REVERT: B 728 LYS cc_start: 0.9221 (mttt) cc_final: 0.8974 (mtmt) REVERT: B 815 ARG cc_start: 0.8869 (mmm160) cc_final: 0.8540 (mmm160) REVERT: B 847 MET cc_start: 0.8933 (mmm) cc_final: 0.8634 (mmm) REVERT: B 862 CYS cc_start: 0.8291 (t) cc_final: 0.7928 (p) REVERT: B 867 PHE cc_start: 0.7171 (m-10) cc_final: 0.6400 (m-10) REVERT: B 952 PRO cc_start: 0.8718 (Cg_endo) cc_final: 0.8498 (Cg_exo) REVERT: B 956 ASP cc_start: 0.8555 (t0) cc_final: 0.8274 (t0) REVERT: B 1000 MET cc_start: 0.8574 (mtt) cc_final: 0.8167 (mpp) REVERT: B 1131 MET cc_start: 0.8955 (ttt) cc_final: 0.8676 (tpp) REVERT: B 1169 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8725 (tm-30) REVERT: B 1178 LEU cc_start: 0.9049 (tt) cc_final: 0.8759 (pp) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1103 time to fit residues: 29.0105 Evaluate side-chains 123 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.0770 chunk 153 optimal weight: 3.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- 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 559 HIS A 708 ASN ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 ASN B 555 ASN B 559 HIS B 708 ASN B 961 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.071514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.058335 restraints weight = 59037.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060541 restraints weight = 32332.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.062082 restraints weight = 21072.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.063213 restraints weight = 15194.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.063986 restraints weight = 11806.387| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13908 Z= 0.189 Angle : 0.624 7.210 19030 Z= 0.326 Chirality : 0.041 0.159 2094 Planarity : 0.004 0.034 2220 Dihedral : 17.996 174.473 2420 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.08 % Allowed : 1.13 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.22), residues: 1512 helix: 1.66 (0.20), residues: 672 sheet: -1.33 (0.46), residues: 146 loop : -1.59 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 487 TYR 0.019 0.002 TYR B1029 PHE 0.013 0.002 PHE B 867 TRP 0.027 0.003 TRP B1090 HIS 0.003 0.001 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00411 (13908) covalent geometry : angle 0.62432 (19030) hydrogen bonds : bond 0.03769 ( 572) hydrogen bonds : angle 3.82700 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 LEU cc_start: 0.9241 (tp) cc_final: 0.9014 (tp) REVERT: A 675 ARG cc_start: 0.9069 (mtt180) cc_final: 0.8774 (mtp-110) REVERT: A 712 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7983 (mp0) REVERT: A 726 GLN cc_start: 0.8830 (mp10) cc_final: 0.8520 (mp10) REVERT: A 728 LYS cc_start: 0.9170 (mttt) cc_final: 0.8908 (mtpt) REVERT: A 754 MET cc_start: 0.8050 (mpp) cc_final: 0.7621 (mpp) REVERT: A 847 MET cc_start: 0.9198 (mmm) cc_final: 0.8601 (mmm) REVERT: A 862 CYS cc_start: 0.8836 (t) cc_final: 0.8415 (p) REVERT: A 867 PHE cc_start: 0.7977 (m-80) cc_final: 0.6108 (m-10) REVERT: A 956 ASP cc_start: 0.8604 (t0) cc_final: 0.8320 (t0) REVERT: A 1030 TYR cc_start: 0.5734 (m-80) cc_final: 0.4318 (m-80) REVERT: A 1131 MET cc_start: 0.9112 (ttt) cc_final: 0.8835 (tpp) REVERT: B 675 ARG cc_start: 0.9043 (mtt180) cc_final: 0.8737 (mtp-110) REVERT: B 712 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7991 (mp0) REVERT: B 728 LYS cc_start: 0.9162 (mttt) cc_final: 0.8917 (mtpt) REVERT: B 754 MET cc_start: 0.8018 (mpp) cc_final: 0.7588 (mpp) REVERT: B 805 TYR cc_start: 0.8177 (m-80) cc_final: 0.7872 (m-10) REVERT: B 847 MET cc_start: 0.9248 (mmm) cc_final: 0.8552 (mmm) REVERT: B 862 CYS cc_start: 0.8539 (t) cc_final: 0.8326 (p) REVERT: B 867 PHE cc_start: 0.7829 (m-10) cc_final: 0.7243 (m-10) REVERT: B 917 ASN cc_start: 0.9081 (t0) cc_final: 0.8881 (t0) REVERT: B 956 ASP cc_start: 0.8534 (t0) cc_final: 0.8239 (t0) REVERT: B 1131 MET cc_start: 0.9107 (ttt) cc_final: 0.8828 (tpp) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1092 time to fit residues: 25.3631 Evaluate side-chains 100 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 0.0040 overall best weight: 1.5198 ------------------------------------------------------------------------------- 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 ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN B 708 ASN B1067 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058611 restraints weight = 58905.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060788 restraints weight = 31879.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062320 restraints weight = 20590.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.063418 restraints weight = 14789.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.064239 restraints weight = 11482.353| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13908 Z= 0.154 Angle : 0.557 6.596 19030 Z= 0.294 Chirality : 0.040 0.182 2094 Planarity : 0.004 0.036 2220 Dihedral : 18.014 177.084 2420 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1512 helix: 1.62 (0.20), residues: 682 sheet: -1.33 (0.46), residues: 146 loop : -1.46 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 982 TYR 0.012 0.001 TYR B1029 PHE 0.015 0.001 PHE A1054 TRP 0.018 0.002 TRP A1090 HIS 0.004 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00331 (13908) covalent geometry : angle 0.55739 (19030) hydrogen bonds : bond 0.03323 ( 572) hydrogen bonds : angle 3.76175 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.524 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 489 LYS cc_start: 0.7960 (mmpt) cc_final: 0.7717 (mmmm) REVERT: A 675 ARG cc_start: 0.9117 (mtt180) cc_final: 0.8812 (mtp-110) REVERT: A 712 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7929 (mp0) REVERT: A 728 LYS cc_start: 0.9165 (mttt) cc_final: 0.8904 (mtpt) REVERT: A 754 MET cc_start: 0.8021 (mpp) cc_final: 0.7598 (mpp) REVERT: A 847 MET cc_start: 0.9126 (mmm) cc_final: 0.8670 (mmm) REVERT: A 862 CYS cc_start: 0.8504 (t) cc_final: 0.8252 (p) REVERT: A 956 ASP cc_start: 0.8656 (t0) cc_final: 0.8398 (t0) REVERT: A 1030 TYR cc_start: 0.5820 (m-80) cc_final: 0.5536 (m-80) REVERT: A 1054 PHE cc_start: 0.9252 (t80) cc_final: 0.9018 (t80) REVERT: A 1131 MET cc_start: 0.9118 (ttt) cc_final: 0.8900 (tpp) REVERT: A 1178 LEU cc_start: 0.9135 (tt) cc_final: 0.8785 (pp) REVERT: B 510 ILE cc_start: 0.9255 (mm) cc_final: 0.9039 (mm) REVERT: B 675 ARG cc_start: 0.9113 (mtt180) cc_final: 0.8804 (mtp-110) REVERT: B 728 LYS cc_start: 0.9167 (mttt) cc_final: 0.8906 (mtpt) REVERT: B 754 MET cc_start: 0.8013 (mpp) cc_final: 0.7589 (mpp) REVERT: B 847 MET cc_start: 0.9196 (mmm) cc_final: 0.8629 (mmm) REVERT: B 867 PHE cc_start: 0.7713 (m-10) cc_final: 0.6896 (m-10) REVERT: B 956 ASP cc_start: 0.8544 (t0) cc_final: 0.8303 (t0) REVERT: B 1054 PHE cc_start: 0.9247 (t80) cc_final: 0.9010 (t80) REVERT: B 1131 MET cc_start: 0.9105 (ttt) cc_final: 0.8892 (tpp) REVERT: B 1169 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8635 (tm-30) REVERT: B 1178 LEU cc_start: 0.9135 (tt) cc_final: 0.8793 (pp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1131 time to fit residues: 26.6774 Evaluate side-chains 115 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 0.0570 chunk 97 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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 A 961 HIS A1067 ASN B 708 ASN B1067 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.060122 restraints weight = 57872.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.062401 restraints weight = 31147.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064004 restraints weight = 20010.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065131 restraints weight = 14274.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.065975 restraints weight = 11031.055| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6819 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= 0.110 Angle : 0.525 6.886 19030 Z= 0.274 Chirality : 0.038 0.134 2094 Planarity : 0.003 0.036 2220 Dihedral : 18.022 179.253 2420 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.23), residues: 1512 helix: 1.81 (0.21), residues: 682 sheet: -1.34 (0.48), residues: 132 loop : -1.38 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 487 TYR 0.011 0.001 TYR A1030 PHE 0.015 0.001 PHE B1054 TRP 0.013 0.002 TRP A1090 HIS 0.003 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00239 (13908) covalent geometry : angle 0.52491 (19030) hydrogen bonds : bond 0.02897 ( 572) hydrogen bonds : angle 3.59190 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.7690 (mm110) cc_final: 0.7296 (mm110) REVERT: A 663 GLU cc_start: 0.9008 (pp20) cc_final: 0.8729 (pp20) REVERT: A 675 ARG cc_start: 0.9136 (mtt180) cc_final: 0.8859 (mtp-110) REVERT: A 712 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8015 (mt-10) REVERT: A 728 LYS cc_start: 0.9135 (mttt) cc_final: 0.8876 (mtpt) REVERT: A 754 MET cc_start: 0.8035 (mpp) cc_final: 0.7581 (mpp) REVERT: A 805 TYR cc_start: 0.8145 (m-80) cc_final: 0.7846 (m-10) REVERT: A 847 MET cc_start: 0.9128 (mmm) cc_final: 0.8639 (mmm) REVERT: A 862 CYS cc_start: 0.8335 (t) cc_final: 0.8128 (p) REVERT: A 956 ASP cc_start: 0.8656 (t0) cc_final: 0.8355 (t0) REVERT: A 1030 TYR cc_start: 0.5925 (m-80) cc_final: 0.5667 (m-80) REVERT: A 1054 PHE cc_start: 0.9265 (t80) cc_final: 0.9026 (t80) REVERT: A 1131 MET cc_start: 0.9115 (ttt) cc_final: 0.8882 (tpp) REVERT: A 1178 LEU cc_start: 0.9132 (tt) cc_final: 0.8786 (pp) REVERT: B 499 LYS cc_start: 0.9435 (tttp) cc_final: 0.9200 (ttmm) REVERT: B 542 GLN cc_start: 0.7688 (mm110) cc_final: 0.7268 (mm110) REVERT: B 675 ARG cc_start: 0.9117 (mtt180) cc_final: 0.8821 (mtp-110) REVERT: B 728 LYS cc_start: 0.9143 (mttt) cc_final: 0.8900 (mtpt) REVERT: B 754 MET cc_start: 0.8029 (mpp) cc_final: 0.7579 (mpp) REVERT: B 804 ARG cc_start: 0.7416 (ptm-80) cc_final: 0.6941 (tmm160) REVERT: B 847 MET cc_start: 0.9162 (mmm) cc_final: 0.8628 (mmm) REVERT: B 867 PHE cc_start: 0.7543 (m-10) cc_final: 0.7052 (m-10) REVERT: B 956 ASP cc_start: 0.8596 (t0) cc_final: 0.8314 (t0) REVERT: B 1054 PHE cc_start: 0.9257 (t80) cc_final: 0.9015 (t80) REVERT: B 1131 MET cc_start: 0.9106 (ttt) cc_final: 0.8880 (tpp) REVERT: B 1178 LEU cc_start: 0.9135 (tt) cc_final: 0.8794 (pp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1102 time to fit residues: 28.3961 Evaluate side-chains 122 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 116 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 A1067 ASN A1149 ASN B 708 ASN B1067 ASN B1149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.058752 restraints weight = 58512.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060948 restraints weight = 31868.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062421 restraints weight = 20601.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.063536 restraints weight = 14899.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064304 restraints weight = 11549.295| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13908 Z= 0.150 Angle : 0.572 6.916 19030 Z= 0.301 Chirality : 0.039 0.153 2094 Planarity : 0.004 0.037 2220 Dihedral : 18.123 178.485 2420 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1512 helix: 1.71 (0.21), residues: 678 sheet: -1.38 (0.45), residues: 146 loop : -1.36 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1148 TYR 0.011 0.001 TYR A 907 PHE 0.015 0.001 PHE A1054 TRP 0.028 0.002 TRP A1090 HIS 0.004 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00329 (13908) covalent geometry : angle 0.57246 (19030) hydrogen bonds : bond 0.03332 ( 572) hydrogen bonds : angle 3.76886 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 ARG cc_start: 0.9155 (mtt180) cc_final: 0.8867 (mtp-110) REVERT: A 712 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7922 (mp0) REVERT: A 728 LYS cc_start: 0.9156 (mttt) cc_final: 0.8892 (mtpt) REVERT: A 754 MET cc_start: 0.8047 (mpp) cc_final: 0.7600 (mpp) REVERT: A 805 TYR cc_start: 0.8145 (m-80) cc_final: 0.7884 (m-10) REVERT: A 847 MET cc_start: 0.9185 (mmm) cc_final: 0.8403 (mmm) REVERT: A 862 CYS cc_start: 0.8487 (t) cc_final: 0.8236 (p) REVERT: A 867 PHE cc_start: 0.7286 (m-10) cc_final: 0.6799 (m-10) REVERT: A 956 ASP cc_start: 0.8716 (t0) cc_final: 0.8403 (t0) REVERT: A 1030 TYR cc_start: 0.5720 (m-80) cc_final: 0.5475 (m-80) REVERT: A 1054 PHE cc_start: 0.9285 (t80) cc_final: 0.9039 (t80) REVERT: A 1131 MET cc_start: 0.9117 (ttt) cc_final: 0.8902 (tpp) REVERT: A 1178 LEU cc_start: 0.9129 (tt) cc_final: 0.8782 (pp) REVERT: B 499 LYS cc_start: 0.9512 (tttp) cc_final: 0.9287 (ttmm) REVERT: B 675 ARG cc_start: 0.9128 (mtt180) cc_final: 0.8827 (mtp-110) REVERT: B 728 LYS cc_start: 0.9169 (mttt) cc_final: 0.8922 (mtpt) REVERT: B 754 MET cc_start: 0.8060 (mpp) cc_final: 0.7600 (mpp) REVERT: B 847 MET cc_start: 0.9201 (mmm) cc_final: 0.8723 (mmm) REVERT: B 867 PHE cc_start: 0.7869 (m-10) cc_final: 0.7193 (m-10) REVERT: B 956 ASP cc_start: 0.8649 (t0) cc_final: 0.8388 (t0) REVERT: B 1054 PHE cc_start: 0.9286 (t80) cc_final: 0.9036 (t80) REVERT: B 1131 MET cc_start: 0.9119 (ttt) cc_final: 0.8899 (tpp) REVERT: B 1178 LEU cc_start: 0.9135 (tt) cc_final: 0.8789 (pp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1072 time to fit residues: 25.8889 Evaluate side-chains 105 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 93 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 A1067 ASN B 708 ASN B1067 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.073007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.059883 restraints weight = 58601.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.062113 restraints weight = 31699.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.063703 restraints weight = 20473.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.064812 restraints weight = 14657.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.065496 restraints weight = 11372.782| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.7249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13908 Z= 0.116 Angle : 0.548 7.239 19030 Z= 0.288 Chirality : 0.039 0.155 2094 Planarity : 0.004 0.039 2220 Dihedral : 18.156 179.632 2420 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.08 % Allowed : 0.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1512 helix: 1.80 (0.21), residues: 680 sheet: -1.51 (0.48), residues: 126 loop : -1.31 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 804 TYR 0.015 0.001 TYR A1030 PHE 0.015 0.001 PHE B1054 TRP 0.013 0.002 TRP A1090 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00256 (13908) covalent geometry : angle 0.54833 (19030) hydrogen bonds : bond 0.02962 ( 572) hydrogen bonds : angle 3.77598 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.83 seconds wall clock time: 36 minutes 36.77 seconds (2196.77 seconds total)