Starting phenix.real_space_refine on Mon Dec 30 19:26:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f5z_28869/12_2024/8f5z_28869.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f5z_28869/12_2024/8f5z_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_28869/12_2024/8f5z_28869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f5z_28869/12_2024/8f5z_28869.map" model { file = "/net/cci-nas-00/data/ceres_data/8f5z_28869/12_2024/8f5z_28869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f5z_28869/12_2024/8f5z_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.49, per 1000 atoms: 0.62 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: 3.53 Conformation dependent library (CDL) restraints added in 2.0 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: 1.68 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: 5.80 Time building geometry restraints manager: 4.07 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: 1.850 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.890 Find NCS groups from input model: 0.640 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- 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 13850 Z= 0.223 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 *********************** 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 : 1.623 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: 0.3131 time to fit residues: 174.8100 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 : 1.685 ------------------------------------------------------------------------------- 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: 10.0000 chunk 72 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 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: 0.8380 ------------------------------------------------------------------------------- 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 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13850 Z= 0.240 Angle : 0.585 11.390 18707 Z= 0.299 Chirality : 0.042 0.176 2134 Planarity : 0.005 0.083 2385 Dihedral : 5.727 88.678 1938 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.96 % Allowed : 27.32 % Favored : 68.72 % 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: 0.27 (0.21), residues: 1704 helix: 0.97 (0.20), residues: 639 sheet: 0.18 (0.29), residues: 357 loop : -0.46 (0.24), residues: 708 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 0.027 0.002 PHE A1111 TYR 0.016 0.001 TYR B 327 ARG 0.008 0.000 ARG A 547 *********************** 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 464 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 405 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: B 339 MET cc_start: 0.8394 (mpp) cc_final: 0.7912 (mpp) REVERT: B 373 ASN cc_start: 0.8157 (t0) cc_final: 0.7830 (t0) REVERT: B 408 MET cc_start: 0.7548 (mmm) cc_final: 0.7245 (mmm) REVERT: B 518 MET cc_start: 0.7923 (ptp) cc_final: 0.7692 (mtm) REVERT: B 538 ASP cc_start: 0.7751 (p0) cc_final: 0.7546 (p0) REVERT: B 784 LYS cc_start: 0.8121 (pptt) cc_final: 0.7883 (pptt) REVERT: B 836 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7767 (mtpp) REVERT: B 883 LEU cc_start: 0.8591 (mm) cc_final: 0.8329 (mm) REVERT: B 905 ARG cc_start: 0.7069 (ttm170) cc_final: 0.6818 (mtp180) REVERT: B 941 GLN cc_start: 0.7843 (mt0) cc_final: 0.7572 (mt0) REVERT: B 973 VAL cc_start: 0.7990 (p) cc_final: 0.7746 (t) REVERT: B 1091 LYS cc_start: 0.7390 (tttm) cc_final: 0.7018 (tttm) REVERT: A 210 ARG cc_start: 0.7497 (mtm110) cc_final: 0.7280 (mtm110) REVERT: A 229 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6844 (mm-30) REVERT: A 303 ASP cc_start: 0.7036 (t0) cc_final: 0.6808 (t70) REVERT: A 328 MET cc_start: 0.8154 (mtm) cc_final: 0.7858 (mtt) REVERT: A 422 ASP cc_start: 0.7752 (t0) cc_final: 0.7352 (t0) REVERT: A 435 GLN cc_start: 0.7369 (mp10) cc_final: 0.6950 (mp10) REVERT: A 446 ASP cc_start: 0.7522 (m-30) cc_final: 0.7292 (m-30) REVERT: A 877 HIS cc_start: 0.7375 (m90) cc_final: 0.6535 (m90) REVERT: A 881 GLN cc_start: 0.7839 (mp10) cc_final: 0.7353 (mp10) REVERT: A 949 ASP cc_start: 0.6614 (m-30) cc_final: 0.6281 (m-30) REVERT: A 977 SER cc_start: 0.8310 (p) cc_final: 0.7841 (p) REVERT: A 1091 LYS cc_start: 0.7536 (mttm) cc_final: 0.7220 (mttm) outliers start: 59 outliers final: 33 residues processed: 426 average time/residue: 0.3105 time to fit residues: 184.0155 Evaluate side-chains 433 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 400 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 181 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 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 855 VAL 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 86 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 129 optimal weight: 0.0050 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 156 optimal weight: 0.0030 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 155 optimal weight: 0.0670 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.1340 ------------------------------------------------------------------------------- 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 880 GLN ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 GLN A 980 GLN A1013 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13850 Z= 0.139 Angle : 0.509 9.431 18707 Z= 0.258 Chirality : 0.039 0.150 2134 Planarity : 0.004 0.060 2385 Dihedral : 4.917 87.427 1930 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.89 % Allowed : 27.79 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.54 (0.21), residues: 1704 helix: 1.43 (0.21), residues: 638 sheet: 0.17 (0.29), residues: 367 loop : -0.46 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 521 HIS 0.005 0.001 HIS B 877 PHE 0.015 0.001 PHE A1111 TYR 0.014 0.001 TYR B 327 ARG 0.009 0.000 ARG A 547 *********************** 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 458 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 400 time to evaluate : 1.616 Fit side-chains REVERT: B 206 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7731 (mtpp) REVERT: B 373 ASN cc_start: 0.8101 (t0) cc_final: 0.7842 (t0) REVERT: B 403 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7102 (mt-10) REVERT: B 408 MET cc_start: 0.7569 (mmm) cc_final: 0.7337 (tpp) REVERT: B 435 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7168 (mm-40) REVERT: B 538 ASP cc_start: 0.7844 (p0) cc_final: 0.7500 (p0) REVERT: B 554 PHE cc_start: 0.8303 (m-80) cc_final: 0.8001 (m-80) REVERT: B 784 LYS cc_start: 0.8126 (pptt) cc_final: 0.7861 (pptt) REVERT: B 811 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7415 (mtp-110) REVERT: B 815 GLN cc_start: 0.7876 (tp40) cc_final: 0.7461 (tp40) REVERT: B 836 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7831 (mtpp) REVERT: B 883 LEU cc_start: 0.8563 (mm) cc_final: 0.8201 (mm) REVERT: B 945 SER cc_start: 0.8400 (p) cc_final: 0.8148 (m) REVERT: B 946 LYS cc_start: 0.7822 (tppt) cc_final: 0.7617 (tppt) REVERT: B 967 GLU cc_start: 0.7986 (mp0) cc_final: 0.7459 (mm-30) REVERT: B 1082 GLU cc_start: 0.7016 (tp30) cc_final: 0.6688 (tp30) REVERT: B 1091 LYS cc_start: 0.7051 (tttm) cc_final: 0.6431 (tttt) REVERT: B 1116 GLU cc_start: 0.5979 (tm-30) cc_final: 0.5656 (tm-30) REVERT: A 130 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7817 (mtm110) REVERT: A 210 ARG cc_start: 0.7390 (mtm110) cc_final: 0.7095 (mtm180) REVERT: A 229 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6817 (mm-30) REVERT: A 232 GLU cc_start: 0.7229 (tt0) cc_final: 0.6817 (tt0) REVERT: A 422 ASP cc_start: 0.7734 (t0) cc_final: 0.7416 (t0) REVERT: A 435 GLN cc_start: 0.7389 (mp10) cc_final: 0.7023 (mp10) REVERT: A 446 ASP cc_start: 0.7555 (m-30) cc_final: 0.7353 (m-30) REVERT: A 495 PHE cc_start: 0.8721 (t80) cc_final: 0.8436 (t80) REVERT: A 497 ARG cc_start: 0.6231 (mmm160) cc_final: 0.5990 (mmm160) REVERT: A 815 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: A 877 HIS cc_start: 0.7399 (m90) cc_final: 0.6569 (m90) REVERT: A 881 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7259 (mp10) outliers start: 58 outliers final: 32 residues processed: 425 average time/residue: 0.3098 time to fit residues: 183.5572 Evaluate side-chains 417 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 383 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 171 ILE 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 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 968 PHE 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 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 815 GLN 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 1010 ILE Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 17 optimal weight: 0.0470 chunk 74 optimal weight: 0.0000 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 overall best weight: 0.3882 ------------------------------------------------------------------------------- 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 B1101 GLN ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN A1013 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13850 Z= 0.157 Angle : 0.523 9.846 18707 Z= 0.261 Chirality : 0.040 0.267 2134 Planarity : 0.004 0.048 2385 Dihedral : 4.759 85.141 1925 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.43 % Allowed : 27.32 % 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: 0.60 (0.21), residues: 1704 helix: 1.49 (0.21), residues: 640 sheet: 0.28 (0.28), residues: 372 loop : -0.51 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 521 HIS 0.003 0.001 HIS A1059 PHE 0.019 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.005 0.000 ARG A 547 *********************** 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 477 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 411 time to evaluate : 1.680 Fit side-chains revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7757 (mtpp) REVERT: B 279 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7934 (mtm-85) REVERT: B 373 ASN cc_start: 0.8156 (t0) cc_final: 0.7873 (t0) REVERT: B 403 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7147 (mt-10) REVERT: B 408 MET cc_start: 0.7589 (mmm) cc_final: 0.7287 (tpp) REVERT: B 412 ASN cc_start: 0.8028 (m-40) cc_final: 0.7621 (t0) REVERT: B 422 ASP cc_start: 0.7908 (t0) cc_final: 0.7274 (t0) REVERT: B 538 ASP cc_start: 0.7855 (p0) cc_final: 0.7470 (p0) REVERT: B 554 PHE cc_start: 0.8322 (m-80) cc_final: 0.7987 (m-80) REVERT: B 782 MET cc_start: 0.8485 (tpt) cc_final: 0.7898 (tpt) REVERT: B 784 LYS cc_start: 0.8122 (pptt) cc_final: 0.7738 (pptt) REVERT: B 811 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7401 (ttp80) REVERT: B 815 GLN cc_start: 0.8041 (tp40) cc_final: 0.7611 (tp40) REVERT: B 836 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7837 (mtpp) REVERT: B 883 LEU cc_start: 0.8558 (mm) cc_final: 0.8223 (mm) REVERT: B 931 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6934 (mtt180) REVERT: B 945 SER cc_start: 0.8417 (p) cc_final: 0.8122 (m) REVERT: B 967 GLU cc_start: 0.8039 (mp0) cc_final: 0.7398 (mm-30) REVERT: B 1054 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.5108 (tt0) REVERT: B 1082 GLU cc_start: 0.7066 (tp30) cc_final: 0.6661 (tp30) REVERT: B 1091 LYS cc_start: 0.7123 (tttm) cc_final: 0.6508 (tttt) REVERT: A 210 ARG cc_start: 0.7353 (mtm110) cc_final: 0.7152 (mtm180) REVERT: A 229 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6753 (mm-30) REVERT: A 303 ASP cc_start: 0.7106 (t0) cc_final: 0.6869 (t70) REVERT: A 378 PHE cc_start: 0.8033 (t80) cc_final: 0.7796 (t80) REVERT: A 422 ASP cc_start: 0.7783 (t0) cc_final: 0.7382 (t0) REVERT: A 446 ASP cc_start: 0.7586 (m-30) cc_final: 0.7362 (m-30) REVERT: A 497 ARG cc_start: 0.6304 (mmm160) cc_final: 0.6008 (mmm160) REVERT: A 811 ARG cc_start: 0.7793 (ttp-110) cc_final: 0.7398 (ttp80) REVERT: A 815 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: A 881 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: A 988 LYS cc_start: 0.6954 (mmmt) cc_final: 0.6239 (mmtm) REVERT: A 1072 MET cc_start: 0.7537 (ppp) cc_final: 0.6892 (ptt) outliers start: 66 outliers final: 41 residues processed: 440 average time/residue: 0.3084 time to fit residues: 189.4236 Evaluate side-chains 437 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 393 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 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 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 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 789 LYS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 815 GLN 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 944 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.0070 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 123 optimal weight: 0.0670 chunk 68 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 577 HIS A1014 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13850 Z= 0.195 Angle : 0.538 9.821 18707 Z= 0.268 Chirality : 0.041 0.297 2134 Planarity : 0.004 0.042 2385 Dihedral : 4.776 77.956 1925 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.83 % Allowed : 28.39 % Favored : 67.79 % 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: 0.65 (0.21), residues: 1704 helix: 1.47 (0.21), residues: 640 sheet: 0.29 (0.29), residues: 364 loop : -0.39 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 521 HIS 0.004 0.001 HIS A1059 PHE 0.020 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.008 0.000 ARG B 512 *********************** 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 465 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 408 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7755 (mtpp) REVERT: B 279 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: B 373 ASN cc_start: 0.8103 (t0) cc_final: 0.7835 (t0) REVERT: B 403 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7145 (mt-10) REVERT: B 408 MET cc_start: 0.7585 (mmm) cc_final: 0.7302 (tpp) REVERT: B 422 ASP cc_start: 0.7940 (t0) cc_final: 0.7298 (t0) REVERT: B 489 SER cc_start: 0.8304 (t) cc_final: 0.7801 (p) REVERT: B 554 PHE cc_start: 0.8348 (m-80) cc_final: 0.8015 (m-80) REVERT: B 782 MET cc_start: 0.8506 (tpt) cc_final: 0.7928 (tpt) REVERT: B 784 LYS cc_start: 0.8134 (pptt) cc_final: 0.7755 (pptt) REVERT: B 811 ARG cc_start: 0.7667 (ttt180) cc_final: 0.7424 (ttp80) REVERT: B 836 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7746 (mtpp) REVERT: B 852 LEU cc_start: 0.8439 (mt) cc_final: 0.7915 (mt) REVERT: B 883 LEU cc_start: 0.8549 (mm) cc_final: 0.8222 (mm) REVERT: B 905 ARG cc_start: 0.7016 (ttm170) cc_final: 0.6753 (mtp180) REVERT: B 1054 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.5056 (tt0) REVERT: B 1086 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7584 (tp) REVERT: B 1091 LYS cc_start: 0.7141 (tttm) cc_final: 0.6513 (tttt) REVERT: A 210 ARG cc_start: 0.7444 (mtm110) cc_final: 0.7205 (mtm110) REVERT: A 229 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6700 (mm-30) REVERT: A 378 PHE cc_start: 0.8145 (t80) cc_final: 0.7823 (t80) REVERT: A 422 ASP cc_start: 0.7802 (t0) cc_final: 0.7394 (t0) REVERT: A 435 GLN cc_start: 0.7479 (mp10) cc_final: 0.7005 (mp10) REVERT: A 446 ASP cc_start: 0.7582 (m-30) cc_final: 0.7373 (m-30) REVERT: A 497 ARG cc_start: 0.6385 (mmm160) cc_final: 0.6051 (mmm160) REVERT: A 878 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7383 (mt-10) REVERT: A 881 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: A 904 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7358 (mttm) REVERT: A 1072 MET cc_start: 0.7541 (ppp) cc_final: 0.7011 (ptt) outliers start: 57 outliers final: 44 residues processed: 430 average time/residue: 0.3153 time to fit residues: 188.7880 Evaluate side-chains 452 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 405 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 287 VAL 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 501 LEU 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 847 LYS 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 1086 LEU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1092 LEU 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 55 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 77 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 160 optimal weight: 1.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- 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 ** B 906 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13850 Z= 0.147 Angle : 0.525 9.863 18707 Z= 0.260 Chirality : 0.040 0.273 2134 Planarity : 0.004 0.047 2385 Dihedral : 4.599 66.302 1925 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.96 % Allowed : 28.72 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.21), residues: 1704 helix: 1.59 (0.21), residues: 642 sheet: 0.34 (0.29), residues: 366 loop : -0.42 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 521 HIS 0.003 0.001 HIS A1059 PHE 0.017 0.001 PHE A1111 TYR 0.014 0.001 TYR B 327 ARG 0.012 0.000 ARG A 547 *********************** 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 460 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 401 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7768 (mtpp) REVERT: B 279 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: B 373 ASN cc_start: 0.8108 (t0) cc_final: 0.7792 (t0) REVERT: B 403 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7151 (mt-10) REVERT: B 408 MET cc_start: 0.7581 (mmm) cc_final: 0.7261 (tpp) REVERT: B 412 ASN cc_start: 0.8016 (m-40) cc_final: 0.7638 (t0) REVERT: B 422 ASP cc_start: 0.7946 (t0) cc_final: 0.7310 (t0) REVERT: B 489 SER cc_start: 0.8318 (t) cc_final: 0.7799 (p) REVERT: B 554 PHE cc_start: 0.8291 (m-80) cc_final: 0.7966 (m-80) REVERT: B 782 MET cc_start: 0.8464 (tpt) cc_final: 0.7924 (tpt) REVERT: B 784 LYS cc_start: 0.8118 (pptt) cc_final: 0.7735 (pptt) REVERT: B 807 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7749 (tmtt) REVERT: B 811 ARG cc_start: 0.7647 (ttt180) cc_final: 0.7413 (ttp80) REVERT: B 836 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7820 (mtpp) REVERT: B 883 LEU cc_start: 0.8516 (mm) cc_final: 0.8221 (mm) REVERT: B 920 MET cc_start: 0.6762 (mtm) cc_final: 0.6516 (mmm) REVERT: B 945 SER cc_start: 0.8389 (p) cc_final: 0.8097 (m) REVERT: B 965 MET cc_start: 0.5163 (tpt) cc_final: 0.4711 (tpt) REVERT: B 1054 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.5045 (tt0) REVERT: B 1091 LYS cc_start: 0.7071 (tttm) cc_final: 0.6449 (tttt) REVERT: A 229 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6515 (mm-30) REVERT: A 378 PHE cc_start: 0.8069 (t80) cc_final: 0.7810 (t80) REVERT: A 422 ASP cc_start: 0.7782 (t0) cc_final: 0.7413 (t0) REVERT: A 435 GLN cc_start: 0.7514 (mp10) cc_final: 0.6951 (mp10) REVERT: A 446 ASP cc_start: 0.7599 (m-30) cc_final: 0.7386 (m-30) REVERT: A 470 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6854 (mm-30) REVERT: A 497 ARG cc_start: 0.6378 (mmm160) cc_final: 0.5998 (mmm160) REVERT: A 815 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: A 878 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7382 (mt-10) REVERT: A 881 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: A 884 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7438 (m-70) REVERT: A 988 LYS cc_start: 0.6822 (mmmt) cc_final: 0.5812 (mmtm) REVERT: A 1072 MET cc_start: 0.7504 (ppp) cc_final: 0.7021 (ptt) outliers start: 59 outliers final: 45 residues processed: 425 average time/residue: 0.3243 time to fit residues: 191.3515 Evaluate side-chains 443 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 394 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 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 232 GLU 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 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 501 LEU Chi-restraints excluded: chain B residue 560 VAL 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 795 ASP Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 246 GLU 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 801 GLU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1092 LEU 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 18 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 overall best weight: 0.5456 ------------------------------------------------------------------------------- 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 ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 980 GLN A1013 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13850 Z= 0.179 Angle : 0.546 11.924 18707 Z= 0.268 Chirality : 0.040 0.286 2134 Planarity : 0.004 0.044 2385 Dihedral : 4.565 58.286 1925 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.63 % Allowed : 28.52 % Favored : 66.85 % 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: 0.69 (0.21), residues: 1704 helix: 1.55 (0.21), residues: 640 sheet: 0.33 (0.29), residues: 364 loop : -0.43 (0.24), residues: 700 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 0.010 0.000 ARG A 547 *********************** 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 479 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 410 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7738 (mtpp) REVERT: B 339 MET cc_start: 0.8473 (mtm) cc_final: 0.8231 (mtm) REVERT: B 373 ASN cc_start: 0.8156 (t0) cc_final: 0.7864 (t0) REVERT: B 403 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7152 (mt-10) REVERT: B 408 MET cc_start: 0.7580 (mmm) cc_final: 0.7267 (tpp) REVERT: B 412 ASN cc_start: 0.8011 (m-40) cc_final: 0.7620 (t0) REVERT: B 422 ASP cc_start: 0.7980 (t0) cc_final: 0.7363 (t0) REVERT: B 489 SER cc_start: 0.8325 (t) cc_final: 0.7820 (p) REVERT: B 554 PHE cc_start: 0.8302 (m-80) cc_final: 0.7990 (m-80) REVERT: B 782 MET cc_start: 0.8499 (tpt) cc_final: 0.7974 (tpt) REVERT: B 784 LYS cc_start: 0.8132 (pptt) cc_final: 0.7738 (pptt) REVERT: B 811 ARG cc_start: 0.7676 (ttt180) cc_final: 0.7402 (ttp80) REVERT: B 836 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7711 (mtpp) REVERT: B 852 LEU cc_start: 0.8468 (mt) cc_final: 0.7828 (mt) REVERT: B 883 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8233 (mm) REVERT: B 905 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6713 (mtp85) REVERT: B 920 MET cc_start: 0.6736 (mtm) cc_final: 0.6483 (mmm) REVERT: B 945 SER cc_start: 0.8400 (p) cc_final: 0.8112 (m) REVERT: B 965 MET cc_start: 0.5176 (tpt) cc_final: 0.4745 (tpt) REVERT: B 1054 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.5090 (tt0) REVERT: B 1091 LYS cc_start: 0.7151 (tttm) cc_final: 0.6566 (tttt) REVERT: A 210 ARG cc_start: 0.7317 (mtm180) cc_final: 0.6809 (mtm110) REVERT: A 288 ARG cc_start: 0.8463 (tpt-90) cc_final: 0.8138 (tpt90) REVERT: A 378 PHE cc_start: 0.8157 (t80) cc_final: 0.7873 (t80) REVERT: A 422 ASP cc_start: 0.7798 (t0) cc_final: 0.7432 (t0) REVERT: A 435 GLN cc_start: 0.7562 (mp10) cc_final: 0.6982 (mp10) REVERT: A 446 ASP cc_start: 0.7600 (m-30) cc_final: 0.7365 (m-30) REVERT: A 470 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6885 (mm-30) REVERT: A 497 ARG cc_start: 0.6395 (mmm160) cc_final: 0.6020 (mmm160) REVERT: A 878 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 881 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: A 884 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.7453 (m-70) REVERT: A 904 LYS cc_start: 0.7674 (ttmm) cc_final: 0.7351 (mttm) REVERT: A 988 LYS cc_start: 0.6920 (mmmt) cc_final: 0.6156 (mmtm) REVERT: A 1072 MET cc_start: 0.7548 (ppp) cc_final: 0.7113 (ptt) outliers start: 69 outliers final: 51 residues processed: 438 average time/residue: 0.3198 time to fit residues: 193.9240 Evaluate side-chains 455 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 400 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 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 287 VAL Chi-restraints excluded: chain B residue 299 ARG 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 501 LEU 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 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 246 GLU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU 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 801 GLU Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1092 LEU 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 99 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 105 optimal weight: 0.4980 chunk 112 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 158 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 0.044 13850 Z= 0.177 Angle : 0.557 12.208 18707 Z= 0.273 Chirality : 0.040 0.292 2134 Planarity : 0.004 0.079 2385 Dihedral : 4.449 54.715 1925 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.30 % Allowed : 28.93 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.21), residues: 1704 helix: 1.60 (0.21), residues: 634 sheet: 0.37 (0.29), residues: 364 loop : -0.48 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 521 HIS 0.003 0.001 HIS A1059 PHE 0.020 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.015 0.000 ARG A 547 *********************** 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 463 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 399 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7732 (mtpp) REVERT: B 339 MET cc_start: 0.8447 (mtm) cc_final: 0.8216 (mtm) REVERT: B 373 ASN cc_start: 0.8158 (t0) cc_final: 0.7896 (t0) REVERT: B 403 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7144 (mt-10) REVERT: B 408 MET cc_start: 0.7573 (mmm) cc_final: 0.7260 (tpp) REVERT: B 412 ASN cc_start: 0.8031 (m-40) cc_final: 0.7650 (t0) REVERT: B 422 ASP cc_start: 0.7990 (t0) cc_final: 0.7375 (t0) REVERT: B 489 SER cc_start: 0.8331 (t) cc_final: 0.7832 (p) REVERT: B 508 MET cc_start: 0.7519 (ttp) cc_final: 0.7224 (ttp) REVERT: B 554 PHE cc_start: 0.8287 (m-80) cc_final: 0.7975 (m-80) REVERT: B 584 ARG cc_start: 0.7422 (mtm180) cc_final: 0.7194 (mtm180) REVERT: B 782 MET cc_start: 0.8494 (tpt) cc_final: 0.8019 (tpt) REVERT: B 784 LYS cc_start: 0.8132 (pptt) cc_final: 0.7743 (pptt) REVERT: B 807 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7763 (tmtt) REVERT: B 811 ARG cc_start: 0.7671 (ttt180) cc_final: 0.7400 (ttp80) REVERT: B 836 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7796 (mtpp) REVERT: B 852 LEU cc_start: 0.8462 (mt) cc_final: 0.7839 (mt) REVERT: B 883 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8245 (mm) REVERT: B 905 ARG cc_start: 0.7011 (ttm170) cc_final: 0.6709 (mtp180) REVERT: B 906 GLN cc_start: 0.7462 (tp40) cc_final: 0.7185 (tt0) REVERT: B 920 MET cc_start: 0.6734 (mtm) cc_final: 0.6483 (mmm) REVERT: B 924 THR cc_start: 0.4670 (OUTLIER) cc_final: 0.3843 (p) REVERT: B 965 MET cc_start: 0.5185 (tpt) cc_final: 0.4814 (tpt) REVERT: B 1054 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.5413 (tt0) REVERT: B 1091 LYS cc_start: 0.7146 (tttm) cc_final: 0.6529 (tttt) REVERT: A 210 ARG cc_start: 0.7353 (mtm180) cc_final: 0.6836 (mtm110) REVERT: A 378 PHE cc_start: 0.8156 (t80) cc_final: 0.7866 (t80) REVERT: A 422 ASP cc_start: 0.7785 (t0) cc_final: 0.7414 (t0) REVERT: A 435 GLN cc_start: 0.7570 (mp10) cc_final: 0.7004 (mp10) REVERT: A 446 ASP cc_start: 0.7590 (m-30) cc_final: 0.7357 (m-30) REVERT: A 470 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6900 (mm-30) REVERT: A 497 ARG cc_start: 0.6407 (mmm160) cc_final: 0.5999 (mmm160) REVERT: A 573 MET cc_start: 0.7777 (tpp) cc_final: 0.7505 (tpp) REVERT: A 878 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 881 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: A 904 LYS cc_start: 0.7677 (ttmm) cc_final: 0.7343 (mttm) REVERT: A 949 ASP cc_start: 0.6665 (m-30) cc_final: 0.6281 (m-30) REVERT: A 988 LYS cc_start: 0.6868 (mmmt) cc_final: 0.6091 (mmtm) REVERT: A 1021 LEU cc_start: 0.8188 (tp) cc_final: 0.7961 (tp) REVERT: A 1072 MET cc_start: 0.7530 (ppp) cc_final: 0.7113 (ptm) outliers start: 64 outliers final: 52 residues processed: 426 average time/residue: 0.3198 time to fit residues: 187.1227 Evaluate side-chains 460 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 404 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 ARG 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 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 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 881 GLN 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 246 GLU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU 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 801 GLU Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1092 LEU 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 154 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ** B 941 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13850 Z= 0.176 Angle : 0.570 12.512 18707 Z= 0.277 Chirality : 0.040 0.292 2134 Planarity : 0.004 0.075 2385 Dihedral : 4.378 49.123 1925 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.16 % Allowed : 29.19 % 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: 0.71 (0.21), residues: 1704 helix: 1.61 (0.21), residues: 636 sheet: 0.40 (0.29), residues: 364 loop : -0.49 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 521 HIS 0.003 0.001 HIS A1059 PHE 0.022 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.015 0.000 ARG A 547 *********************** 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: 62 poor density : 401 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7729 (mtpp) REVERT: B 339 MET cc_start: 0.8432 (mtm) cc_final: 0.8215 (mtm) REVERT: B 373 ASN cc_start: 0.8128 (t0) cc_final: 0.7847 (t0) REVERT: B 403 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7141 (mt-10) REVERT: B 408 MET cc_start: 0.7564 (mmm) cc_final: 0.7246 (tpp) REVERT: B 412 ASN cc_start: 0.8022 (m-40) cc_final: 0.7650 (t0) REVERT: B 422 ASP cc_start: 0.7986 (t0) cc_final: 0.7371 (t0) REVERT: B 489 SER cc_start: 0.8331 (t) cc_final: 0.7828 (p) REVERT: B 508 MET cc_start: 0.7513 (ttp) cc_final: 0.7205 (ttp) REVERT: B 554 PHE cc_start: 0.8276 (m-80) cc_final: 0.7958 (m-80) REVERT: B 584 ARG cc_start: 0.7427 (mtm180) cc_final: 0.7204 (mtm180) REVERT: B 782 MET cc_start: 0.8477 (tpt) cc_final: 0.8003 (tpt) REVERT: B 784 LYS cc_start: 0.8133 (pptt) cc_final: 0.7752 (pptt) REVERT: B 807 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7761 (tmtt) REVERT: B 811 ARG cc_start: 0.7633 (ttt180) cc_final: 0.7323 (ttp80) REVERT: B 836 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7919 (mtpp) REVERT: B 883 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 905 ARG cc_start: 0.7023 (ttm170) cc_final: 0.6722 (mtp180) REVERT: B 920 MET cc_start: 0.6741 (mtm) cc_final: 0.6491 (mmm) REVERT: B 924 THR cc_start: 0.4657 (OUTLIER) cc_final: 0.3823 (p) REVERT: B 950 ASP cc_start: 0.7224 (t0) cc_final: 0.6945 (t70) REVERT: B 965 MET cc_start: 0.5171 (tpt) cc_final: 0.4792 (tpt) REVERT: B 1054 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.5397 (tt0) REVERT: B 1082 GLU cc_start: 0.7030 (tp30) cc_final: 0.6611 (tp30) REVERT: B 1091 LYS cc_start: 0.7132 (tttm) cc_final: 0.6516 (tttt) REVERT: A 210 ARG cc_start: 0.7345 (mtm180) cc_final: 0.6867 (mtm110) REVERT: A 229 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6599 (mm-30) REVERT: A 288 ARG cc_start: 0.8455 (tpt-90) cc_final: 0.8183 (tpt90) REVERT: A 378 PHE cc_start: 0.8156 (t80) cc_final: 0.7862 (t80) REVERT: A 422 ASP cc_start: 0.7781 (t0) cc_final: 0.7434 (t0) REVERT: A 435 GLN cc_start: 0.7526 (mp10) cc_final: 0.6970 (mp10) REVERT: A 446 ASP cc_start: 0.7591 (m-30) cc_final: 0.7346 (m-30) REVERT: A 450 LEU cc_start: 0.8758 (tt) cc_final: 0.8429 (tp) REVERT: A 470 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6877 (mm-30) REVERT: A 497 ARG cc_start: 0.6426 (mmm160) cc_final: 0.6064 (mmm160) REVERT: A 573 MET cc_start: 0.7840 (tpp) cc_final: 0.7569 (tpp) REVERT: A 878 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 881 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: A 904 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7347 (mttm) REVERT: A 949 ASP cc_start: 0.6628 (m-30) cc_final: 0.6260 (m-30) REVERT: A 988 LYS cc_start: 0.6858 (mmmt) cc_final: 0.6062 (mmtm) REVERT: A 1021 LEU cc_start: 0.8091 (tp) cc_final: 0.7881 (tp) REVERT: A 1072 MET cc_start: 0.7531 (ppp) cc_final: 0.7118 (ptm) outliers start: 62 outliers final: 50 residues processed: 425 average time/residue: 0.3147 time to fit residues: 185.4857 Evaluate side-chains 450 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 396 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 299 ARG 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 501 LEU 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 881 GLN 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 246 GLU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU 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 789 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1092 LEU 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 99 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 171 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 0.0000 chunk 14 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13850 Z= 0.194 Angle : 0.582 12.631 18707 Z= 0.283 Chirality : 0.041 0.291 2134 Planarity : 0.004 0.072 2385 Dihedral : 4.361 40.361 1925 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.96 % Allowed : 29.53 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1704 helix: 1.64 (0.21), residues: 626 sheet: 0.39 (0.29), residues: 365 loop : -0.49 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 521 HIS 0.003 0.001 HIS A1059 PHE 0.027 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.016 0.000 ARG A 547 ********************** 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 460 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 401 time to evaluate : 1.637 Fit side-chains revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7739 (mtpp) REVERT: B 373 ASN cc_start: 0.8110 (t0) cc_final: 0.7861 (t0) REVERT: B 408 MET cc_start: 0.7560 (mmm) cc_final: 0.7248 (tpp) REVERT: B 412 ASN cc_start: 0.8014 (m-40) cc_final: 0.7627 (t0) REVERT: B 422 ASP cc_start: 0.8000 (t0) cc_final: 0.7402 (t0) REVERT: B 489 SER cc_start: 0.8338 (t) cc_final: 0.7843 (p) REVERT: B 508 MET cc_start: 0.7529 (ttp) cc_final: 0.7097 (ttp) REVERT: B 518 MET cc_start: 0.7803 (ptp) cc_final: 0.7555 (mtm) REVERT: B 554 PHE cc_start: 0.8288 (m-80) cc_final: 0.7961 (m-80) REVERT: B 584 ARG cc_start: 0.7436 (mtm180) cc_final: 0.7211 (mtm180) REVERT: B 782 MET cc_start: 0.8500 (tpt) cc_final: 0.8062 (tpt) REVERT: B 784 LYS cc_start: 0.8129 (pptt) cc_final: 0.7754 (pptt) REVERT: B 807 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7768 (tmtt) REVERT: B 811 ARG cc_start: 0.7642 (ttt180) cc_final: 0.7312 (ttp80) REVERT: B 836 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7882 (mtpp) REVERT: B 883 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8262 (mm) REVERT: B 905 ARG cc_start: 0.7017 (ttm170) cc_final: 0.6717 (mtp180) REVERT: B 924 THR cc_start: 0.4621 (OUTLIER) cc_final: 0.3770 (p) REVERT: B 965 MET cc_start: 0.5205 (tpt) cc_final: 0.4868 (tpt) REVERT: B 1054 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.5443 (tt0) REVERT: B 1082 GLU cc_start: 0.7038 (tp30) cc_final: 0.6617 (tp30) REVERT: B 1091 LYS cc_start: 0.7126 (tttm) cc_final: 0.6525 (tttt) REVERT: A 229 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7001 (mm-30) REVERT: A 288 ARG cc_start: 0.8473 (tpt-90) cc_final: 0.8179 (tpt90) REVERT: A 378 PHE cc_start: 0.8178 (t80) cc_final: 0.7878 (t80) REVERT: A 422 ASP cc_start: 0.7783 (t0) cc_final: 0.7418 (t0) REVERT: A 435 GLN cc_start: 0.7540 (mp10) cc_final: 0.6981 (mp10) REVERT: A 446 ASP cc_start: 0.7586 (m-30) cc_final: 0.7354 (m-30) REVERT: A 450 LEU cc_start: 0.8781 (tt) cc_final: 0.8430 (tp) REVERT: A 470 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6873 (mm-30) REVERT: A 495 PHE cc_start: 0.8785 (t80) cc_final: 0.8507 (t80) REVERT: A 497 ARG cc_start: 0.6457 (mmm160) cc_final: 0.6098 (mmm160) REVERT: A 573 MET cc_start: 0.7884 (tpp) cc_final: 0.7486 (tpp) REVERT: A 878 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 881 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: A 904 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7365 (mttm) REVERT: A 949 ASP cc_start: 0.6658 (m-30) cc_final: 0.6277 (m-30) REVERT: A 988 LYS cc_start: 0.6881 (mmmt) cc_final: 0.6097 (mmtm) REVERT: A 1072 MET cc_start: 0.7553 (ppp) cc_final: 0.7167 (ptm) outliers start: 59 outliers final: 51 residues processed: 425 average time/residue: 0.3222 time to fit residues: 188.8383 Evaluate side-chains 452 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 397 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 299 ARG 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 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 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 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 246 GLU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU 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 789 LYS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1092 LEU 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 41 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 136 optimal weight: 0.0010 chunk 57 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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 906 GLN ** B 941 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** A1014 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138453 restraints weight = 20499.556| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.68 r_work: 0.3640 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13850 Z= 0.166 Angle : 0.571 12.816 18707 Z= 0.278 Chirality : 0.040 0.282 2134 Planarity : 0.004 0.069 2385 Dihedral : 4.236 32.248 1925 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.62 % Allowed : 30.00 % Favored : 66.38 % 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: 0.70 (0.21), residues: 1704 helix: 1.61 (0.21), residues: 636 sheet: 0.41 (0.29), residues: 365 loop : -0.51 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 PHE 0.023 0.001 PHE A1111 TYR 0.015 0.001 TYR B 327 ARG 0.016 0.000 ARG A 547 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3954.82 seconds wall clock time: 72 minutes 34.22 seconds (4354.22 seconds total)