Starting phenix.real_space_refine on Fri Jul 3 11:02:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f5z_28869/07_2026/8f5z_28869.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f5z_28869/07_2026/8f5z_28869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f5z_28869/07_2026/8f5z_28869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f5z_28869/07_2026/8f5z_28869.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f5z_28869/07_2026/8f5z_28869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f5z_28869/07_2026/8f5z_28869.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8f5z_28869/07_2026/8f5z_28869.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f5z_28869/07_2026/8f5z_28869.cif" } resolution = 3.2 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 8641 2.51 5 N 2344 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13598 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6753 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 829} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 6759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6759 Classifications: {'peptide': 862} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 829} Chain breaks: 4 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.38, per 1000 atoms: 0.18 Number of scatterers: 13598 At special positions: 0 Unit cell: (113.436, 121.716, 139.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 2512 8.00 N 2344 7.00 C 8641 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 565.6 milliseconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 14 sheets defined 42.9% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.635A pdb=" N THR B 108 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.044A pdb=" N LEU B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 146 Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.617A pdb=" N ARG B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.515A pdb=" N ILE B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 380 through 426 removed outlier: 3.858A pdb=" N MET B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.710A pdb=" N GLN B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 479 removed outlier: 3.602A pdb=" N GLU B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 494 Processing helix chain 'B' and resid 569 through 587 removed outlier: 3.583A pdb=" N ASP B 574 " --> pdb=" O ASP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 787 Processing helix chain 'B' and resid 790 through 794 removed outlier: 3.595A pdb=" N ILE B 794 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 831 removed outlier: 3.649A pdb=" N PHE B 818 " --> pdb=" O ASN B 814 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR B 830 " --> pdb=" O ASN B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 889 removed outlier: 3.771A pdb=" N ALA B 889 " --> pdb=" O VAL B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 896 Processing helix chain 'B' and resid 896 through 922 removed outlier: 3.691A pdb=" N LEU B 900 " --> pdb=" O ARG B 896 " (cutoff:3.500A) Proline residue: B 910 - end of helix removed outlier: 3.610A pdb=" N ILE B 921 " --> pdb=" O THR B 917 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 922 " --> pdb=" O ARG B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 950 removed outlier: 3.834A pdb=" N GLN B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 removed outlier: 4.162A pdb=" N GLU B 958 " --> pdb=" O GLU B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 988 removed outlier: 3.939A pdb=" N VAL B 973 " --> pdb=" O THR B 969 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 974 " --> pdb=" O LEU B 970 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 980 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 981 " --> pdb=" O SER B 977 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET B 983 " --> pdb=" O SER B 979 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS B 984 " --> pdb=" O GLN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1001 removed outlier: 3.505A pdb=" N MET B1001 " --> pdb=" O GLU B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1027 removed outlier: 3.607A pdb=" N ALA B1023 " --> pdb=" O PHE B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1065 through 1071 removed outlier: 3.533A pdb=" N GLN B1071 " --> pdb=" O PHE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1075 Processing helix chain 'B' and resid 1082 through 1095 removed outlier: 4.294A pdb=" N LEU B1086 " --> pdb=" O GLU B1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 Processing helix chain 'A' and resid 101 through 107 removed outlier: 4.464A pdb=" N GLU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.564A pdb=" N LEU A 152 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 202 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.793A pdb=" N ARG A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 235 removed outlier: 3.775A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.571A pdb=" N MET A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.561A pdb=" N MET A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 426 removed outlier: 3.536A pdb=" N MET A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.817A pdb=" N SER A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 435' Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.578A pdb=" N GLN A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 470 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 497 through 502 removed outlier: 4.048A pdb=" N LEU A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 502' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.600A pdb=" N LEU A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.598A pdb=" N PHE A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 removed outlier: 3.521A pdb=" N ALA A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 892 " --> pdb=" O LEU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 922 removed outlier: 3.589A pdb=" N ARG A 896 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Proline residue: A 910 - end of helix removed outlier: 3.627A pdb=" N GLU A 922 " --> pdb=" O ARG A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 3.956A pdb=" N ARG A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 944 " --> pdb=" O CYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 954 removed outlier: 4.484A pdb=" N GLU A 954 " --> pdb=" O SER A 951 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 951 through 954' Processing helix chain 'A' and resid 969 through 988 removed outlier: 4.151A pdb=" N VAL A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS A 984 " --> pdb=" O GLN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1008 through 1026 removed outlier: 3.790A pdb=" N PHE A1026 " --> pdb=" O MET A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.573A pdb=" N VAL A1048 " --> pdb=" O GLY A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1073 removed outlier: 4.315A pdb=" N GLN A1071 " --> pdb=" O PHE A1067 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET A1072 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1095 removed outlier: 3.709A pdb=" N LEU A1086 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A1091 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1092 " --> pdb=" O VAL A1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.792A pdb=" N ALA B 88 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 287 through 290 removed outlier: 3.989A pdb=" N VAL B 369 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 367 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 287 through 290 removed outlier: 3.989A pdb=" N VAL B 369 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 239 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 255 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA B 241 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU B 267 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 530 " --> pdb=" O GLU B 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 455 through 456 removed outlier: 3.660A pdb=" N ALA B 449 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 523 " --> pdb=" O GLY B 507 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY B 484 " --> pdb=" O THR B 746 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 748 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER B 486 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 755 " --> pdb=" O ARG B 747 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 775 through 778 removed outlier: 6.165A pdb=" N GLY B 768 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP B 778 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 766 " --> pdb=" O TRP B 778 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 870 " --> pdb=" O PHE B 767 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 867 " --> pdb=" O LYS B 858 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 993 through 994 removed outlier: 3.545A pdb=" N THR B1058 " --> pdb=" O THR B1034 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1053 through 1055 removed outlier: 3.569A pdb=" N ALA B1115 " --> pdb=" O LEU B1053 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.603A pdb=" N ILE A 80 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 298 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A 88 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR A 99 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU A 86 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 290 removed outlier: 3.538A pdb=" N GLY A 367 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP A 366 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 239 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 255 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 241 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 267 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 530 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 559 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 456 through 460 removed outlier: 6.314A pdb=" N GLY A 484 " --> pdb=" O THR A 746 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE A 748 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 486 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 745 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 775 through 778 removed outlier: 6.174A pdb=" N GLY A 768 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP A 778 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 766 " --> pdb=" O TRP A 778 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 769 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 867 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 855 " --> pdb=" O GLU A 835 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 994 removed outlier: 6.317A pdb=" N ARG A 991 " --> pdb=" O LEU A1033 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL A1035 " --> pdb=" O ARG A 991 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR A 993 " --> pdb=" O VAL A1035 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N ALA A1037 " --> pdb=" O THR A 993 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A1056 " --> pdb=" O SER A1036 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1053 " --> pdb=" O ALA A1115 " (cutoff:3.500A) 642 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2818 1.33 - 1.45: 3000 1.45 - 1.57: 7869 1.57 - 1.69: 1 1.69 - 1.81: 162 Bond restraints: 13850 Sorted by residual: bond pdb=" CAL O6E A1201 " pdb=" OAZ O6E A1201 " ideal model delta sigma weight residual 1.247 1.341 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" CAL O6E B1201 " pdb=" OAZ O6E B1201 " ideal model delta sigma weight residual 1.247 1.340 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CAM O6E A1201 " pdb=" OBG O6E A1201 " ideal model delta sigma weight residual 1.248 1.340 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" CAM O6E B1201 " pdb=" OBG O6E B1201 " ideal model delta sigma weight residual 1.248 1.340 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" CAW O6E A1201 " pdb=" CBC O6E A1201 " ideal model delta sigma weight residual 1.460 1.408 0.052 2.00e-02 2.50e+03 6.75e+00 ... (remaining 13845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 18384 1.95 - 3.89: 250 3.89 - 5.84: 53 5.84 - 7.79: 18 7.79 - 9.73: 2 Bond angle restraints: 18707 Sorted by residual: angle pdb=" N GLY B 250 " pdb=" CA GLY B 250 " pdb=" C GLY B 250 " ideal model delta sigma weight residual 111.18 115.59 -4.41 1.54e+00 4.22e-01 8.19e+00 angle pdb=" CB GLU A 262 " pdb=" CG GLU A 262 " pdb=" CD GLU A 262 " ideal model delta sigma weight residual 112.60 117.35 -4.75 1.70e+00 3.46e-01 7.81e+00 angle pdb=" CA LEU A 953 " pdb=" CB LEU A 953 " pdb=" CG LEU A 953 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.73e+00 angle pdb=" C GLN A 435 " pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta sigma weight residual 120.09 123.51 -3.42 1.25e+00 6.40e-01 7.49e+00 angle pdb=" CA PRO B 759 " pdb=" N PRO B 759 " pdb=" CD PRO B 759 " ideal model delta sigma weight residual 112.00 108.17 3.83 1.40e+00 5.10e-01 7.47e+00 ... (remaining 18702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7135 17.93 - 35.86: 952 35.86 - 53.79: 262 53.79 - 71.72: 41 71.72 - 89.65: 13 Dihedral angle restraints: 8403 sinusoidal: 3413 harmonic: 4990 Sorted by residual: dihedral pdb=" CG ARG A 299 " pdb=" CD ARG A 299 " pdb=" NE ARG A 299 " pdb=" CZ ARG A 299 " ideal model delta sinusoidal sigma weight residual 90.00 133.85 -43.85 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG B1090 " pdb=" CD ARG B1090 " pdb=" NE ARG B1090 " pdb=" CZ ARG B1090 " ideal model delta sinusoidal sigma weight residual -90.00 -133.85 43.85 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA ASP A1078 " pdb=" CB ASP A1078 " pdb=" CG ASP A1078 " pdb=" OD1 ASP A1078 " ideal model delta sinusoidal sigma weight residual -30.00 -84.48 54.48 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 8400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1498 0.035 - 0.069: 456 0.069 - 0.104: 125 0.104 - 0.138: 51 0.138 - 0.173: 4 Chirality restraints: 2134 Sorted by residual: chirality pdb=" CBJ O6E A1201 " pdb=" CAC O6E A1201 " pdb=" CBD O6E A1201 " pdb=" CBN O6E A1201 " both_signs ideal model delta sigma weight residual False 2.70 2.88 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CBD O6E A1201 " pdb=" CAT O6E A1201 " pdb=" CAX O6E A1201 " pdb=" CBJ O6E A1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.85 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CBD O6E B1201 " pdb=" CAT O6E B1201 " pdb=" CAX O6E B1201 " pdb=" CBJ O6E B1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.85 0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 2131 not shown) Planarity restraints: 2385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " 0.202 2.00e-02 2.50e+03 2.06e-01 1.06e+03 pdb=" CAP O6E B1201 " -0.308 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " -0.027 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.181 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " -0.054 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " 0.052 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " 0.471 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " -0.023 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.162 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " -0.197 2.00e-02 2.50e+03 1.99e-01 9.92e+02 pdb=" CAP O6E A1201 " 0.295 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " 0.020 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.177 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " 0.050 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " -0.050 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.456 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " 0.026 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.159 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " 0.003 2.00e-02 2.50e+03 3.52e-02 3.09e+01 pdb=" CAO O6E A1201 " 0.051 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " -0.005 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " -0.038 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.032 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.006 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " -0.008 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.011 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.079 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.027 2.00e-02 2.50e+03 ... (remaining 2382 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2411 2.77 - 3.30: 12650 3.30 - 3.83: 21854 3.83 - 4.37: 25580 4.37 - 4.90: 44235 Nonbonded interactions: 106730 Sorted by model distance: nonbonded pdb=" OG SER A 434 " pdb=" OE1 GLN A 435 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP B 273 " pdb=" OH TYR B 327 " model vdw 2.245 3.040 nonbonded pdb=" OD2 ASP A 90 " pdb=" OG1 THR A 93 " model vdw 2.249 3.040 nonbonded pdb=" O ASP A 446 " pdb=" OG1 THR A 461 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR B 924 " pdb=" OE1 GLN A 930 " model vdw 2.273 3.040 ... (remaining 106725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 69 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB )) or resid 129 through 587 or resid 743 through 1201)) \ selection = (chain 'B' and (resid 69 through 1119 or resid 1201)) } 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 individual isotropic 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.710 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.003 0.098 13852 Z= 0.162 Angle : 0.588 9.734 18707 Z= 0.282 Chirality : 0.039 0.173 2134 Planarity : 0.008 0.206 2385 Dihedral : 17.312 89.652 5163 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.47 % Allowed : 31.28 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.05 (0.21), residues: 1704 helix: 0.62 (0.22), residues: 596 sheet: 0.14 (0.29), residues: 353 loop : -0.36 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 547 TYR 0.012 0.001 TYR B 168 PHE 0.031 0.001 PHE A 83 TRP 0.007 0.001 TRP A 568 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (13850) covalent geometry : angle 0.58780 / 0.28 (18707) hydrogen bonds : bond 0.26737 / 17.62 ( 633) hydrogen bonds : angle 8.48896 / 5.92 ( 1803) Misc. bond : bond 0.03174 / 1.60 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 398 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 MET cc_start: 0.7380 (mmm) cc_final: 0.7136 (mmm) REVERT: B 554 PHE cc_start: 0.8402 (m-80) cc_final: 0.8117 (m-80) REVERT: B 967 GLU cc_start: 0.8021 (mp0) cc_final: 0.7596 (mm-30) outliers start: 7 outliers final: 6 residues processed: 401 average time/residue: 0.1169 time to fit residues: 66.2961 Evaluate side-chains 386 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 380 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 1101 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN B 245 HIS ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN B 438 ASN B 827 ASN B 880 GLN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135834 restraints weight = 20412.191| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.66 r_work: 0.3610 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13852 Z= 0.148 Angle : 0.574 11.847 18707 Z= 0.293 Chirality : 0.041 0.166 2134 Planarity : 0.005 0.084 2385 Dihedral : 5.646 88.814 1878 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.03 % Allowed : 27.52 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.21), residues: 1704 helix: 0.99 (0.20), residues: 638 sheet: 0.17 (0.28), residues: 363 loop : -0.49 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 547 TYR 0.015 0.001 TYR A 242 PHE 0.026 0.002 PHE A1111 TRP 0.010 0.001 TRP A 521 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (13850) covalent geometry : angle 0.57437 / 0.29 (18707) hydrogen bonds : bond 0.05123 / 3.40 ( 633) hydrogen bonds : angle 5.54145 / 3.82 ( 1803) Misc. bond : bond 0.00115 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 406 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 339 MET cc_start: 0.8077 (mpp) cc_final: 0.7607 (mpp) REVERT: B 373 ASN cc_start: 0.7828 (t0) cc_final: 0.7543 (t0) REVERT: B 408 MET cc_start: 0.7439 (mmm) cc_final: 0.7145 (mmm) REVERT: B 518 MET cc_start: 0.7828 (ptp) cc_final: 0.7602 (mtm) REVERT: B 784 LYS cc_start: 0.8068 (pptt) cc_final: 0.7834 (pptt) REVERT: B 836 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7612 (mtpp) REVERT: B 883 LEU cc_start: 0.8536 (mm) cc_final: 0.8267 (mm) REVERT: B 905 ARG cc_start: 0.7147 (ttm170) cc_final: 0.6919 (mtp180) REVERT: B 973 VAL cc_start: 0.7835 (p) cc_final: 0.7587 (t) REVERT: B 1091 LYS cc_start: 0.7207 (tttm) cc_final: 0.6862 (tttm) REVERT: B 1116 GLU cc_start: 0.5793 (tm-30) cc_final: 0.5556 (tm-30) REVERT: A 210 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7300 (mtm110) REVERT: A 229 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6793 (mm-30) REVERT: A 232 GLU cc_start: 0.7376 (tt0) cc_final: 0.7174 (tt0) REVERT: A 303 ASP cc_start: 0.6953 (t0) cc_final: 0.6704 (t70) REVERT: A 328 MET cc_start: 0.8068 (mtm) cc_final: 0.7818 (mtt) REVERT: A 422 ASP cc_start: 0.7674 (t0) cc_final: 0.7284 (t0) REVERT: A 435 GLN cc_start: 0.7320 (mp10) cc_final: 0.6910 (mp10) REVERT: A 446 ASP cc_start: 0.7414 (m-30) cc_final: 0.7187 (m-30) REVERT: A 877 HIS cc_start: 0.7661 (m90) cc_final: 0.6869 (m90) REVERT: A 878 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 881 GLN cc_start: 0.7883 (mp10) cc_final: 0.7345 (mp10) REVERT: A 949 ASP cc_start: 0.6493 (m-30) cc_final: 0.6175 (m-30) REVERT: A 1091 LYS cc_start: 0.7325 (mttm) cc_final: 0.7103 (mttp) outliers start: 60 outliers final: 31 residues processed: 428 average time/residue: 0.1153 time to fit residues: 69.2583 Evaluate side-chains 431 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 400 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 37 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 136 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN B 438 ASN B 880 GLN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN A1013 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.151843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135373 restraints weight = 20526.177| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.70 r_work: 0.3604 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13852 Z= 0.136 Angle : 0.542 9.497 18707 Z= 0.276 Chirality : 0.040 0.149 2134 Planarity : 0.004 0.061 2385 Dihedral : 4.982 89.743 1865 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.83 % Allowed : 27.05 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.46 (0.21), residues: 1704 helix: 1.32 (0.21), residues: 631 sheet: 0.22 (0.28), residues: 367 loop : -0.50 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 547 TYR 0.015 0.001 TYR B 327 PHE 0.022 0.001 PHE A1111 TRP 0.010 0.001 TRP A 521 HIS 0.005 0.001 HIS B 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (13850) covalent geometry : angle 0.54176 / 0.28 (18707) hydrogen bonds : bond 0.04166 / 2.75 ( 633) hydrogen bonds : angle 4.99892 / 3.44 ( 1803) Misc. bond : bond 0.00093 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 416 time to evaluate : 0.539 Fit side-chains REVERT: B 106 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8469 (tt) REVERT: B 206 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7892 (mtpp) REVERT: B 279 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7899 (mtm-85) REVERT: B 339 MET cc_start: 0.8074 (mpp) cc_final: 0.7598 (mpp) REVERT: B 373 ASN cc_start: 0.7780 (t0) cc_final: 0.7572 (t0) REVERT: B 408 MET cc_start: 0.7560 (mmm) cc_final: 0.7300 (tpp) REVERT: B 435 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7180 (mm-40) REVERT: B 538 ASP cc_start: 0.7903 (p0) cc_final: 0.7700 (p0) REVERT: B 782 MET cc_start: 0.8357 (tpt) cc_final: 0.7752 (tpt) REVERT: B 784 LYS cc_start: 0.8064 (pptt) cc_final: 0.7655 (pptt) REVERT: B 811 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7541 (mtp-110) REVERT: B 836 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7636 (mtpp) REVERT: B 883 LEU cc_start: 0.8530 (mm) cc_final: 0.8157 (mm) REVERT: B 973 VAL cc_start: 0.7813 (p) cc_final: 0.7570 (t) REVERT: B 1091 LYS cc_start: 0.7101 (tttm) cc_final: 0.6485 (tttt) REVERT: A 229 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6897 (mm-30) REVERT: A 232 GLU cc_start: 0.7425 (tt0) cc_final: 0.7075 (tt0) REVERT: A 247 ASP cc_start: 0.6975 (p0) cc_final: 0.6511 (p0) REVERT: A 378 PHE cc_start: 0.8064 (t80) cc_final: 0.7780 (t80) REVERT: A 422 ASP cc_start: 0.7734 (t0) cc_final: 0.7371 (t0) REVERT: A 435 GLN cc_start: 0.7379 (mp10) cc_final: 0.7113 (mp10) REVERT: A 446 ASP cc_start: 0.7471 (m-30) cc_final: 0.7271 (m-30) REVERT: A 497 ARG cc_start: 0.6386 (mmm160) cc_final: 0.6173 (mmm160) REVERT: A 881 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: A 904 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7456 (mttm) REVERT: A 940 CYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6361 (t) REVERT: A 947 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7205 (mt) outliers start: 72 outliers final: 46 residues processed: 446 average time/residue: 0.1333 time to fit residues: 83.4287 Evaluate side-chains 448 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 398 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 4 optimal weight: 0.0020 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 HIS A 980 GLN A1013 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136495 restraints weight = 20525.672| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.69 r_work: 0.3604 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13852 Z= 0.128 Angle : 0.537 9.702 18707 Z= 0.270 Chirality : 0.040 0.290 2134 Planarity : 0.004 0.047 2385 Dihedral : 4.920 87.779 1865 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.90 % Allowed : 26.58 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.55 (0.21), residues: 1704 helix: 1.45 (0.21), residues: 632 sheet: 0.21 (0.28), residues: 366 loop : -0.46 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 547 TYR 0.015 0.001 TYR B 327 PHE 0.022 0.001 PHE A1111 TRP 0.009 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (13850) covalent geometry : angle 0.53670 / 0.27 (18707) hydrogen bonds : bond 0.03754 / 2.48 ( 633) hydrogen bonds : angle 4.81172 / 3.31 ( 1803) Misc. bond : bond 0.00089 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 410 time to evaluate : 0.401 Fit side-chains REVERT: B 206 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7921 (mtpp) REVERT: B 279 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7905 (mtm-85) REVERT: B 339 MET cc_start: 0.8098 (mpp) cc_final: 0.7637 (mpp) REVERT: B 373 ASN cc_start: 0.7796 (t0) cc_final: 0.7548 (t0) REVERT: B 408 MET cc_start: 0.7582 (mmm) cc_final: 0.7296 (tpp) REVERT: B 435 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7237 (mm-40) REVERT: B 538 ASP cc_start: 0.7949 (p0) cc_final: 0.7635 (p0) REVERT: B 554 PHE cc_start: 0.8273 (m-80) cc_final: 0.7988 (m-80) REVERT: B 782 MET cc_start: 0.8366 (tpt) cc_final: 0.7835 (tpt) REVERT: B 784 LYS cc_start: 0.8073 (pptt) cc_final: 0.7665 (pptt) REVERT: B 811 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7462 (mtp-110) REVERT: B 836 LYS cc_start: 0.8049 (mtpp) cc_final: 0.7676 (mtpp) REVERT: B 857 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7831 (mtmt) REVERT: B 883 LEU cc_start: 0.8546 (mm) cc_final: 0.8202 (mm) REVERT: B 941 GLN cc_start: 0.7721 (mt0) cc_final: 0.7450 (mt0) REVERT: B 965 MET cc_start: 0.5328 (tpt) cc_final: 0.4835 (tpt) REVERT: B 973 VAL cc_start: 0.7802 (p) cc_final: 0.7561 (t) REVERT: B 1054 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.5243 (tt0) REVERT: B 1091 LYS cc_start: 0.7047 (tttm) cc_final: 0.6433 (tttt) REVERT: A 229 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6979 (mm-30) REVERT: A 247 ASP cc_start: 0.7072 (p0) cc_final: 0.6749 (p0) REVERT: A 378 PHE cc_start: 0.8102 (t80) cc_final: 0.7799 (t80) REVERT: A 422 ASP cc_start: 0.7782 (t0) cc_final: 0.7370 (t0) REVERT: A 446 ASP cc_start: 0.7478 (m-30) cc_final: 0.7270 (m-30) REVERT: A 497 ARG cc_start: 0.6460 (mmm160) cc_final: 0.6103 (mmm160) REVERT: A 881 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: A 904 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7424 (mttm) REVERT: A 940 CYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6241 (t) REVERT: A 947 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7208 (mt) REVERT: A 1072 MET cc_start: 0.7422 (ppp) cc_final: 0.6783 (ptt) outliers start: 73 outliers final: 52 residues processed: 441 average time/residue: 0.1306 time to fit residues: 80.9696 Evaluate side-chains 456 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 400 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 163 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 165 optimal weight: 0.8980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** 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 = 0.3940 r_free = 0.3940 target = 0.151659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135297 restraints weight = 20448.279| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.68 r_work: 0.3589 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13852 Z= 0.158 Angle : 0.569 9.742 18707 Z= 0.282 Chirality : 0.042 0.291 2134 Planarity : 0.004 0.048 2385 Dihedral : 4.974 83.627 1865 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.37 % Allowed : 27.32 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1704 helix: 1.38 (0.21), residues: 638 sheet: 0.23 (0.29), residues: 360 loop : -0.47 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 547 TYR 0.016 0.001 TYR A 242 PHE 0.025 0.002 PHE A1111 TRP 0.008 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (13850) covalent geometry : angle 0.56873 / 0.28 (18707) hydrogen bonds : bond 0.03898 / 2.58 ( 633) hydrogen bonds : angle 4.81467 / 3.32 ( 1803) Misc. bond : bond 0.00113 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 408 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7899 (mtpp) REVERT: B 339 MET cc_start: 0.8135 (mpp) cc_final: 0.7576 (mpp) REVERT: B 373 ASN cc_start: 0.7782 (t0) cc_final: 0.7560 (t0) REVERT: B 408 MET cc_start: 0.7585 (mmm) cc_final: 0.7294 (tpp) REVERT: B 422 ASP cc_start: 0.7934 (t0) cc_final: 0.7338 (t0) REVERT: B 435 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7220 (mm-40) REVERT: B 489 SER cc_start: 0.8330 (t) cc_final: 0.7812 (p) REVERT: B 538 ASP cc_start: 0.7968 (p0) cc_final: 0.7645 (p0) REVERT: B 554 PHE cc_start: 0.8298 (m-80) cc_final: 0.8060 (m-80) REVERT: B 782 MET cc_start: 0.8354 (tpt) cc_final: 0.7843 (tpt) REVERT: B 784 LYS cc_start: 0.8075 (pptt) cc_final: 0.7698 (pptt) REVERT: B 811 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7622 (ttp80) REVERT: B 836 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7756 (mtpp) REVERT: B 857 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7808 (mtmt) REVERT: B 883 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8213 (mm) REVERT: B 924 THR cc_start: 0.4532 (OUTLIER) cc_final: 0.3725 (p) REVERT: B 941 GLN cc_start: 0.7722 (mt0) cc_final: 0.7463 (mt0) REVERT: B 973 VAL cc_start: 0.7816 (p) cc_final: 0.7588 (t) REVERT: B 1054 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.5191 (tt0) REVERT: B 1056 ARG cc_start: 0.7834 (ttt-90) cc_final: 0.7613 (ttm-80) REVERT: B 1091 LYS cc_start: 0.7063 (tttm) cc_final: 0.6426 (tttt) REVERT: A 229 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6932 (mm-30) REVERT: A 247 ASP cc_start: 0.7062 (p0) cc_final: 0.6726 (p0) REVERT: A 288 ARG cc_start: 0.8505 (tpt-90) cc_final: 0.8205 (tpt90) REVERT: A 422 ASP cc_start: 0.7782 (t0) cc_final: 0.7377 (t0) REVERT: A 435 GLN cc_start: 0.7436 (mp10) cc_final: 0.6953 (mp10) REVERT: A 446 ASP cc_start: 0.7484 (m-30) cc_final: 0.7254 (m-30) REVERT: A 497 ARG cc_start: 0.6522 (mmm160) cc_final: 0.6162 (mmm160) REVERT: A 878 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 881 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: A 940 CYS cc_start: 0.6639 (OUTLIER) cc_final: 0.6258 (t) REVERT: A 947 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7232 (mt) REVERT: A 1021 LEU cc_start: 0.8233 (tp) cc_final: 0.8017 (tp) REVERT: A 1072 MET cc_start: 0.7448 (ppp) cc_final: 0.6992 (ptt) outliers start: 80 outliers final: 58 residues processed: 443 average time/residue: 0.1345 time to fit residues: 83.3127 Evaluate side-chains 461 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 397 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 44 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** 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 = 0.3906 r_free = 0.3906 target = 0.148764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132389 restraints weight = 20452.947| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.67 r_work: 0.3558 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13852 Z= 0.254 Angle : 0.637 10.247 18707 Z= 0.319 Chirality : 0.044 0.327 2134 Planarity : 0.004 0.056 2385 Dihedral : 5.261 78.209 1865 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.77 % Allowed : 27.11 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.29 (0.21), residues: 1704 helix: 1.14 (0.20), residues: 637 sheet: 0.14 (0.29), residues: 352 loop : -0.56 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 547 TYR 0.022 0.002 TYR B1006 PHE 0.027 0.002 PHE A1111 TRP 0.014 0.002 TRP A 521 HIS 0.005 0.001 HIS A1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (13850) covalent geometry : angle 0.63654 / 0.32 (18707) hydrogen bonds : bond 0.04480 / 2.97 ( 633) hydrogen bonds : angle 5.01456 / 3.46 ( 1803) Misc. bond : bond 0.00162 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 417 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7890 (mtpp) REVERT: B 342 VAL cc_start: 0.7358 (t) cc_final: 0.7113 (m) REVERT: B 373 ASN cc_start: 0.7760 (t0) cc_final: 0.7539 (t0) REVERT: B 408 MET cc_start: 0.7522 (mmm) cc_final: 0.7262 (tpp) REVERT: B 422 ASP cc_start: 0.8075 (t0) cc_final: 0.7502 (t0) REVERT: B 435 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7326 (mm-40) REVERT: B 538 ASP cc_start: 0.8003 (p0) cc_final: 0.7645 (p0) REVERT: B 782 MET cc_start: 0.8465 (tpt) cc_final: 0.8055 (tpt) REVERT: B 784 LYS cc_start: 0.8084 (pptt) cc_final: 0.7734 (pptt) REVERT: B 811 ARG cc_start: 0.7922 (ttp-170) cc_final: 0.7610 (ttp80) REVERT: B 836 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7693 (mtpp) REVERT: B 857 LYS cc_start: 0.8018 (mtmt) cc_final: 0.7805 (mtmt) REVERT: B 883 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8203 (mm) REVERT: B 924 THR cc_start: 0.4672 (OUTLIER) cc_final: 0.3803 (p) REVERT: B 1054 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.5307 (tt0) REVERT: B 1056 ARG cc_start: 0.7929 (ttt-90) cc_final: 0.7638 (ttm-80) REVERT: B 1082 GLU cc_start: 0.6990 (tp30) cc_final: 0.6777 (tp30) REVERT: B 1091 LYS cc_start: 0.7269 (tttm) cc_final: 0.6642 (tttt) REVERT: A 210 ARG cc_start: 0.7419 (mtm180) cc_final: 0.6905 (mtm110) REVERT: A 229 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6548 (mm-30) REVERT: A 232 GLU cc_start: 0.7526 (tt0) cc_final: 0.7293 (tt0) REVERT: A 243 LYS cc_start: 0.8404 (tttm) cc_final: 0.8111 (tttm) REVERT: A 247 ASP cc_start: 0.7035 (p0) cc_final: 0.6695 (p0) REVERT: A 288 ARG cc_start: 0.8517 (tpt-90) cc_final: 0.8216 (tpt90) REVERT: A 422 ASP cc_start: 0.7793 (t0) cc_final: 0.7352 (t0) REVERT: A 435 GLN cc_start: 0.7426 (mp10) cc_final: 0.6882 (mp10) REVERT: A 446 ASP cc_start: 0.7485 (m-30) cc_final: 0.7249 (m-30) REVERT: A 470 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7008 (mm-30) REVERT: A 497 ARG cc_start: 0.6633 (mmm160) cc_final: 0.6248 (mmm160) REVERT: A 878 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7551 (mt-10) REVERT: A 881 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: A 940 CYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6299 (t) REVERT: A 947 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7220 (mt) REVERT: A 949 ASP cc_start: 0.6713 (m-30) cc_final: 0.6359 (m-30) REVERT: A 1072 MET cc_start: 0.7519 (ppp) cc_final: 0.7203 (ptt) outliers start: 86 outliers final: 60 residues processed: 453 average time/residue: 0.1315 time to fit residues: 83.3687 Evaluate side-chains 474 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 408 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 163 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** 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 = 0.3935 r_free = 0.3935 target = 0.150920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134565 restraints weight = 20355.159| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.66 r_work: 0.3594 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13852 Z= 0.144 Angle : 0.580 11.323 18707 Z= 0.286 Chirality : 0.041 0.308 2134 Planarity : 0.004 0.050 2385 Dihedral : 4.925 72.029 1865 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.17 % Allowed : 28.05 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.46 (0.21), residues: 1704 helix: 1.38 (0.21), residues: 631 sheet: 0.07 (0.29), residues: 360 loop : -0.47 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 512 TYR 0.017 0.001 TYR B 327 PHE 0.018 0.001 PHE A1111 TRP 0.012 0.001 TRP A 521 HIS 0.006 0.001 HIS B 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (13850) covalent geometry : angle 0.58008 / 0.29 (18707) hydrogen bonds : bond 0.03735 / 2.48 ( 633) hydrogen bonds : angle 4.79730 / 3.31 ( 1803) Misc. bond : bond 0.00071 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 407 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7884 (mtpp) REVERT: B 279 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7839 (mtm-85) REVERT: B 373 ASN cc_start: 0.7774 (t0) cc_final: 0.7568 (t0) REVERT: B 408 MET cc_start: 0.7564 (mmm) cc_final: 0.7294 (tpp) REVERT: B 422 ASP cc_start: 0.7991 (t0) cc_final: 0.7404 (t0) REVERT: B 435 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7294 (mm-40) REVERT: B 518 MET cc_start: 0.7790 (ptp) cc_final: 0.7585 (mtm) REVERT: B 538 ASP cc_start: 0.7951 (p0) cc_final: 0.7565 (p0) REVERT: B 784 LYS cc_start: 0.8048 (pptt) cc_final: 0.7694 (pptt) REVERT: B 807 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7915 (tmtt) REVERT: B 836 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7751 (mtpp) REVERT: B 857 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7800 (mtmt) REVERT: B 883 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8214 (mm) REVERT: B 920 MET cc_start: 0.6798 (mtm) cc_final: 0.6540 (mmm) REVERT: B 924 THR cc_start: 0.4583 (OUTLIER) cc_final: 0.3786 (p) REVERT: B 965 MET cc_start: 0.5324 (tpt) cc_final: 0.5002 (tpt) REVERT: B 1054 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.5163 (tt0) REVERT: B 1091 LYS cc_start: 0.7069 (tttm) cc_final: 0.6449 (tttt) REVERT: B 1116 GLU cc_start: 0.5813 (tm-30) cc_final: 0.5593 (tm-30) REVERT: A 157 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 229 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 247 ASP cc_start: 0.7011 (p0) cc_final: 0.6656 (p0) REVERT: A 288 ARG cc_start: 0.8508 (tpt-90) cc_final: 0.8205 (tpt90) REVERT: A 422 ASP cc_start: 0.7769 (t0) cc_final: 0.7414 (t0) REVERT: A 446 ASP cc_start: 0.7436 (m-30) cc_final: 0.7213 (m-30) REVERT: A 470 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6979 (mm-30) REVERT: A 497 ARG cc_start: 0.6609 (mmm160) cc_final: 0.6258 (mmm160) REVERT: A 569 LYS cc_start: 0.7925 (mptm) cc_final: 0.7703 (mptm) REVERT: A 878 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 881 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: A 940 CYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6174 (t) REVERT: A 947 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7260 (mt) REVERT: A 949 ASP cc_start: 0.6658 (m-30) cc_final: 0.6304 (m-30) REVERT: A 1072 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7127 (ptt) outliers start: 77 outliers final: 55 residues processed: 440 average time/residue: 0.1374 time to fit residues: 84.5633 Evaluate side-chains 460 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 397 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 0.0000 chunk 131 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** 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 = 0.3943 r_free = 0.3943 target = 0.151401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135041 restraints weight = 20221.940| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.68 r_work: 0.3602 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13852 Z= 0.121 Angle : 0.572 11.315 18707 Z= 0.281 Chirality : 0.041 0.307 2134 Planarity : 0.004 0.048 2385 Dihedral : 4.662 58.259 1865 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.63 % Allowed : 28.72 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.58 (0.21), residues: 1704 helix: 1.53 (0.21), residues: 629 sheet: 0.11 (0.28), residues: 366 loop : -0.43 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 512 TYR 0.017 0.001 TYR B 327 PHE 0.021 0.001 PHE A1111 TRP 0.011 0.001 TRP A 521 HIS 0.005 0.001 HIS B 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13850) covalent geometry : angle 0.57164 / 0.28 (18707) hydrogen bonds : bond 0.03475 / 2.30 ( 633) hydrogen bonds : angle 4.67944 / 3.21 ( 1803) Misc. bond : bond 0.00050 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 403 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7904 (mtpp) REVERT: B 279 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7863 (mtm-85) REVERT: B 339 MET cc_start: 0.8187 (mpp) cc_final: 0.7590 (mpp) REVERT: B 373 ASN cc_start: 0.7800 (t0) cc_final: 0.7535 (t0) REVERT: B 408 MET cc_start: 0.7613 (mmm) cc_final: 0.7310 (tpp) REVERT: B 422 ASP cc_start: 0.7981 (t0) cc_final: 0.7380 (t0) REVERT: B 435 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7299 (mm-40) REVERT: B 489 SER cc_start: 0.8300 (t) cc_final: 0.7811 (p) REVERT: B 538 ASP cc_start: 0.7950 (p0) cc_final: 0.7558 (p0) REVERT: B 784 LYS cc_start: 0.8066 (pptt) cc_final: 0.7694 (pptt) REVERT: B 807 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7880 (tmtt) REVERT: B 836 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7772 (mtpp) REVERT: B 857 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7776 (mtmt) REVERT: B 883 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8192 (mm) REVERT: B 914 ILE cc_start: 0.7649 (mt) cc_final: 0.7425 (tt) REVERT: B 920 MET cc_start: 0.6801 (mtm) cc_final: 0.6556 (mmm) REVERT: B 924 THR cc_start: 0.4608 (OUTLIER) cc_final: 0.3803 (p) REVERT: B 965 MET cc_start: 0.5322 (tpt) cc_final: 0.4968 (tpt) REVERT: B 1054 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.5088 (tt0) REVERT: B 1082 GLU cc_start: 0.6878 (tp30) cc_final: 0.6555 (tp30) REVERT: B 1091 LYS cc_start: 0.7026 (tttm) cc_final: 0.6412 (tttt) REVERT: B 1116 GLU cc_start: 0.5822 (tm-30) cc_final: 0.5599 (tm-30) REVERT: A 157 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8027 (tt) REVERT: A 210 ARG cc_start: 0.7481 (mtm180) cc_final: 0.6959 (mtm110) REVERT: A 247 ASP cc_start: 0.6997 (p0) cc_final: 0.6635 (p0) REVERT: A 422 ASP cc_start: 0.7755 (t0) cc_final: 0.7423 (t0) REVERT: A 435 GLN cc_start: 0.7445 (mp10) cc_final: 0.6991 (mp10) REVERT: A 446 ASP cc_start: 0.7465 (m-30) cc_final: 0.7231 (m-30) REVERT: A 470 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6971 (mm-30) REVERT: A 497 ARG cc_start: 0.6608 (mmm160) cc_final: 0.6209 (mmm160) REVERT: A 878 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7495 (mt-10) REVERT: A 881 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: A 940 CYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6130 (t) REVERT: A 949 ASP cc_start: 0.6632 (m-30) cc_final: 0.6280 (m-30) REVERT: A 1021 LEU cc_start: 0.8236 (tp) cc_final: 0.8032 (tp) REVERT: A 1072 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7142 (ptt) outliers start: 69 outliers final: 54 residues processed: 436 average time/residue: 0.1273 time to fit residues: 77.4144 Evaluate side-chains 456 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 395 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN A 980 GLN A1013 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.150164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133833 restraints weight = 20399.646| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.66 r_work: 0.3573 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13852 Z= 0.182 Angle : 0.610 10.698 18707 Z= 0.302 Chirality : 0.043 0.321 2134 Planarity : 0.004 0.050 2385 Dihedral : 4.723 43.403 1865 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.63 % Allowed : 29.06 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.46 (0.21), residues: 1704 helix: 1.35 (0.21), residues: 632 sheet: 0.12 (0.29), residues: 362 loop : -0.47 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 512 TYR 0.017 0.002 TYR B 327 PHE 0.035 0.002 PHE A1111 TRP 0.013 0.002 TRP A 521 HIS 0.006 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (13850) covalent geometry : angle 0.61044 / 0.30 (18707) hydrogen bonds : bond 0.03926 / 2.59 ( 633) hydrogen bonds : angle 4.81606 / 3.31 ( 1803) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 406 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7883 (mtpp) REVERT: B 373 ASN cc_start: 0.7786 (t0) cc_final: 0.7569 (t0) REVERT: B 408 MET cc_start: 0.7563 (mmm) cc_final: 0.7291 (tpp) REVERT: B 422 ASP cc_start: 0.7959 (t0) cc_final: 0.7422 (t0) REVERT: B 435 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7218 (mm-40) REVERT: B 538 ASP cc_start: 0.7966 (p0) cc_final: 0.7674 (p0) REVERT: B 784 LYS cc_start: 0.8092 (pptt) cc_final: 0.7730 (pptt) REVERT: B 807 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7883 (tmtt) REVERT: B 811 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.7573 (mtp-110) REVERT: B 824 VAL cc_start: 0.8452 (t) cc_final: 0.8247 (p) REVERT: B 836 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7816 (mtpp) REVERT: B 857 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7773 (mtmt) REVERT: B 883 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8215 (mm) REVERT: B 920 MET cc_start: 0.6735 (mtm) cc_final: 0.6486 (mmm) REVERT: B 924 THR cc_start: 0.4646 (OUTLIER) cc_final: 0.3789 (p) REVERT: B 1054 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.5185 (tt0) REVERT: B 1091 LYS cc_start: 0.7146 (tttm) cc_final: 0.6525 (tttt) REVERT: A 210 ARG cc_start: 0.7463 (mtm180) cc_final: 0.6908 (mtm110) REVERT: A 247 ASP cc_start: 0.7059 (p0) cc_final: 0.6636 (p0) REVERT: A 288 ARG cc_start: 0.8510 (tpt-90) cc_final: 0.8194 (tpt90) REVERT: A 422 ASP cc_start: 0.7783 (t0) cc_final: 0.7423 (t0) REVERT: A 435 GLN cc_start: 0.7469 (mp10) cc_final: 0.6982 (mp10) REVERT: A 446 ASP cc_start: 0.7479 (m-30) cc_final: 0.7238 (m-30) REVERT: A 470 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6919 (mm-30) REVERT: A 495 PHE cc_start: 0.8798 (t80) cc_final: 0.8546 (t80) REVERT: A 497 ARG cc_start: 0.6653 (mmm160) cc_final: 0.6260 (mmm160) REVERT: A 878 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7548 (mt-10) REVERT: A 881 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: A 940 CYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6267 (t) REVERT: A 947 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7241 (mt) REVERT: A 949 ASP cc_start: 0.6695 (m-30) cc_final: 0.6351 (m-30) REVERT: A 1072 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7186 (ptt) outliers start: 69 outliers final: 53 residues processed: 443 average time/residue: 0.1328 time to fit residues: 82.2911 Evaluate side-chains 461 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 401 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 8 optimal weight: 0.0030 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN A1013 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135631 restraints weight = 20413.711| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.68 r_work: 0.3607 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13852 Z= 0.123 Angle : 0.581 11.181 18707 Z= 0.285 Chirality : 0.041 0.310 2134 Planarity : 0.004 0.049 2385 Dihedral : 4.501 35.963 1865 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.56 % Allowed : 28.93 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.58 (0.21), residues: 1704 helix: 1.51 (0.21), residues: 630 sheet: 0.14 (0.29), residues: 362 loop : -0.44 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 512 TYR 0.016 0.001 TYR B 327 PHE 0.024 0.001 PHE A1111 TRP 0.014 0.001 TRP A 521 HIS 0.005 0.001 HIS B 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (13850) covalent geometry : angle 0.58100 / 0.29 (18707) hydrogen bonds : bond 0.03456 / 2.28 ( 633) hydrogen bonds : angle 4.67582 / 3.22 ( 1803) Misc. bond : bond 0.00043 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 399 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7894 (mtpp) REVERT: B 373 ASN cc_start: 0.7827 (t0) cc_final: 0.7576 (t0) REVERT: B 408 MET cc_start: 0.7591 (mmm) cc_final: 0.7287 (tpp) REVERT: B 422 ASP cc_start: 0.7939 (t0) cc_final: 0.7367 (t0) REVERT: B 423 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8021 (mmm) REVERT: B 435 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7199 (mm-40) REVERT: B 489 SER cc_start: 0.8307 (t) cc_final: 0.7826 (p) REVERT: B 538 ASP cc_start: 0.7923 (p0) cc_final: 0.7632 (p0) REVERT: B 782 MET cc_start: 0.8351 (tpt) cc_final: 0.7913 (tpt) REVERT: B 784 LYS cc_start: 0.8080 (pptt) cc_final: 0.7691 (pptt) REVERT: B 807 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7860 (tmtt) REVERT: B 811 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.7583 (ttp80) REVERT: B 836 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7768 (mtpp) REVERT: B 857 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7765 (mtmt) REVERT: B 883 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8184 (mm) REVERT: B 924 THR cc_start: 0.4655 (OUTLIER) cc_final: 0.3840 (p) REVERT: B 1054 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.5071 (tt0) REVERT: B 1082 GLU cc_start: 0.6897 (tp30) cc_final: 0.6528 (tp30) REVERT: B 1091 LYS cc_start: 0.7018 (tttm) cc_final: 0.6387 (tttt) REVERT: B 1108 LYS cc_start: 0.6650 (mmmt) cc_final: 0.6405 (mmmt) REVERT: A 210 ARG cc_start: 0.7519 (mtm180) cc_final: 0.7008 (mtm110) REVERT: A 247 ASP cc_start: 0.7068 (p0) cc_final: 0.6638 (p0) REVERT: A 288 ARG cc_start: 0.8513 (tpt-90) cc_final: 0.8208 (tpt90) REVERT: A 422 ASP cc_start: 0.7756 (t0) cc_final: 0.7420 (t0) REVERT: A 435 GLN cc_start: 0.7457 (mp10) cc_final: 0.6956 (mp10) REVERT: A 446 ASP cc_start: 0.7473 (m-30) cc_final: 0.7235 (m-30) REVERT: A 470 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6944 (mm-30) REVERT: A 497 ARG cc_start: 0.6639 (mmm160) cc_final: 0.6265 (mmm160) REVERT: A 569 LYS cc_start: 0.7926 (mptm) cc_final: 0.7709 (mptm) REVERT: A 878 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7536 (mt-10) REVERT: A 881 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: A 949 ASP cc_start: 0.6640 (m-30) cc_final: 0.6292 (m-30) REVERT: A 1021 LEU cc_start: 0.8243 (tp) cc_final: 0.8026 (tp) REVERT: A 1072 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7108 (ptt) outliers start: 68 outliers final: 56 residues processed: 435 average time/residue: 0.1315 time to fit residues: 79.9173 Evaluate side-chains 454 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 392 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** 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 = 0.3920 r_free = 0.3920 target = 0.149854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133564 restraints weight = 20417.872| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.68 r_work: 0.3561 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13852 Z= 0.203 Angle : 0.629 10.745 18707 Z= 0.313 Chirality : 0.043 0.323 2134 Planarity : 0.004 0.050 2385 Dihedral : 4.707 32.423 1865 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.56 % Allowed : 29.33 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.39 (0.21), residues: 1704 helix: 1.29 (0.21), residues: 631 sheet: 0.11 (0.29), residues: 353 loop : -0.51 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 512 TYR 0.018 0.002 TYR B1006 PHE 0.041 0.002 PHE A1111 TRP 0.013 0.002 TRP A 521 HIS 0.006 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (13850) covalent geometry : angle 0.62921 / 0.31 (18707) hydrogen bonds : bond 0.04036 / 2.66 ( 633) hydrogen bonds : angle 4.82559 / 3.33 ( 1803) Misc. bond : bond 0.00098 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.00 seconds wall clock time: 55 minutes 27.15 seconds (3327.15 seconds total)