Starting phenix.real_space_refine on Sat Aug 23 18:05:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f5z_28869/08_2025/8f5z_28869.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f5z_28869/08_2025/8f5z_28869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f5z_28869/08_2025/8f5z_28869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f5z_28869/08_2025/8f5z_28869.map" model { file = "/net/cci-nas-00/data/ceres_data/8f5z_28869/08_2025/8f5z_28869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f5z_28869/08_2025/8f5z_28869.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 8641 2.51 5 N 2344 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13598 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6753 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 829} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 6759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6759 Classifications: {'peptide': 862} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 829} Chain breaks: 4 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.23, per 1000 atoms: 0.24 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: 1.29 Conformation dependent library (CDL) restraints added in 682.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 14 sheets defined 42.9% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.635A pdb=" N THR B 108 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.044A pdb=" N LEU B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 146 Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.617A pdb=" N ARG B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.515A pdb=" N ILE B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 380 through 426 removed outlier: 3.858A pdb=" N MET B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.710A pdb=" N GLN B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 479 removed outlier: 3.602A pdb=" N GLU B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 494 Processing helix chain 'B' and resid 569 through 587 removed outlier: 3.583A pdb=" N ASP B 574 " --> pdb=" O ASP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 787 Processing helix chain 'B' and resid 790 through 794 removed outlier: 3.595A pdb=" N ILE B 794 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 831 removed outlier: 3.649A pdb=" N PHE B 818 " --> pdb=" O ASN B 814 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR B 830 " --> pdb=" O ASN B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 889 removed outlier: 3.771A pdb=" N ALA B 889 " --> pdb=" O VAL B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 896 Processing helix chain 'B' and resid 896 through 922 removed outlier: 3.691A pdb=" N LEU B 900 " --> pdb=" O ARG B 896 " (cutoff:3.500A) Proline residue: B 910 - end of helix removed outlier: 3.610A pdb=" N ILE B 921 " --> pdb=" O THR B 917 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 922 " --> pdb=" O ARG B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 950 removed outlier: 3.834A pdb=" N GLN B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 removed outlier: 4.162A pdb=" N GLU B 958 " --> pdb=" O GLU B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 988 removed outlier: 3.939A pdb=" N VAL B 973 " --> pdb=" O THR B 969 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 974 " --> pdb=" O LEU B 970 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 980 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 981 " --> pdb=" O SER B 977 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET B 983 " --> pdb=" O SER B 979 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS B 984 " --> pdb=" O GLN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1001 removed outlier: 3.505A pdb=" N MET B1001 " --> pdb=" O GLU B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1027 removed outlier: 3.607A pdb=" N ALA B1023 " --> pdb=" O PHE B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1065 through 1071 removed outlier: 3.533A pdb=" N GLN B1071 " --> pdb=" O PHE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1075 Processing helix chain 'B' and resid 1082 through 1095 removed outlier: 4.294A pdb=" N LEU B1086 " --> pdb=" O GLU B1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 Processing helix chain 'A' and resid 101 through 107 removed outlier: 4.464A pdb=" N GLU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.564A pdb=" N LEU A 152 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 202 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.793A pdb=" N ARG A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 235 removed outlier: 3.775A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.571A pdb=" N MET A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.561A pdb=" N MET A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 426 removed outlier: 3.536A pdb=" N MET A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.817A pdb=" N SER A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 435' Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.578A pdb=" N GLN A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 470 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 497 through 502 removed outlier: 4.048A pdb=" N LEU A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 502' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.600A pdb=" N LEU A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.598A pdb=" N PHE A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 removed outlier: 3.521A pdb=" N ALA A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 892 " --> pdb=" O LEU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 922 removed outlier: 3.589A pdb=" N ARG A 896 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Proline residue: A 910 - end of helix removed outlier: 3.627A pdb=" N GLU A 922 " --> pdb=" O ARG A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 3.956A pdb=" N ARG A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 944 " --> pdb=" O CYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 954 removed outlier: 4.484A pdb=" N GLU A 954 " --> pdb=" O SER A 951 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 951 through 954' Processing helix chain 'A' and resid 969 through 988 removed outlier: 4.151A pdb=" N VAL A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS A 984 " --> pdb=" O GLN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1008 through 1026 removed outlier: 3.790A pdb=" N PHE A1026 " --> pdb=" O MET A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.573A pdb=" N VAL A1048 " --> pdb=" O GLY A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1073 removed outlier: 4.315A pdb=" N GLN A1071 " --> pdb=" O PHE A1067 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET A1072 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1095 removed outlier: 3.709A pdb=" N LEU A1086 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A1091 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1092 " --> pdb=" O VAL A1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.792A pdb=" N ALA B 88 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 287 through 290 removed outlier: 3.989A pdb=" N VAL B 369 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 367 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 287 through 290 removed outlier: 3.989A pdb=" N VAL B 369 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 239 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 255 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA B 241 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU B 267 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 530 " --> pdb=" O GLU B 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 455 through 456 removed outlier: 3.660A pdb=" N ALA B 449 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 523 " --> pdb=" O GLY B 507 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY B 484 " --> pdb=" O THR B 746 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 748 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER B 486 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 755 " --> pdb=" O ARG B 747 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 775 through 778 removed outlier: 6.165A pdb=" N GLY B 768 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP B 778 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 766 " --> pdb=" O TRP B 778 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 870 " --> pdb=" O PHE B 767 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 867 " --> pdb=" O LYS B 858 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 993 through 994 removed outlier: 3.545A pdb=" N THR B1058 " --> pdb=" O THR B1034 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1053 through 1055 removed outlier: 3.569A pdb=" N ALA B1115 " --> pdb=" O LEU B1053 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.603A pdb=" N ILE A 80 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 298 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A 88 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR A 99 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU A 86 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 290 removed outlier: 3.538A pdb=" N GLY A 367 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP A 366 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 239 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 255 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 241 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 267 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 530 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 559 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 456 through 460 removed outlier: 6.314A pdb=" N GLY A 484 " --> pdb=" O THR A 746 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE A 748 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 486 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 745 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 775 through 778 removed outlier: 6.174A pdb=" N GLY A 768 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP A 778 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 766 " --> pdb=" O TRP A 778 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 769 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 867 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 855 " --> pdb=" O GLU A 835 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 994 removed outlier: 6.317A pdb=" N ARG A 991 " --> pdb=" O LEU A1033 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL A1035 " --> pdb=" O ARG A 991 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR A 993 " --> pdb=" O VAL A1035 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N ALA A1037 " --> pdb=" O THR A 993 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A1056 " --> pdb=" O SER A1036 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1053 " --> pdb=" O ALA A1115 " (cutoff:3.500A) 642 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.67 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 1201)) \ selection = (chain 'B' and (resid 69 through 1119 or resid 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 13852 Z= 0.162 Angle : 0.588 9.734 18707 Z= 0.282 Chirality : 0.039 0.173 2134 Planarity : 0.008 0.206 2385 Dihedral : 17.242 89.652 5223 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.47 % Allowed : 31.28 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.21), residues: 1704 helix: 0.62 (0.22), residues: 596 sheet: 0.14 (0.29), residues: 353 loop : -0.36 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 547 TYR 0.012 0.001 TYR B 168 PHE 0.031 0.001 PHE A 83 TRP 0.007 0.001 TRP A 568 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00337 (13850) covalent geometry : angle 0.58780 (18707) hydrogen bonds : bond 0.26737 ( 633) hydrogen bonds : angle 8.48896 ( 1803) Misc. bond : bond 0.03174 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 398 time to evaluate : 0.516 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: 0.1291 time to fit residues: 72.5320 Evaluate side-chains 386 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 380 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 1101 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.151861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135474 restraints weight = 20422.153| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.70 r_work: 0.3605 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13852 Z= 0.148 Angle : 0.574 11.487 18707 Z= 0.292 Chirality : 0.041 0.165 2134 Planarity : 0.005 0.084 2385 Dihedral : 5.662 89.603 1938 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.23 % Allowed : 27.18 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.21), residues: 1704 helix: 0.96 (0.20), residues: 639 sheet: 0.15 (0.28), residues: 363 loop : -0.50 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 547 TYR 0.015 0.001 TYR B 327 PHE 0.025 0.002 PHE A1111 TRP 0.010 0.001 TRP A 521 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00327 (13850) covalent geometry : angle 0.57377 (18707) hydrogen bonds : bond 0.04984 ( 633) hydrogen bonds : angle 5.50682 ( 1803) Misc. bond : bond 0.00139 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 406 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 339 MET cc_start: 0.8082 (mpp) cc_final: 0.7622 (mpp) REVERT: B 373 ASN cc_start: 0.7842 (t0) cc_final: 0.7597 (t0) REVERT: B 518 MET cc_start: 0.7837 (ptp) cc_final: 0.7618 (mtm) REVERT: B 538 ASP cc_start: 0.7897 (p0) cc_final: 0.7695 (p0) REVERT: B 784 LYS cc_start: 0.8068 (pptt) cc_final: 0.7834 (pptt) REVERT: B 836 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7619 (mtpp) REVERT: B 883 LEU cc_start: 0.8538 (mm) cc_final: 0.8282 (mm) REVERT: B 905 ARG cc_start: 0.7156 (ttm170) cc_final: 0.6937 (mtp180) REVERT: B 973 VAL cc_start: 0.7828 (p) cc_final: 0.7578 (t) REVERT: B 1091 LYS cc_start: 0.7208 (tttm) cc_final: 0.6856 (tttm) REVERT: B 1108 LYS cc_start: 0.6783 (mmmt) cc_final: 0.6544 (mmmt) REVERT: B 1116 GLU cc_start: 0.5801 (tm-30) cc_final: 0.5562 (tm-30) REVERT: A 210 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7024 (mtm110) REVERT: A 229 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6846 (mm-30) REVERT: A 232 GLU cc_start: 0.7394 (tt0) cc_final: 0.7175 (tt0) REVERT: A 303 ASP cc_start: 0.6967 (t0) cc_final: 0.6724 (t70) REVERT: A 328 MET cc_start: 0.8078 (mtm) cc_final: 0.7829 (mtt) REVERT: A 422 ASP cc_start: 0.7686 (t0) cc_final: 0.7298 (t0) REVERT: A 446 ASP cc_start: 0.7426 (m-30) cc_final: 0.7190 (m-30) REVERT: A 877 HIS cc_start: 0.7684 (m90) cc_final: 0.6889 (m90) REVERT: A 878 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7547 (mt-10) REVERT: A 881 GLN cc_start: 0.7896 (mp10) cc_final: 0.7366 (mp10) REVERT: A 949 ASP cc_start: 0.6491 (m-30) cc_final: 0.6153 (m-30) REVERT: A 1091 LYS cc_start: 0.7332 (mttm) cc_final: 0.7111 (mttp) outliers start: 63 outliers final: 33 residues processed: 430 average time/residue: 0.1330 time to fit residues: 79.5060 Evaluate side-chains 436 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 37 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN B 438 ASN ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 GLN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134852 restraints weight = 20535.922| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.69 r_work: 0.3597 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13852 Z= 0.149 Angle : 0.548 9.777 18707 Z= 0.279 Chirality : 0.041 0.160 2134 Planarity : 0.004 0.061 2385 Dihedral : 5.036 89.029 1925 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.50 % Allowed : 27.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.21), residues: 1704 helix: 1.26 (0.21), residues: 635 sheet: 0.21 (0.28), residues: 366 loop : -0.49 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 547 TYR 0.015 0.001 TYR B 327 PHE 0.023 0.002 PHE A1111 TRP 0.010 0.001 TRP A 521 HIS 0.005 0.001 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00336 (13850) covalent geometry : angle 0.54810 (18707) hydrogen bonds : bond 0.04349 ( 633) hydrogen bonds : angle 5.06239 ( 1803) Misc. bond : bond 0.00147 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 412 time to evaluate : 0.525 Fit side-chains REVERT: B 106 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8453 (tt) REVERT: B 202 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8239 (mttp) REVERT: B 206 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7879 (mtpp) REVERT: B 339 MET cc_start: 0.8095 (mpp) cc_final: 0.7591 (mpp) REVERT: B 373 ASN cc_start: 0.7784 (t0) cc_final: 0.7567 (t0) REVERT: B 408 MET cc_start: 0.7705 (tpp) cc_final: 0.7381 (mpp) REVERT: B 435 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7196 (mm-40) REVERT: B 538 ASP cc_start: 0.7957 (p0) cc_final: 0.7662 (p0) REVERT: B 784 LYS cc_start: 0.8058 (pptt) cc_final: 0.7653 (pptt) REVERT: B 811 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7520 (mtp-110) REVERT: B 836 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7596 (mtpp) REVERT: B 883 LEU cc_start: 0.8551 (mm) cc_final: 0.8173 (mm) REVERT: B 905 ARG cc_start: 0.7165 (ttm170) cc_final: 0.6956 (mtp180) REVERT: B 973 VAL cc_start: 0.7826 (p) cc_final: 0.7579 (t) REVERT: B 1091 LYS cc_start: 0.7119 (tttm) cc_final: 0.6498 (tttt) REVERT: A 210 ARG cc_start: 0.7445 (mtm110) cc_final: 0.6851 (mtm180) REVERT: A 229 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6815 (mm-30) REVERT: A 247 ASP cc_start: 0.6892 (p0) cc_final: 0.6492 (p0) REVERT: A 378 PHE cc_start: 0.8085 (t80) cc_final: 0.7795 (t80) REVERT: A 422 ASP cc_start: 0.7739 (t0) cc_final: 0.7368 (t0) REVERT: A 435 GLN cc_start: 0.7380 (mp10) cc_final: 0.7111 (mp10) REVERT: A 446 ASP cc_start: 0.7481 (m-30) cc_final: 0.7278 (m-30) REVERT: A 497 ARG cc_start: 0.6392 (mmm160) cc_final: 0.6142 (mmm160) REVERT: A 816 GLU cc_start: 0.7357 (tp30) cc_final: 0.7149 (tp30) REVERT: A 878 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 881 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7354 (mp10) REVERT: A 896 ARG cc_start: 0.7003 (ptt-90) cc_final: 0.6753 (ptt90) REVERT: A 940 CYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6378 (t) outliers start: 67 outliers final: 45 residues processed: 440 average time/residue: 0.1254 time to fit residues: 77.1817 Evaluate side-chains 446 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 398 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 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 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 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.0010 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN A1013 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.151369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134861 restraints weight = 20511.210| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.70 r_work: 0.3589 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13852 Z= 0.173 Angle : 0.572 10.094 18707 Z= 0.289 Chirality : 0.042 0.308 2134 Planarity : 0.004 0.051 2385 Dihedral : 5.116 89.077 1925 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.23 % Allowed : 26.71 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.21), residues: 1704 helix: 1.24 (0.21), residues: 636 sheet: 0.23 (0.29), residues: 360 loop : -0.44 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 547 TYR 0.016 0.002 TYR A 242 PHE 0.027 0.002 PHE A1111 TRP 0.010 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00393 (13850) covalent geometry : angle 0.57238 (18707) hydrogen bonds : bond 0.04168 ( 633) hydrogen bonds : angle 4.95709 ( 1803) Misc. bond : bond 0.00175 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 410 time to evaluate : 0.462 Fit side-chains REVERT: B 206 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7925 (mtpp) REVERT: B 373 ASN cc_start: 0.7792 (t0) cc_final: 0.7568 (t0) REVERT: B 408 MET cc_start: 0.7742 (tpp) cc_final: 0.7388 (mpp) REVERT: B 435 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7228 (mm-40) REVERT: B 538 ASP cc_start: 0.7980 (p0) cc_final: 0.7631 (p0) REVERT: B 784 LYS cc_start: 0.8070 (pptt) cc_final: 0.7687 (pptt) REVERT: B 836 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7670 (mtpp) REVERT: B 883 LEU cc_start: 0.8543 (mm) cc_final: 0.8182 (mm) REVERT: B 905 ARG cc_start: 0.7230 (ttm170) cc_final: 0.7002 (mtp180) REVERT: B 965 MET cc_start: 0.5324 (tpt) cc_final: 0.4892 (tpt) REVERT: B 973 VAL cc_start: 0.7838 (p) cc_final: 0.7602 (t) REVERT: B 1054 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.5101 (tt0) REVERT: B 1091 LYS cc_start: 0.7147 (tttm) cc_final: 0.6513 (tttt) REVERT: A 206 LYS cc_start: 0.7929 (tmtt) cc_final: 0.7680 (tmtt) REVERT: A 210 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6782 (mtm110) REVERT: A 229 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6341 (mm-30) REVERT: A 247 ASP cc_start: 0.6977 (p0) cc_final: 0.6581 (p0) REVERT: A 422 ASP cc_start: 0.7791 (t0) cc_final: 0.7345 (t0) REVERT: A 435 GLN cc_start: 0.7417 (mp10) cc_final: 0.6825 (mp10) REVERT: A 446 ASP cc_start: 0.7464 (m-30) cc_final: 0.7260 (m-30) REVERT: A 497 ARG cc_start: 0.6498 (mmm160) cc_final: 0.6204 (mmm160) REVERT: A 881 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: A 896 ARG cc_start: 0.7048 (ptt-90) cc_final: 0.6754 (ptt90) REVERT: A 940 CYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6359 (t) REVERT: A 1072 MET cc_start: 0.7470 (ppp) cc_final: 0.6890 (ptt) REVERT: A 1091 LYS cc_start: 0.7321 (mttp) cc_final: 0.7085 (mttm) outliers start: 78 outliers final: 58 residues processed: 447 average time/residue: 0.1354 time to fit residues: 84.9642 Evaluate side-chains 456 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 395 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 847 LYS 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 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 163 optimal weight: 0.0870 chunk 120 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.0050 chunk 165 optimal weight: 2.9990 overall best weight: 0.5572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.152394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135932 restraints weight = 20547.206| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.72 r_work: 0.3609 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13852 Z= 0.124 Angle : 0.554 10.034 18707 Z= 0.275 Chirality : 0.041 0.294 2134 Planarity : 0.004 0.047 2385 Dihedral : 4.960 88.076 1925 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.90 % Allowed : 27.79 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.21), residues: 1704 helix: 1.39 (0.21), residues: 637 sheet: 0.23 (0.29), residues: 358 loop : -0.42 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 547 TYR 0.015 0.001 TYR B 327 PHE 0.019 0.001 PHE A1111 TRP 0.010 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00282 (13850) covalent geometry : angle 0.55445 (18707) hydrogen bonds : bond 0.03645 ( 633) hydrogen bonds : angle 4.76636 ( 1803) Misc. bond : bond 0.00117 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 408 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7865 (mtpp) REVERT: B 279 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7872 (mtm-85) REVERT: B 339 MET cc_start: 0.8111 (mpp) cc_final: 0.7567 (mpp) REVERT: B 373 ASN cc_start: 0.7806 (t0) cc_final: 0.7567 (t0) REVERT: B 408 MET cc_start: 0.7714 (tpp) cc_final: 0.7364 (mpp) REVERT: B 422 ASP cc_start: 0.7915 (t0) cc_final: 0.7314 (t0) REVERT: B 435 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7231 (mm-40) REVERT: B 538 ASP cc_start: 0.7954 (p0) cc_final: 0.7603 (p0) REVERT: B 784 LYS cc_start: 0.8070 (pptt) cc_final: 0.7685 (pptt) REVERT: B 836 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7742 (mtpp) REVERT: B 842 PHE cc_start: 0.8105 (m-10) cc_final: 0.7854 (m-10) REVERT: B 883 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8197 (mm) REVERT: B 905 ARG cc_start: 0.7133 (ttm170) cc_final: 0.6919 (mtp180) REVERT: B 941 GLN cc_start: 0.7694 (mt0) cc_final: 0.7438 (mt0) REVERT: B 965 MET cc_start: 0.5317 (tpt) cc_final: 0.4855 (tpt) REVERT: B 973 VAL cc_start: 0.7801 (p) cc_final: 0.7569 (t) REVERT: B 1054 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.5763 (tt0) REVERT: B 1091 LYS cc_start: 0.7039 (tttm) cc_final: 0.6410 (tttt) REVERT: B 1116 GLU cc_start: 0.5842 (tm-30) cc_final: 0.5527 (tm-30) REVERT: A 206 LYS cc_start: 0.7955 (tmtt) cc_final: 0.7660 (tmtt) REVERT: A 210 ARG cc_start: 0.7309 (mtm110) cc_final: 0.6727 (mtm110) REVERT: A 247 ASP cc_start: 0.6975 (p0) cc_final: 0.6470 (p0) REVERT: A 288 ARG cc_start: 0.8497 (tpt-90) cc_final: 0.8164 (tpt90) REVERT: A 422 ASP cc_start: 0.7770 (t0) cc_final: 0.7348 (t0) REVERT: A 435 GLN cc_start: 0.7386 (mp10) cc_final: 0.6820 (mp10) REVERT: A 446 ASP cc_start: 0.7491 (m-30) cc_final: 0.7264 (m-30) REVERT: A 497 ARG cc_start: 0.6505 (mmm160) cc_final: 0.6113 (mmm160) REVERT: A 881 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: A 1072 MET cc_start: 0.7424 (ppp) cc_final: 0.6956 (ptt) REVERT: A 1091 LYS cc_start: 0.7215 (mttp) cc_final: 0.6983 (mttm) outliers start: 73 outliers final: 52 residues processed: 443 average time/residue: 0.1349 time to fit residues: 82.5286 Evaluate side-chains 450 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 395 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 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 257 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 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 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 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU 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 948 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 44 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 0.0060 chunk 39 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 130 optimal weight: 0.0870 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136009 restraints weight = 20633.356| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.72 r_work: 0.3615 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13852 Z= 0.114 Angle : 0.560 12.152 18707 Z= 0.274 Chirality : 0.041 0.303 2134 Planarity : 0.004 0.052 2385 Dihedral : 4.832 83.667 1925 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.57 % Allowed : 27.11 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.21), residues: 1704 helix: 1.49 (0.21), residues: 632 sheet: 0.23 (0.29), residues: 361 loop : -0.41 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 547 TYR 0.015 0.001 TYR B 327 PHE 0.017 0.001 PHE A1111 TRP 0.009 0.001 TRP A 521 HIS 0.003 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00260 (13850) covalent geometry : angle 0.55984 (18707) hydrogen bonds : bond 0.03456 ( 633) hydrogen bonds : angle 4.66749 ( 1803) Misc. bond : bond 0.00103 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 411 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7874 (mtpp) REVERT: B 279 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7878 (mtm-85) REVERT: B 339 MET cc_start: 0.8134 (mpp) cc_final: 0.7583 (mpp) REVERT: B 373 ASN cc_start: 0.7804 (t0) cc_final: 0.7546 (t0) REVERT: B 408 MET cc_start: 0.7703 (tpp) cc_final: 0.7388 (mpp) REVERT: B 422 ASP cc_start: 0.7905 (t0) cc_final: 0.7287 (t0) REVERT: B 435 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7130 (mm-40) REVERT: B 489 SER cc_start: 0.8329 (t) cc_final: 0.7819 (p) REVERT: B 538 ASP cc_start: 0.7960 (p0) cc_final: 0.7582 (p0) REVERT: B 782 MET cc_start: 0.8340 (tpt) cc_final: 0.7840 (tpt) REVERT: B 784 LYS cc_start: 0.8057 (pptt) cc_final: 0.7672 (pptt) REVERT: B 811 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7584 (ttp80) REVERT: B 836 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7824 (mtpp) REVERT: B 883 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8197 (mm) REVERT: B 905 ARG cc_start: 0.7154 (ttm170) cc_final: 0.6939 (mtp180) REVERT: B 965 MET cc_start: 0.5307 (tpt) cc_final: 0.4876 (tpt) REVERT: B 973 VAL cc_start: 0.7780 (p) cc_final: 0.7535 (t) REVERT: B 1054 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.4942 (tt0) REVERT: B 1091 LYS cc_start: 0.6996 (tttm) cc_final: 0.6381 (tttt) REVERT: A 206 LYS cc_start: 0.7973 (tmtt) cc_final: 0.7671 (tmtt) REVERT: A 210 ARG cc_start: 0.7330 (mtm110) cc_final: 0.6683 (mtm110) REVERT: A 247 ASP cc_start: 0.7101 (p0) cc_final: 0.6690 (p0) REVERT: A 422 ASP cc_start: 0.7762 (t0) cc_final: 0.7361 (t0) REVERT: A 435 GLN cc_start: 0.7409 (mp10) cc_final: 0.7183 (mp10) REVERT: A 446 ASP cc_start: 0.7501 (m-30) cc_final: 0.7267 (m-30) REVERT: A 470 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7020 (mm-30) REVERT: A 497 ARG cc_start: 0.6528 (mmm160) cc_final: 0.6161 (mmm160) REVERT: A 573 MET cc_start: 0.7817 (mmm) cc_final: 0.7410 (tpp) REVERT: A 815 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: A 881 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: A 1021 LEU cc_start: 0.8197 (tp) cc_final: 0.7965 (tp) REVERT: A 1072 MET cc_start: 0.7431 (ppp) cc_final: 0.7014 (ptt) outliers start: 83 outliers final: 58 residues processed: 450 average time/residue: 0.1175 time to fit residues: 73.1999 Evaluate side-chains 467 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 405 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 336 SER 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 769 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 789 LYS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 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 942 LYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 163 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 70 optimal weight: 0.0670 chunk 146 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.149090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132623 restraints weight = 20439.733| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.70 r_work: 0.3559 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13852 Z= 0.220 Angle : 0.629 10.602 18707 Z= 0.312 Chirality : 0.044 0.327 2134 Planarity : 0.004 0.059 2385 Dihedral : 5.071 69.942 1925 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.70 % Allowed : 27.38 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1704 helix: 1.18 (0.21), residues: 638 sheet: 0.19 (0.29), residues: 352 loop : -0.46 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 547 TYR 0.020 0.002 TYR B1006 PHE 0.030 0.002 PHE A1111 TRP 0.013 0.002 TRP A 521 HIS 0.005 0.001 HIS A1049 Details of bonding type rmsd covalent geometry : bond 0.00502 (13850) covalent geometry : angle 0.62920 (18707) hydrogen bonds : bond 0.04243 ( 633) hydrogen bonds : angle 4.92307 ( 1803) Misc. bond : bond 0.00221 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 411 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7880 (mtpp) REVERT: B 373 ASN cc_start: 0.7769 (t0) cc_final: 0.7527 (t0) REVERT: B 408 MET cc_start: 0.7759 (tpp) cc_final: 0.7415 (mpp) REVERT: B 422 ASP cc_start: 0.7957 (t0) cc_final: 0.7393 (t0) REVERT: B 435 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7216 (mm-40) REVERT: B 538 ASP cc_start: 0.7949 (p0) cc_final: 0.7566 (p0) REVERT: B 784 LYS cc_start: 0.8063 (pptt) cc_final: 0.7703 (pptt) REVERT: B 811 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7695 (ttp80) REVERT: B 824 VAL cc_start: 0.8449 (t) cc_final: 0.8239 (p) REVERT: B 836 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7787 (mtpp) REVERT: B 883 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8185 (mm) REVERT: B 905 ARG cc_start: 0.7295 (ttm170) cc_final: 0.7004 (mtp180) REVERT: B 924 THR cc_start: 0.4579 (OUTLIER) cc_final: 0.3783 (p) REVERT: B 1054 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.5053 (tt0) REVERT: B 1091 LYS cc_start: 0.7262 (tttm) cc_final: 0.6634 (tttt) REVERT: B 1108 LYS cc_start: 0.6921 (mmmt) cc_final: 0.6696 (mmmm) REVERT: B 1116 GLU cc_start: 0.5790 (tm-30) cc_final: 0.5580 (tm-30) REVERT: A 157 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8154 (tt) REVERT: A 206 LYS cc_start: 0.8000 (tmtt) cc_final: 0.7715 (tmtt) REVERT: A 210 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6700 (mtm110) REVERT: A 229 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6146 (mm-30) REVERT: A 247 ASP cc_start: 0.7147 (p0) cc_final: 0.6761 (p0) REVERT: A 288 ARG cc_start: 0.8480 (tpt-90) cc_final: 0.8177 (tpt90) REVERT: A 422 ASP cc_start: 0.7798 (t0) cc_final: 0.7359 (t0) REVERT: A 435 GLN cc_start: 0.7469 (mp10) cc_final: 0.6897 (mp10) REVERT: A 446 ASP cc_start: 0.7491 (m-30) cc_final: 0.7258 (m-30) REVERT: A 470 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7002 (mm-30) REVERT: A 497 ARG cc_start: 0.6632 (mmm160) cc_final: 0.6230 (mmm160) REVERT: A 569 LYS cc_start: 0.7902 (mptm) cc_final: 0.7564 (mptm) REVERT: A 881 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: A 949 ASP cc_start: 0.6528 (m-30) cc_final: 0.6205 (m-30) REVERT: A 1072 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7174 (ptm) outliers start: 85 outliers final: 57 residues processed: 452 average time/residue: 0.1473 time to fit residues: 92.3102 Evaluate side-chains 468 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 404 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.151576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135330 restraints weight = 20176.582| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.67 r_work: 0.3602 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13852 Z= 0.131 Angle : 0.581 11.196 18707 Z= 0.286 Chirality : 0.042 0.306 2134 Planarity : 0.004 0.049 2385 Dihedral : 4.794 64.273 1925 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.90 % Allowed : 28.32 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.21), residues: 1704 helix: 1.37 (0.21), residues: 630 sheet: 0.16 (0.29), residues: 362 loop : -0.42 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 512 TYR 0.015 0.001 TYR B 327 PHE 0.018 0.001 PHE A1111 TRP 0.013 0.001 TRP A 521 HIS 0.005 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00301 (13850) covalent geometry : angle 0.58115 (18707) hydrogen bonds : bond 0.03603 ( 633) hydrogen bonds : angle 4.73743 ( 1803) Misc. bond : bond 0.00128 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 412 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7892 (mtpp) REVERT: B 373 ASN cc_start: 0.7778 (t0) cc_final: 0.7569 (t0) REVERT: B 408 MET cc_start: 0.7713 (tpp) cc_final: 0.7396 (mpp) REVERT: B 422 ASP cc_start: 0.7935 (t0) cc_final: 0.7366 (t0) REVERT: B 435 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7156 (mm-40) REVERT: B 489 SER cc_start: 0.8296 (t) cc_final: 0.7819 (p) REVERT: B 538 ASP cc_start: 0.7915 (p0) cc_final: 0.7567 (p0) REVERT: B 554 PHE cc_start: 0.8302 (m-80) cc_final: 0.8079 (m-80) REVERT: B 784 LYS cc_start: 0.8051 (pptt) cc_final: 0.7684 (pptt) REVERT: B 811 ARG cc_start: 0.7922 (ttp-170) cc_final: 0.7686 (ttp80) REVERT: B 836 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7817 (mtpp) REVERT: B 883 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8187 (mm) REVERT: B 905 ARG cc_start: 0.7201 (ttm170) cc_final: 0.6945 (mtp180) REVERT: B 920 MET cc_start: 0.6701 (mtm) cc_final: 0.6454 (mmm) REVERT: B 924 THR cc_start: 0.4699 (OUTLIER) cc_final: 0.3898 (p) REVERT: B 1054 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.4914 (tt0) REVERT: B 1091 LYS cc_start: 0.7041 (tttm) cc_final: 0.6419 (tttt) REVERT: A 206 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7804 (tmtt) REVERT: A 210 ARG cc_start: 0.7351 (mtm110) cc_final: 0.6733 (mtm110) REVERT: A 247 ASP cc_start: 0.7092 (p0) cc_final: 0.6690 (p0) REVERT: A 422 ASP cc_start: 0.7770 (t0) cc_final: 0.7350 (t0) REVERT: A 435 GLN cc_start: 0.7447 (mp10) cc_final: 0.6892 (mp10) REVERT: A 446 ASP cc_start: 0.7469 (m-30) cc_final: 0.7239 (m-30) REVERT: A 470 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6976 (mm-30) REVERT: A 495 PHE cc_start: 0.8798 (t80) cc_final: 0.8529 (t80) REVERT: A 497 ARG cc_start: 0.6591 (mmm160) cc_final: 0.6196 (mmm160) REVERT: A 569 LYS cc_start: 0.7761 (mptm) cc_final: 0.7424 (mptm) REVERT: A 573 MET cc_start: 0.7814 (tpp) cc_final: 0.7505 (tpp) REVERT: A 881 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: A 949 ASP cc_start: 0.6481 (m-30) cc_final: 0.6136 (m-30) REVERT: A 1021 LEU cc_start: 0.8203 (tp) cc_final: 0.7975 (tp) REVERT: A 1072 MET cc_start: 0.7411 (ppp) cc_final: 0.7078 (ptm) outliers start: 73 outliers final: 56 residues processed: 445 average time/residue: 0.1448 time to fit residues: 89.1083 Evaluate side-chains 460 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 399 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 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 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.0040 chunk 134 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135604 restraints weight = 20446.704| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.68 r_work: 0.3609 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13852 Z= 0.122 Angle : 0.586 11.203 18707 Z= 0.287 Chirality : 0.042 0.309 2134 Planarity : 0.004 0.063 2385 Dihedral : 4.598 50.879 1925 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.70 % Allowed : 28.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.21), residues: 1704 helix: 1.38 (0.21), residues: 639 sheet: 0.20 (0.29), residues: 364 loop : -0.44 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 547 TYR 0.015 0.001 TYR B 327 PHE 0.020 0.001 PHE A1111 TRP 0.012 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00281 (13850) covalent geometry : angle 0.58582 (18707) hydrogen bonds : bond 0.03472 ( 633) hydrogen bonds : angle 4.68128 ( 1803) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 407 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7901 (mtpp) REVERT: B 279 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7984 (mtm-85) REVERT: B 339 MET cc_start: 0.8158 (mpp) cc_final: 0.7551 (mpp) REVERT: B 373 ASN cc_start: 0.7815 (t0) cc_final: 0.7596 (t0) REVERT: B 403 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6970 (mp0) REVERT: B 408 MET cc_start: 0.7708 (tpp) cc_final: 0.7381 (mpp) REVERT: B 412 ASN cc_start: 0.7964 (m-40) cc_final: 0.7582 (t0) REVERT: B 422 ASP cc_start: 0.7948 (t0) cc_final: 0.7373 (t0) REVERT: B 423 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7962 (mmm) REVERT: B 435 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7135 (mm-40) REVERT: B 489 SER cc_start: 0.8350 (t) cc_final: 0.7875 (p) REVERT: B 538 ASP cc_start: 0.7916 (p0) cc_final: 0.7609 (p0) REVERT: B 554 PHE cc_start: 0.8283 (m-80) cc_final: 0.8050 (m-80) REVERT: B 784 LYS cc_start: 0.8076 (pptt) cc_final: 0.7696 (pptt) REVERT: B 807 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7907 (tmtt) REVERT: B 811 ARG cc_start: 0.7933 (ttp-170) cc_final: 0.7697 (ttp80) REVERT: B 836 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7795 (mtpp) REVERT: B 883 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8193 (mm) REVERT: B 905 ARG cc_start: 0.7137 (ttm170) cc_final: 0.6887 (mtp180) REVERT: B 920 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6426 (mmm) REVERT: B 924 THR cc_start: 0.4659 (OUTLIER) cc_final: 0.3832 (p) REVERT: B 965 MET cc_start: 0.5299 (tpt) cc_final: 0.4923 (tpt) REVERT: B 1054 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.5104 (tt0) REVERT: B 1091 LYS cc_start: 0.7029 (tttm) cc_final: 0.6412 (tttt) REVERT: A 210 ARG cc_start: 0.7384 (mtm110) cc_final: 0.6767 (mtm110) REVERT: A 247 ASP cc_start: 0.7091 (p0) cc_final: 0.6701 (p0) REVERT: A 288 ARG cc_start: 0.8464 (tpt-90) cc_final: 0.8203 (tpt90) REVERT: A 422 ASP cc_start: 0.7776 (t0) cc_final: 0.7379 (t0) REVERT: A 435 GLN cc_start: 0.7466 (mp10) cc_final: 0.6906 (mp10) REVERT: A 446 ASP cc_start: 0.7485 (m-30) cc_final: 0.7251 (m-30) REVERT: A 470 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6959 (mm-30) REVERT: A 497 ARG cc_start: 0.6581 (mmm160) cc_final: 0.6194 (mmm160) REVERT: A 569 LYS cc_start: 0.7758 (mptm) cc_final: 0.7437 (mptm) REVERT: A 573 MET cc_start: 0.7786 (tpp) cc_final: 0.7469 (tpp) REVERT: A 881 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: A 1021 LEU cc_start: 0.8197 (tp) cc_final: 0.7966 (tp) REVERT: A 1072 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7082 (ptm) outliers start: 70 outliers final: 55 residues processed: 437 average time/residue: 0.1465 time to fit residues: 88.1917 Evaluate side-chains 460 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 398 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.151536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135296 restraints weight = 20410.505| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.66 r_work: 0.3598 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13852 Z= 0.143 Angle : 0.599 11.032 18707 Z= 0.294 Chirality : 0.042 0.316 2134 Planarity : 0.004 0.068 2385 Dihedral : 4.559 41.162 1925 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.50 % Allowed : 29.40 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.21), residues: 1704 helix: 1.36 (0.21), residues: 631 sheet: 0.24 (0.29), residues: 359 loop : -0.47 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 547 TYR 0.016 0.001 TYR B 327 PHE 0.022 0.002 PHE A1111 TRP 0.012 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00331 (13850) covalent geometry : angle 0.59905 (18707) hydrogen bonds : bond 0.03570 ( 633) hydrogen bonds : angle 4.70221 ( 1803) Misc. bond : bond 0.00137 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 400 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7886 (mtpp) REVERT: B 373 ASN cc_start: 0.7795 (t0) cc_final: 0.7593 (t0) REVERT: B 403 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6976 (mp0) REVERT: B 408 MET cc_start: 0.7709 (tpp) cc_final: 0.7396 (mpp) REVERT: B 412 ASN cc_start: 0.7965 (m-40) cc_final: 0.7591 (t0) REVERT: B 422 ASP cc_start: 0.7959 (t0) cc_final: 0.7374 (t0) REVERT: B 423 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7947 (mmm) REVERT: B 435 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7295 (mm-40) REVERT: B 489 SER cc_start: 0.8303 (t) cc_final: 0.7829 (p) REVERT: B 518 MET cc_start: 0.7761 (ptp) cc_final: 0.7511 (mtm) REVERT: B 538 ASP cc_start: 0.7923 (p0) cc_final: 0.7623 (p0) REVERT: B 554 PHE cc_start: 0.8288 (m-80) cc_final: 0.8049 (m-80) REVERT: B 782 MET cc_start: 0.8365 (tpt) cc_final: 0.7928 (tpt) REVERT: B 784 LYS cc_start: 0.8086 (pptt) cc_final: 0.7709 (pptt) REVERT: B 807 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7895 (tmtt) REVERT: B 811 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7653 (ttp80) REVERT: B 836 LYS cc_start: 0.8123 (mtpp) cc_final: 0.7807 (mtpp) REVERT: B 883 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8212 (mm) REVERT: B 905 ARG cc_start: 0.7052 (ttm170) cc_final: 0.6768 (mtp180) REVERT: B 924 THR cc_start: 0.4684 (OUTLIER) cc_final: 0.3853 (p) REVERT: B 965 MET cc_start: 0.5316 (tpt) cc_final: 0.4935 (tpt) REVERT: B 1054 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.4954 (tt0) REVERT: B 1091 LYS cc_start: 0.7066 (tttm) cc_final: 0.6443 (tttt) REVERT: B 1116 GLU cc_start: 0.5815 (tm-30) cc_final: 0.5586 (tm-30) REVERT: A 206 LYS cc_start: 0.8137 (tmtt) cc_final: 0.7771 (tmtt) REVERT: A 210 ARG cc_start: 0.7419 (mtm110) cc_final: 0.6670 (mtm110) REVERT: A 247 ASP cc_start: 0.7090 (p0) cc_final: 0.6718 (p0) REVERT: A 288 ARG cc_start: 0.8482 (tpt-90) cc_final: 0.8198 (tpt90) REVERT: A 317 LEU cc_start: 0.8775 (mp) cc_final: 0.8567 (mt) REVERT: A 422 ASP cc_start: 0.7806 (t0) cc_final: 0.7397 (t0) REVERT: A 435 GLN cc_start: 0.7497 (mp10) cc_final: 0.6941 (mp10) REVERT: A 446 ASP cc_start: 0.7492 (m-30) cc_final: 0.7257 (m-30) REVERT: A 495 PHE cc_start: 0.8751 (t80) cc_final: 0.8470 (t80) REVERT: A 497 ARG cc_start: 0.6578 (mmm160) cc_final: 0.6220 (mmm160) REVERT: A 569 LYS cc_start: 0.7755 (mptm) cc_final: 0.7445 (mptm) REVERT: A 573 MET cc_start: 0.7811 (tpp) cc_final: 0.7490 (tpp) REVERT: A 881 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: A 949 ASP cc_start: 0.6635 (m-30) cc_final: 0.6284 (m-30) REVERT: A 1021 LEU cc_start: 0.8242 (tp) cc_final: 0.8023 (tp) REVERT: A 1072 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7119 (ptm) outliers start: 67 outliers final: 55 residues processed: 431 average time/residue: 0.1480 time to fit residues: 88.1399 Evaluate side-chains 457 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 396 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 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 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 112 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 111 optimal weight: 0.0060 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135583 restraints weight = 20464.817| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.65 r_work: 0.3608 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13852 Z= 0.134 Angle : 0.596 11.028 18707 Z= 0.293 Chirality : 0.042 0.306 2134 Planarity : 0.004 0.067 2385 Dihedral : 4.469 33.685 1925 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.50 % Allowed : 29.66 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.21), residues: 1704 helix: 1.38 (0.21), residues: 634 sheet: 0.23 (0.29), residues: 362 loop : -0.44 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 547 TYR 0.015 0.001 TYR B 327 PHE 0.023 0.001 PHE A1111 TRP 0.011 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00309 (13850) covalent geometry : angle 0.59617 (18707) hydrogen bonds : bond 0.03494 ( 633) hydrogen bonds : angle 4.67342 ( 1803) Misc. bond : bond 0.00127 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3354.09 seconds wall clock time: 58 minutes 24.04 seconds (3504.04 seconds total)