Starting phenix.real_space_refine on Thu Jun 12 10:19:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f5z_28869/06_2025/8f5z_28869.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f5z_28869/06_2025/8f5z_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f5z_28869/06_2025/8f5z_28869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f5z_28869/06_2025/8f5z_28869.map" model { file = "/net/cci-nas-00/data/ceres_data/8f5z_28869/06_2025/8f5z_28869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f5z_28869/06_2025/8f5z_28869.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.94, per 1000 atoms: 0.66 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: 3.42 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.73 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: 5.37 Time building geometry restraints manager: 4.06 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: 7189 17.93 - 35.86: 958 35.86 - 53.79: 262 53.79 - 71.72: 41 71.72 - 89.65: 13 Dihedral angle restraints: 8463 sinusoidal: 3473 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 8460 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 1119 o \ r resid 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.550 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 17.242 89.652 5223 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (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 TRP 0.007 0.001 TRP A 568 HIS 0.004 0.001 HIS A1059 PHE 0.031 0.001 PHE A 83 TYR 0.012 0.001 TYR B 168 ARG 0.016 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.26737 ( 633) hydrogen bonds : angle 8.48896 ( 1803) covalent geometry : bond 0.00337 (13850) covalent geometry : angle 0.58780 (18707) Misc. bond : bond 0.03174 ( 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 : 1.495 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: 0.2936 time to fit residues: 163.5360 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 : 1.420 ------------------------------------------------------------------------------- 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 145 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 285 ASN ** 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 = 0.3940 r_free = 0.3940 target = 0.151338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135112 restraints weight = 20334.221| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.64 r_work: 0.3598 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13852 Z= 0.172 Angle : 0.589 11.658 18707 Z= 0.301 Chirality : 0.042 0.170 2134 Planarity : 0.005 0.083 2385 Dihedral : 5.737 89.750 1938 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.16 % Allowed : 27.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1704 helix: 0.97 (0.20), residues: 635 sheet: 0.15 (0.28), residues: 362 loop : -0.48 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 521 HIS 0.004 0.001 HIS A 372 PHE 0.028 0.002 PHE A1111 TYR 0.016 0.001 TYR A 242 ARG 0.010 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 633) hydrogen bonds : angle 5.50882 ( 1803) covalent geometry : bond 0.00382 (13850) covalent geometry : angle 0.58868 (18707) Misc. bond : bond 0.00183 ( 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 469 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 407 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: B 339 MET cc_start: 0.8098 (mpp) cc_final: 0.7608 (mpp) REVERT: B 373 ASN cc_start: 0.7832 (t0) cc_final: 0.7588 (t0) REVERT: B 408 MET cc_start: 0.7445 (mmm) cc_final: 0.7155 (mmm) REVERT: B 518 MET cc_start: 0.7827 (ptp) cc_final: 0.7520 (mtm) REVERT: B 538 ASP cc_start: 0.7899 (p0) cc_final: 0.7695 (p0) REVERT: B 784 LYS cc_start: 0.8059 (pptt) cc_final: 0.7833 (pptt) REVERT: B 836 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7627 (mtpp) REVERT: B 883 LEU cc_start: 0.8543 (mm) cc_final: 0.8257 (mm) REVERT: B 905 ARG cc_start: 0.7183 (ttm170) cc_final: 0.6965 (mtp180) REVERT: B 941 GLN cc_start: 0.7706 (mt0) cc_final: 0.7425 (mt0) REVERT: B 973 VAL cc_start: 0.7856 (p) cc_final: 0.7610 (t) REVERT: B 1091 LYS cc_start: 0.7235 (tttm) cc_final: 0.6888 (tttm) REVERT: A 210 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7071 (mtm110) REVERT: A 229 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 232 GLU cc_start: 0.7389 (tt0) cc_final: 0.7169 (tt0) REVERT: A 303 ASP cc_start: 0.7039 (t0) cc_final: 0.6806 (t70) REVERT: A 328 MET cc_start: 0.8104 (mtm) cc_final: 0.7841 (mtt) REVERT: A 422 ASP cc_start: 0.7711 (t0) cc_final: 0.7317 (t0) REVERT: A 446 ASP cc_start: 0.7435 (m-30) cc_final: 0.7212 (m-30) REVERT: A 877 HIS cc_start: 0.7681 (m90) cc_final: 0.6863 (m90) REVERT: A 878 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 881 GLN cc_start: 0.7897 (mp10) cc_final: 0.7369 (mp10) REVERT: A 949 ASP cc_start: 0.6494 (m-30) cc_final: 0.6169 (m-30) REVERT: A 1091 LYS cc_start: 0.7365 (mttm) cc_final: 0.7070 (mttm) outliers start: 62 outliers final: 35 residues processed: 429 average time/residue: 0.2912 time to fit residues: 173.2177 Evaluate side-chains 437 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 402 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 171 ILE 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 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 52 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 125 optimal weight: 0.0270 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN B 438 ASN ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.150866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134518 restraints weight = 20396.956| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.68 r_work: 0.3587 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13852 Z= 0.171 Angle : 0.561 9.875 18707 Z= 0.287 Chirality : 0.041 0.196 2134 Planarity : 0.004 0.060 2385 Dihedral : 5.283 89.285 1930 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.70 % Allowed : 26.64 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1704 helix: 1.18 (0.21), residues: 638 sheet: 0.21 (0.29), residues: 360 loop : -0.48 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 521 HIS 0.005 0.001 HIS B 877 PHE 0.025 0.002 PHE A1111 TYR 0.016 0.001 TYR B 327 ARG 0.009 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 633) hydrogen bonds : angle 5.11364 ( 1803) covalent geometry : bond 0.00385 (13850) covalent geometry : angle 0.56146 (18707) Misc. bond : bond 0.00169 ( 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 487 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 417 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: B 106 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8448 (tt) REVERT: B 202 LYS cc_start: 0.8473 (mtmm) cc_final: 0.8229 (mttp) REVERT: B 206 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7900 (mtpp) REVERT: B 339 MET cc_start: 0.8120 (mpp) cc_final: 0.7613 (mpp) REVERT: B 373 ASN cc_start: 0.7796 (t0) cc_final: 0.7571 (t0) REVERT: B 408 MET cc_start: 0.7516 (mmm) cc_final: 0.7282 (tpp) REVERT: B 435 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7270 (mm-40) REVERT: B 538 ASP cc_start: 0.7943 (p0) cc_final: 0.7662 (p0) REVERT: B 782 MET cc_start: 0.8400 (tpt) cc_final: 0.7849 (tpt) REVERT: B 784 LYS cc_start: 0.8072 (pptt) cc_final: 0.7682 (pptt) REVERT: B 811 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.7540 (mtp-110) REVERT: B 836 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7625 (mtpp) REVERT: B 883 LEU cc_start: 0.8547 (mm) cc_final: 0.8170 (mm) REVERT: B 905 ARG cc_start: 0.7198 (ttm170) cc_final: 0.6969 (mtp180) REVERT: B 973 VAL cc_start: 0.7833 (p) cc_final: 0.7600 (t) REVERT: B 1091 LYS cc_start: 0.7165 (tttm) cc_final: 0.6538 (tttt) REVERT: A 206 LYS cc_start: 0.7942 (tmtt) cc_final: 0.7712 (tmtt) REVERT: A 229 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6875 (mm-30) REVERT: A 378 PHE cc_start: 0.8108 (t80) cc_final: 0.7842 (t80) REVERT: A 422 ASP cc_start: 0.7740 (t0) cc_final: 0.7370 (t0) REVERT: A 435 GLN cc_start: 0.7362 (mp10) cc_final: 0.7091 (mp10) REVERT: A 446 ASP cc_start: 0.7475 (m-30) cc_final: 0.7270 (m-30) REVERT: A 816 GLU cc_start: 0.7367 (tp30) cc_final: 0.7147 (tp30) REVERT: A 881 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: A 896 ARG cc_start: 0.7055 (ptt-90) cc_final: 0.6763 (ptt90) REVERT: A 940 CYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6396 (t) REVERT: A 1091 LYS cc_start: 0.7360 (mttm) cc_final: 0.7150 (mttm) outliers start: 70 outliers final: 50 residues processed: 447 average time/residue: 0.3010 time to fit residues: 187.0092 Evaluate side-chains 453 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 400 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 209 THR 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 385 TYR Chi-restraints excluded: chain B residue 419 LEU 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 843 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 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 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 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 548 MET Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 805 THR 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 948 LEU Chi-restraints excluded: chain A residue 954 GLU 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 1064 ILE 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 62 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 144 optimal weight: 0.0010 chunk 111 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN A1013 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.152435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136066 restraints weight = 20313.855| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.67 r_work: 0.3612 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1894 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= 0.122 Angle : 0.543 9.917 18707 Z= 0.273 Chirality : 0.041 0.300 2134 Planarity : 0.004 0.048 2385 Dihedral : 5.069 89.865 1928 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.83 % Allowed : 27.45 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1704 helix: 1.37 (0.21), residues: 632 sheet: 0.20 (0.29), residues: 359 loop : -0.47 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 521 HIS 0.005 0.001 HIS A1059 PHE 0.021 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.010 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 633) hydrogen bonds : angle 4.87525 ( 1803) covalent geometry : bond 0.00275 (13850) covalent geometry : angle 0.54304 (18707) Misc. bond : bond 0.00116 ( 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 480 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 408 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: B 106 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8453 (tt) REVERT: B 206 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7938 (mtpp) REVERT: B 279 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: B 339 MET cc_start: 0.8093 (mpp) cc_final: 0.7601 (mpp) REVERT: B 373 ASN cc_start: 0.7802 (t0) cc_final: 0.7565 (t0) REVERT: B 408 MET cc_start: 0.7578 (mmm) cc_final: 0.7299 (tpp) REVERT: B 435 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7299 (mm-40) REVERT: B 538 ASP cc_start: 0.7943 (p0) cc_final: 0.7601 (p0) REVERT: B 782 MET cc_start: 0.8350 (tpt) cc_final: 0.7839 (tpt) REVERT: B 784 LYS cc_start: 0.8076 (pptt) cc_final: 0.7671 (pptt) REVERT: B 811 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7404 (mtp-110) REVERT: B 836 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7643 (mtpp) REVERT: B 857 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7805 (mtmt) REVERT: B 883 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8197 (mm) REVERT: B 965 MET cc_start: 0.5344 (tpt) cc_final: 0.4872 (tpt) REVERT: B 973 VAL cc_start: 0.7813 (p) cc_final: 0.7571 (t) REVERT: B 1054 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.5717 (tt0) REVERT: B 1091 LYS cc_start: 0.7056 (tttm) cc_final: 0.6431 (tttt) REVERT: B 1116 GLU cc_start: 0.5847 (tm-30) cc_final: 0.5528 (tm-30) REVERT: A 210 ARG cc_start: 0.7391 (mtm110) cc_final: 0.6884 (mtm110) REVERT: A 325 LEU cc_start: 0.8283 (mt) cc_final: 0.8048 (mm) REVERT: A 378 PHE cc_start: 0.8090 (t80) cc_final: 0.7792 (t80) REVERT: A 422 ASP cc_start: 0.7753 (t0) cc_final: 0.7318 (t0) REVERT: A 423 MET cc_start: 0.7933 (mmm) cc_final: 0.7694 (mmm) REVERT: A 446 ASP cc_start: 0.7458 (m-30) cc_final: 0.7246 (m-30) REVERT: A 881 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: A 904 LYS cc_start: 0.7700 (ttmm) cc_final: 0.7364 (mttm) REVERT: A 1021 LEU cc_start: 0.8164 (tp) cc_final: 0.7955 (tp) REVERT: A 1072 MET cc_start: 0.7410 (ppp) cc_final: 0.6781 (ptt) outliers start: 72 outliers final: 47 residues processed: 439 average time/residue: 0.3039 time to fit residues: 184.4217 Evaluate side-chains 449 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 398 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 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 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 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 883 LEU 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 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 342 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 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 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 948 LEU Chi-restraints excluded: chain A residue 990 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 159 optimal weight: 0.0040 chunk 7 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 103 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 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 = 0.3969 r_free = 0.3969 target = 0.154103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137852 restraints weight = 20401.768| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.67 r_work: 0.3626 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13852 Z= 0.107 Angle : 0.549 10.141 18707 Z= 0.270 Chirality : 0.040 0.288 2134 Planarity : 0.004 0.046 2385 Dihedral : 4.833 85.761 1925 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.03 % Allowed : 27.92 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1704 helix: 1.45 (0.21), residues: 638 sheet: 0.31 (0.29), residues: 364 loop : -0.50 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 474 HIS 0.004 0.001 HIS A1059 PHE 0.019 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.010 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 633) hydrogen bonds : angle 4.71686 ( 1803) covalent geometry : bond 0.00244 (13850) covalent geometry : angle 0.54898 (18707) Misc. bond : bond 0.00089 ( 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 479 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 404 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 106 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8474 (tt) REVERT: B 206 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7900 (mtpp) REVERT: B 339 MET cc_start: 0.8093 (mpp) cc_final: 0.7603 (mpp) REVERT: B 373 ASN cc_start: 0.7804 (t0) cc_final: 0.7571 (t0) REVERT: B 408 MET cc_start: 0.7610 (mmm) cc_final: 0.7308 (tpp) REVERT: B 422 ASP cc_start: 0.7888 (t0) cc_final: 0.7274 (t0) REVERT: B 435 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7270 (mm-40) REVERT: B 538 ASP cc_start: 0.7927 (p0) cc_final: 0.7558 (p0) REVERT: B 554 PHE cc_start: 0.8266 (m-80) cc_final: 0.7988 (m-80) REVERT: B 782 MET cc_start: 0.8373 (tpt) cc_final: 0.7835 (tpt) REVERT: B 784 LYS cc_start: 0.8064 (pptt) cc_final: 0.7683 (pptt) REVERT: B 811 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7611 (ttp80) REVERT: B 836 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7778 (mtpp) REVERT: B 883 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8189 (mm) REVERT: B 941 GLN cc_start: 0.7678 (mt0) cc_final: 0.7423 (mt0) REVERT: B 965 MET cc_start: 0.5247 (tpt) cc_final: 0.4761 (tpt) REVERT: B 1054 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.5153 (tt0) REVERT: B 1091 LYS cc_start: 0.6995 (tttm) cc_final: 0.6378 (tttt) REVERT: A 210 ARG cc_start: 0.7482 (mtm110) cc_final: 0.6905 (mtm110) REVERT: A 288 ARG cc_start: 0.8451 (tpt-90) cc_final: 0.8113 (tpt90) REVERT: A 378 PHE cc_start: 0.8054 (t80) cc_final: 0.7755 (t80) REVERT: A 422 ASP cc_start: 0.7713 (t0) cc_final: 0.7331 (t0) REVERT: A 878 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: A 881 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: A 904 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7308 (mttm) REVERT: A 906 GLN cc_start: 0.6799 (mm-40) cc_final: 0.6470 (mt0) REVERT: A 1072 MET cc_start: 0.7396 (ppp) cc_final: 0.6902 (ptt) outliers start: 75 outliers final: 55 residues processed: 436 average time/residue: 0.3015 time to fit residues: 180.7335 Evaluate side-chains 461 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 400 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU 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 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU 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 501 LEU 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 777 GLU Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 811 ARG 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 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 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 MET 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 483 THR 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 771 GLU 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 878 GLU Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1064 ILE 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 153 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 0.0030 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 0.0020 chunk 162 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.153898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137532 restraints weight = 20541.109| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.69 r_work: 0.3624 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13852 Z= 0.114 Angle : 0.549 10.296 18707 Z= 0.271 Chirality : 0.040 0.299 2134 Planarity : 0.004 0.052 2385 Dihedral : 4.748 78.793 1925 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.97 % Allowed : 27.85 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1704 helix: 1.49 (0.21), residues: 638 sheet: 0.28 (0.29), residues: 367 loop : -0.51 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 PHE 0.020 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.012 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 633) hydrogen bonds : angle 4.62205 ( 1803) covalent geometry : bond 0.00262 (13850) covalent geometry : angle 0.54901 (18707) Misc. bond : bond 0.00105 ( 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 479 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 405 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7899 (mtpp) REVERT: B 339 MET cc_start: 0.8106 (mpp) cc_final: 0.7590 (mpp) REVERT: B 373 ASN cc_start: 0.7809 (t0) cc_final: 0.7551 (t0) REVERT: B 403 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6944 (mp0) REVERT: B 408 MET cc_start: 0.7572 (mmm) cc_final: 0.7259 (tpp) REVERT: B 412 ASN cc_start: 0.7953 (m-40) cc_final: 0.7548 (t0) REVERT: B 422 ASP cc_start: 0.7916 (t0) cc_final: 0.7302 (t0) REVERT: B 489 SER cc_start: 0.8327 (t) cc_final: 0.7809 (p) REVERT: B 554 PHE cc_start: 0.8270 (m-80) cc_final: 0.7997 (m-80) REVERT: B 782 MET cc_start: 0.8373 (tpt) cc_final: 0.7870 (tpt) REVERT: B 784 LYS cc_start: 0.8050 (pptt) cc_final: 0.7674 (pptt) REVERT: B 811 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7616 (ttp80) REVERT: B 836 LYS cc_start: 0.8067 (mtpp) cc_final: 0.7786 (mtpp) REVERT: B 883 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8190 (mm) REVERT: B 965 MET cc_start: 0.5236 (tpt) cc_final: 0.4762 (tpt) REVERT: B 1054 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.4896 (tt0) REVERT: B 1091 LYS cc_start: 0.6979 (tttm) cc_final: 0.6358 (tttt) REVERT: A 210 ARG cc_start: 0.7520 (mtm110) cc_final: 0.6903 (mtm110) REVERT: A 273 ASP cc_start: 0.7779 (m-30) cc_final: 0.7263 (m-30) REVERT: A 288 ARG cc_start: 0.8471 (tpt-90) cc_final: 0.8172 (tpt90) REVERT: A 303 ASP cc_start: 0.7212 (t70) cc_final: 0.6959 (t0) REVERT: A 378 PHE cc_start: 0.8098 (t80) cc_final: 0.7828 (t80) REVERT: A 422 ASP cc_start: 0.7735 (t0) cc_final: 0.7368 (t0) REVERT: A 435 GLN cc_start: 0.7406 (mp10) cc_final: 0.6870 (mp10) REVERT: A 470 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6993 (mm-30) REVERT: A 573 MET cc_start: 0.7858 (mmm) cc_final: 0.7405 (tpp) REVERT: A 811 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7479 (ttp80) REVERT: A 878 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7481 (mt-10) REVERT: A 881 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: A 904 LYS cc_start: 0.7646 (ttmm) cc_final: 0.7338 (mttm) REVERT: A 1072 MET cc_start: 0.7436 (ppp) cc_final: 0.7003 (ptt) outliers start: 74 outliers final: 59 residues processed: 443 average time/residue: 0.3245 time to fit residues: 204.9669 Evaluate side-chains 455 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 393 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 125 ILE 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 209 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 287 VAL 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 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 771 GLU 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 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 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 240 MET 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 483 THR Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU 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 953 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1064 ILE 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 92 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.148286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131854 restraints weight = 20358.789| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.69 r_work: 0.3549 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 13852 Z= 0.276 Angle : 0.651 10.629 18707 Z= 0.328 Chirality : 0.045 0.332 2134 Planarity : 0.005 0.060 2385 Dihedral : 5.221 69.290 1925 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.37 % Allowed : 27.58 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1704 helix: 1.09 (0.20), residues: 638 sheet: 0.22 (0.29), residues: 351 loop : -0.54 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 521 HIS 0.006 0.001 HIS A1049 PHE 0.035 0.002 PHE A1111 TYR 0.025 0.002 TYR B1006 ARG 0.014 0.001 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 633) hydrogen bonds : angle 4.99457 ( 1803) covalent geometry : bond 0.00626 (13850) covalent geometry : angle 0.65118 (18707) Misc. bond : bond 0.00274 ( 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 490 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 410 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7913 (mtpp) REVERT: B 373 ASN cc_start: 0.7772 (t0) cc_final: 0.7550 (t0) REVERT: B 408 MET cc_start: 0.7519 (mmm) cc_final: 0.7268 (tpp) REVERT: B 422 ASP cc_start: 0.8020 (t0) cc_final: 0.7453 (t0) REVERT: B 538 ASP cc_start: 0.7963 (p0) cc_final: 0.7585 (p0) REVERT: B 554 PHE cc_start: 0.8348 (m-80) cc_final: 0.8146 (m-80) REVERT: B 782 MET cc_start: 0.8462 (tpt) cc_final: 0.8044 (tpt) REVERT: B 784 LYS cc_start: 0.8076 (pptt) cc_final: 0.7729 (pptt) REVERT: B 811 ARG cc_start: 0.7927 (ttp-170) cc_final: 0.7559 (mtp-110) REVERT: B 836 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7606 (mtpp) REVERT: B 883 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8212 (mm) REVERT: B 924 THR cc_start: 0.4640 (OUTLIER) cc_final: 0.3811 (p) REVERT: B 1054 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.5099 (tt0) REVERT: B 1091 LYS cc_start: 0.7245 (tttm) cc_final: 0.6623 (tttt) REVERT: B 1108 LYS cc_start: 0.6913 (mmmt) cc_final: 0.6713 (mmmm) REVERT: A 157 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 210 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6941 (mtm110) REVERT: A 273 ASP cc_start: 0.7866 (m-30) cc_final: 0.7339 (m-30) REVERT: A 422 ASP cc_start: 0.7825 (t0) cc_final: 0.7428 (t0) REVERT: A 435 GLN cc_start: 0.7388 (mp10) cc_final: 0.6858 (mp10) REVERT: A 470 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6962 (mm-30) REVERT: A 495 PHE cc_start: 0.8829 (t80) cc_final: 0.8615 (t80) REVERT: A 569 LYS cc_start: 0.7986 (mptm) cc_final: 0.7752 (mptm) REVERT: A 878 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 881 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: A 949 ASP cc_start: 0.6645 (m-30) cc_final: 0.6309 (m-30) REVERT: A 1072 MET cc_start: 0.7509 (ppp) cc_final: 0.7182 (ptm) outliers start: 80 outliers final: 56 residues processed: 446 average time/residue: 0.2930 time to fit residues: 181.8772 Evaluate side-chains 461 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 399 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 TYR 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 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 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 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 847 LYS Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain B residue 883 LEU 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 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 240 MET 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 483 THR Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU 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 966 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1064 ILE 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 61 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 163 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** 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 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 = 0.3948 r_free = 0.3948 target = 0.152151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135883 restraints weight = 20349.228| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.66 r_work: 0.3607 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13852 Z= 0.126 Angle : 0.590 12.571 18707 Z= 0.290 Chirality : 0.041 0.300 2134 Planarity : 0.004 0.054 2385 Dihedral : 4.778 56.975 1925 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.43 % Allowed : 28.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1704 helix: 1.37 (0.21), residues: 632 sheet: 0.15 (0.29), residues: 360 loop : -0.47 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 521 HIS 0.005 0.001 HIS A1059 PHE 0.018 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.012 0.000 ARG B 512 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 633) hydrogen bonds : angle 4.72971 ( 1803) covalent geometry : bond 0.00288 (13850) covalent geometry : angle 0.58971 (18707) Misc. bond : bond 0.00121 ( 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 470 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 404 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7921 (mtpp) REVERT: B 251 GLU cc_start: 0.7840 (tt0) cc_final: 0.7591 (tt0) REVERT: B 373 ASN cc_start: 0.7802 (t0) cc_final: 0.7575 (t0) REVERT: B 403 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6930 (mp0) REVERT: B 408 MET cc_start: 0.7577 (mmm) cc_final: 0.7296 (tpp) REVERT: B 422 ASP cc_start: 0.7934 (t0) cc_final: 0.7361 (t0) REVERT: B 489 SER cc_start: 0.8320 (t) cc_final: 0.7842 (p) REVERT: B 538 ASP cc_start: 0.7902 (p0) cc_final: 0.7557 (p0) REVERT: B 554 PHE cc_start: 0.8319 (m-80) cc_final: 0.8113 (m-80) REVERT: B 784 LYS cc_start: 0.8041 (pptt) cc_final: 0.7679 (pptt) REVERT: B 807 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7907 (tmtt) REVERT: B 811 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7533 (mtp-110) REVERT: B 836 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7767 (mtpp) REVERT: B 883 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8185 (mm) REVERT: B 924 THR cc_start: 0.4679 (OUTLIER) cc_final: 0.3865 (p) REVERT: B 965 MET cc_start: 0.5318 (tpt) cc_final: 0.4975 (tpt) REVERT: B 1054 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.4995 (tt0) REVERT: B 1091 LYS cc_start: 0.7037 (tttm) cc_final: 0.6417 (tttt) REVERT: A 210 ARG cc_start: 0.7522 (mtm110) cc_final: 0.6895 (mtm110) REVERT: A 288 ARG cc_start: 0.8470 (tpt-90) cc_final: 0.8161 (tpt90) REVERT: A 378 PHE cc_start: 0.8126 (t80) cc_final: 0.7839 (t80) REVERT: A 422 ASP cc_start: 0.7761 (t0) cc_final: 0.7434 (t0) REVERT: A 435 GLN cc_start: 0.7355 (mp10) cc_final: 0.6824 (mp10) REVERT: A 470 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6974 (mm-30) REVERT: A 569 LYS cc_start: 0.7821 (mptm) cc_final: 0.7569 (mptm) REVERT: A 573 MET cc_start: 0.7815 (tpp) cc_final: 0.7474 (tpp) REVERT: A 878 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 881 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: A 949 ASP cc_start: 0.6539 (m-30) cc_final: 0.6217 (m-30) REVERT: A 1072 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7076 (ptm) outliers start: 66 outliers final: 48 residues processed: 435 average time/residue: 0.3682 time to fit residues: 221.9076 Evaluate side-chains 454 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 401 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 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 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 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 771 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 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 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 240 MET 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 477 GLU Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU 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 942 LYS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1064 ILE 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 67 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 149 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** 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 980 GLN A1013 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136223 restraints weight = 20294.500| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.67 r_work: 0.3616 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13852 Z= 0.119 Angle : 0.593 12.647 18707 Z= 0.289 Chirality : 0.041 0.307 2134 Planarity : 0.004 0.060 2385 Dihedral : 4.508 42.998 1925 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.89 % Allowed : 29.66 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1704 helix: 1.50 (0.21), residues: 638 sheet: 0.20 (0.29), residues: 361 loop : -0.45 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 PHE 0.020 0.001 PHE A1111 TYR 0.016 0.001 TYR B 327 ARG 0.014 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 633) hydrogen bonds : angle 4.67279 ( 1803) covalent geometry : bond 0.00276 (13850) covalent geometry : angle 0.59288 (18707) Misc. bond : bond 0.00103 ( 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 463 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 405 time to evaluate : 3.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7944 (mtpp) REVERT: B 251 GLU cc_start: 0.7830 (tt0) cc_final: 0.7566 (tt0) REVERT: B 339 MET cc_start: 0.8163 (mpp) cc_final: 0.7586 (mpp) REVERT: B 373 ASN cc_start: 0.7799 (t0) cc_final: 0.7583 (t0) REVERT: B 408 MET cc_start: 0.7607 (mmm) cc_final: 0.7301 (tpp) REVERT: B 422 ASP cc_start: 0.7953 (t0) cc_final: 0.7498 (t0) REVERT: B 489 SER cc_start: 0.8362 (t) cc_final: 0.7892 (p) REVERT: B 538 ASP cc_start: 0.7898 (p0) cc_final: 0.7593 (p0) REVERT: B 554 PHE cc_start: 0.8293 (m-80) cc_final: 0.8063 (m-80) REVERT: B 784 LYS cc_start: 0.8065 (pptt) cc_final: 0.7695 (pptt) REVERT: B 807 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7845 (tmtt) REVERT: B 811 ARG cc_start: 0.7869 (ttp-170) cc_final: 0.7610 (mtp-110) REVERT: B 836 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7784 (mtpp) REVERT: B 883 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8213 (mm) REVERT: B 920 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6423 (mmm) REVERT: B 924 THR cc_start: 0.4631 (OUTLIER) cc_final: 0.3785 (p) REVERT: B 965 MET cc_start: 0.5315 (tpt) cc_final: 0.4929 (tpt) REVERT: B 1054 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.5101 (tt0) REVERT: B 1091 LYS cc_start: 0.6992 (tttm) cc_final: 0.6375 (tttt) REVERT: A 210 ARG cc_start: 0.7554 (mtm110) cc_final: 0.6975 (mtm110) REVERT: A 273 ASP cc_start: 0.7831 (m-30) cc_final: 0.7310 (m-30) REVERT: A 288 ARG cc_start: 0.8462 (tpt-90) cc_final: 0.8153 (tpt90) REVERT: A 317 LEU cc_start: 0.8788 (mp) cc_final: 0.8580 (mt) REVERT: A 378 PHE cc_start: 0.8120 (t80) cc_final: 0.7826 (t80) REVERT: A 422 ASP cc_start: 0.7779 (t0) cc_final: 0.7420 (t0) REVERT: A 435 GLN cc_start: 0.7354 (mp10) cc_final: 0.6816 (mp10) REVERT: A 470 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6920 (mm-30) REVERT: A 495 PHE cc_start: 0.8831 (t80) cc_final: 0.8576 (t80) REVERT: A 569 LYS cc_start: 0.7824 (mptm) cc_final: 0.7596 (mptm) REVERT: A 573 MET cc_start: 0.7788 (tpp) cc_final: 0.7464 (tpp) REVERT: A 878 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7529 (mt-10) REVERT: A 881 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: A 904 LYS cc_start: 0.7697 (ttmm) cc_final: 0.7407 (mttm) REVERT: A 949 ASP cc_start: 0.6544 (m-30) cc_final: 0.6170 (m-30) REVERT: A 1021 LEU cc_start: 0.8223 (tp) cc_final: 0.8013 (tp) REVERT: A 1072 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7060 (ptm) outliers start: 58 outliers final: 48 residues processed: 434 average time/residue: 0.4605 time to fit residues: 286.4212 Evaluate side-chains 453 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 399 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 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 439 ILE Chi-restraints excluded: chain B residue 462 THR 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 771 GLU 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 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 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 240 MET 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 477 GLU Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU 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 942 LYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1064 ILE 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 40 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 0.0060 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** 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 = 0.3946 r_free = 0.3946 target = 0.152088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135853 restraints weight = 20318.062| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.65 r_work: 0.3606 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13852 Z= 0.142 Angle : 0.606 12.149 18707 Z= 0.296 Chirality : 0.042 0.319 2134 Planarity : 0.004 0.068 2385 Dihedral : 4.510 36.056 1925 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.09 % Allowed : 29.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1704 helix: 1.43 (0.21), residues: 640 sheet: 0.24 (0.29), residues: 360 loop : -0.46 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 PHE 0.025 0.002 PHE A1111 TYR 0.016 0.001 TYR B 327 ARG 0.016 0.001 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 633) hydrogen bonds : angle 4.68515 ( 1803) covalent geometry : bond 0.00328 (13850) covalent geometry : angle 0.60571 (18707) Misc. bond : bond 0.00135 ( 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 457 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 396 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 SER cc_start: 0.4394 (OUTLIER) cc_final: 0.4174 (p) REVERT: B 206 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7903 (mtpp) REVERT: B 251 GLU cc_start: 0.7831 (tt0) cc_final: 0.7570 (tt0) REVERT: B 339 MET cc_start: 0.8167 (mpp) cc_final: 0.7561 (mpp) REVERT: B 373 ASN cc_start: 0.7783 (t0) cc_final: 0.7566 (t0) REVERT: B 408 MET cc_start: 0.7615 (mmm) cc_final: 0.7304 (tpp) REVERT: B 412 ASN cc_start: 0.8003 (m-40) cc_final: 0.7590 (t0) REVERT: B 422 ASP cc_start: 0.7956 (t0) cc_final: 0.7391 (t0) REVERT: B 489 SER cc_start: 0.8321 (t) cc_final: 0.7848 (p) REVERT: B 538 ASP cc_start: 0.7915 (p0) cc_final: 0.7614 (p0) REVERT: B 554 PHE cc_start: 0.8296 (m-80) cc_final: 0.8055 (m-80) REVERT: B 782 MET cc_start: 0.8385 (tpt) cc_final: 0.7943 (tpt) REVERT: B 784 LYS cc_start: 0.8070 (pptt) cc_final: 0.7684 (pptt) REVERT: B 807 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7837 (tmtt) REVERT: B 811 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7516 (mtp-110) REVERT: B 836 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7769 (mtpp) REVERT: B 883 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8206 (mm) REVERT: B 920 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6442 (mmm) REVERT: B 924 THR cc_start: 0.4679 (OUTLIER) cc_final: 0.3834 (p) REVERT: B 965 MET cc_start: 0.5327 (tpt) cc_final: 0.4937 (tpt) REVERT: B 1054 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.5058 (tt0) REVERT: B 1091 LYS cc_start: 0.7042 (tttm) cc_final: 0.6417 (tttt) REVERT: A 210 ARG cc_start: 0.7544 (mtm110) cc_final: 0.6953 (mtm110) REVERT: A 288 ARG cc_start: 0.8501 (tpt-90) cc_final: 0.8190 (tpt90) REVERT: A 422 ASP cc_start: 0.7782 (t0) cc_final: 0.7454 (t0) REVERT: A 435 GLN cc_start: 0.7371 (mp10) cc_final: 0.6835 (mp10) REVERT: A 495 PHE cc_start: 0.8790 (t80) cc_final: 0.8554 (t80) REVERT: A 569 LYS cc_start: 0.7824 (mptm) cc_final: 0.7590 (mptm) REVERT: A 573 MET cc_start: 0.7811 (tpp) cc_final: 0.7498 (tpp) REVERT: A 878 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7569 (mt-10) REVERT: A 881 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: A 904 LYS cc_start: 0.7704 (ttmm) cc_final: 0.7405 (mttm) REVERT: A 949 ASP cc_start: 0.6644 (m-30) cc_final: 0.6277 (m-30) REVERT: A 1021 LEU cc_start: 0.8286 (tp) cc_final: 0.8057 (tp) REVERT: A 1072 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7108 (ptm) outliers start: 61 outliers final: 48 residues processed: 427 average time/residue: 0.3063 time to fit residues: 181.5907 Evaluate side-chains 454 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 399 time to evaluate : 2.353 ------------------------------------------------------------------------------- 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 171 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 209 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 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 771 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 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 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 240 MET 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 477 GLU Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU 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 942 LYS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1064 ILE 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 73 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.150535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134275 restraints weight = 20449.896| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.67 r_work: 0.3582 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13852 Z= 0.179 Angle : 0.632 12.254 18707 Z= 0.311 Chirality : 0.043 0.315 2134 Planarity : 0.004 0.066 2385 Dihedral : 4.630 32.334 1925 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.09 % Allowed : 30.00 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1704 helix: 1.31 (0.21), residues: 636 sheet: 0.18 (0.29), residues: 351 loop : -0.51 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 521 HIS 0.006 0.001 HIS A1059 PHE 0.035 0.002 PHE A1111 TYR 0.021 0.002 TYR A1102 ARG 0.015 0.001 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 633) hydrogen bonds : angle 4.78135 ( 1803) covalent geometry : bond 0.00413 (13850) covalent geometry : angle 0.63188 (18707) Misc. bond : bond 0.00176 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7810.01 seconds wall clock time: 138 minutes 10.01 seconds (8290.01 seconds total)