Starting phenix.real_space_refine on Wed Jun 18 12:11:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t5o_25699/06_2025/7t5o_25699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t5o_25699/06_2025/7t5o_25699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t5o_25699/06_2025/7t5o_25699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t5o_25699/06_2025/7t5o_25699.map" model { file = "/net/cci-nas-00/data/ceres_data/7t5o_25699/06_2025/7t5o_25699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t5o_25699/06_2025/7t5o_25699.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.021 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 105 5.16 5 C 13502 2.51 5 N 3568 2.21 5 O 4088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21263 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3290 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 408} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 7381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7381 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 898} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 7373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7373 Classifications: {'peptide': 947} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 897} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1626 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 207} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 13.52, per 1000 atoms: 0.64 Number of scatterers: 21263 At special positions: 0 Unit cell: (118.8, 158.76, 204.12, 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 105 16.00 O 4088 8.00 N 3568 7.00 C 13502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS C 707 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 707 " - pdb=" SG CYS C 883 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.07 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 3.0 seconds 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5138 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 46 sheets defined 25.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 747 through 755 Processing helix chain 'A' and resid 759 through 782 Processing helix chain 'A' and resid 816 through 826 removed outlier: 4.004A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.669A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 914 through 919 removed outlier: 4.063A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 968 Processing helix chain 'A' and resid 989 through 1002 removed outlier: 4.443A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1033 removed outlier: 3.588A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.913A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.512A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.714A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.566A pdb=" N ARG B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.714A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 897 through 904 Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.632A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 916 " --> pdb=" O GLN B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 916' Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.734A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.762A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1028 removed outlier: 3.831A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.544A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.880A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.512A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.750A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.820A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.589A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 835 through 841 removed outlier: 3.942A pdb=" N GLY C 838 " --> pdb=" O LYS C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.554A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.875A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.989A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.522A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 968 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.763A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1033 removed outlier: 4.389A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 993 " --> pdb=" O ALA C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.767A pdb=" N ASP L 81 " --> pdb=" O GLU L 78 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing helix chain 'L' and resid 125 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 727 removed outlier: 3.648A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.577A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1121 through 1125 removed outlier: 5.810A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.605A pdb=" N THR B 274 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 197 removed outlier: 3.681A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 315 removed outlier: 3.539A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 651 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 359 removed outlier: 3.598A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.899A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.592A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.788A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AB7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.709A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.824A pdb=" N ILE C 788 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 711 through 721 removed outlier: 3.557A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 711 through 721 removed outlier: 3.557A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 734 through 736 removed outlier: 4.103A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1089 through 1090 removed outlier: 4.094A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.577A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 188 through 193 removed outlier: 4.162A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 275 through 279 removed outlier: 3.695A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.718A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 650 " --> pdb=" O PHE C 643 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 317 through 319 Processing sheet with id=AD1, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.374A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.658A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AD5, first strand: chain 'C' and resid 664 through 665 removed outlier: 3.537A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.613A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.706A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1076 through 1078 removed outlier: 4.561A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.298A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.536A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.612A pdb=" N THR H 114 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.612A pdb=" N THR H 114 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.806A pdb=" N LEU H 145 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP H 151 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 188 " --> pdb=" O HIS H 171 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 158 through 161 removed outlier: 3.833A pdb=" N SER H 160 " --> pdb=" O ASN H 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN H 204 " --> pdb=" O SER H 160 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.560A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR L 86 " --> pdb=" O TYR L 35 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 18 through 21 removed outlier: 3.523A pdb=" N THR L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER L 64 " --> pdb=" O THR L 71 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 90 through 91 removed outlier: 3.551A pdb=" N ASP L 91 " --> pdb=" O ASP L 98 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 119 through 122 removed outlier: 6.219A pdb=" N ALA L 177 " --> pdb=" O PRO L 168 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER L 179 " --> pdb=" O THR L 166 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 158 through 159 removed outlier: 4.396A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR L 149 " --> pdb=" O THR L 200 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS L 153 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR L 195 " --> pdb=" O VAL L 210 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL L 210 " --> pdb=" O TYR L 195 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS L 208 " --> pdb=" O CYS L 197 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1926 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: 9.11 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 5955 1.34 - 1.47: 6107 1.47 - 1.60: 9540 1.60 - 1.73: 0 1.73 - 1.87: 134 Bond restraints: 21736 Sorted by residual: bond pdb=" C TYR L 144 " pdb=" N PRO L 145 " ideal model delta sigma weight residual 1.330 1.396 -0.066 1.23e-02 6.61e+03 2.90e+01 bond pdb=" C GLU H 155 " pdb=" N PRO H 156 " ideal model delta sigma weight residual 1.334 1.418 -0.084 2.34e-02 1.83e+03 1.28e+01 bond pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " ideal model delta sigma weight residual 1.533 1.588 -0.055 1.69e-02 3.50e+03 1.07e+01 bond pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.69e+00 bond pdb=" CA VAL C 524 " pdb=" CB VAL C 524 " ideal model delta sigma weight residual 1.532 1.565 -0.033 1.08e-02 8.57e+03 9.32e+00 ... (remaining 21731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 28950 4.20 - 8.40: 548 8.40 - 12.60: 73 12.60 - 16.79: 11 16.79 - 20.99: 3 Bond angle restraints: 29585 Sorted by residual: angle pdb=" N VAL C 362 " pdb=" CA VAL C 362 " pdb=" C VAL C 362 " ideal model delta sigma weight residual 113.53 104.74 8.79 9.80e-01 1.04e+00 8.04e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 134.94 -20.54 2.30e+00 1.89e-01 7.97e+01 angle pdb=" N GLU C 773 " pdb=" CA GLU C 773 " pdb=" CB GLU C 773 " ideal model delta sigma weight residual 110.44 123.07 -12.63 1.53e+00 4.27e-01 6.82e+01 angle pdb=" CA GLU C 773 " pdb=" CB GLU C 773 " pdb=" CG GLU C 773 " ideal model delta sigma weight residual 114.10 129.77 -15.67 2.00e+00 2.50e-01 6.14e+01 angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 102.72 110.99 -8.27 1.06e+00 8.90e-01 6.08e+01 ... (remaining 29580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11943 17.93 - 35.86: 894 35.86 - 53.79: 148 53.79 - 71.73: 31 71.73 - 89.66: 19 Dihedral angle restraints: 13035 sinusoidal: 5042 harmonic: 7993 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 1.47 -87.47 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -160.73 74.73 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 25.94 67.06 1 1.00e+01 1.00e-02 5.86e+01 ... (remaining 13032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2843 0.102 - 0.203: 462 0.203 - 0.305: 54 0.305 - 0.407: 13 0.407 - 0.508: 6 Chirality restraints: 3378 Sorted by residual: chirality pdb=" CB ILE A 993 " pdb=" CA ILE A 993 " pdb=" CG1 ILE A 993 " pdb=" CG2 ILE A 993 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" CB THR B 376 " pdb=" CA THR B 376 " pdb=" OG1 THR B 376 " pdb=" CG2 THR B 376 " both_signs ideal model delta sigma weight residual False 2.55 2.07 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CB THR B 33 " pdb=" CA THR B 33 " pdb=" OG1 THR B 33 " pdb=" CG2 THR B 33 " both_signs ideal model delta sigma weight residual False 2.55 2.07 0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 3375 not shown) Planarity restraints: 3841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 369 " 0.017 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR C 369 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR C 369 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C 369 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR C 369 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 369 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 369 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 369 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.027 2.00e-02 2.50e+03 2.69e-02 1.27e+01 pdb=" CG PHE A 906 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 321 " -0.057 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO C 322 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " -0.046 5.00e-02 4.00e+02 ... (remaining 3838 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5662 2.82 - 3.34: 17545 3.34 - 3.86: 34720 3.86 - 4.38: 38079 4.38 - 4.90: 66394 Nonbonded interactions: 162400 Sorted by model distance: nonbonded pdb=" O ALA B1026 " pdb=" OG SER B1030 " model vdw 2.295 3.040 nonbonded pdb=" O ASP A 994 " pdb=" OG1 THR A 998 " model vdw 2.304 3.040 nonbonded pdb=" O VAL B1040 " pdb=" OG SER C1030 " model vdw 2.307 3.040 nonbonded pdb=" O ASP A 979 " pdb=" OG1 THR C 385 " model vdw 2.314 3.040 nonbonded pdb=" O GLN B1005 " pdb=" OG1 THR B1009 " model vdw 2.335 3.040 ... (remaining 162395 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 'B' and (resid 27 through 829 or resid 832 through 1135)) selection = (chain 'C' and (resid 27 through 240 or resid 265 through 1135)) } 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: 6.320 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: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 50.080 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.140 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4669 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 : 0.007 0.084 21771 Z= 0.355 Angle : 1.387 20.992 29655 Z= 0.750 Chirality : 0.078 0.508 3378 Planarity : 0.010 0.085 3841 Dihedral : 13.253 89.658 7792 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.13), residues: 2730 helix: -3.17 (0.13), residues: 604 sheet: -0.35 (0.26), residues: 388 loop : -1.90 (0.13), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP H 50 HIS 0.016 0.002 HIS A1048 PHE 0.061 0.004 PHE A 906 TYR 0.061 0.003 TYR C 369 ARG 0.018 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.21085 ( 680) hydrogen bonds : angle 9.80958 ( 1926) SS BOND : bond 0.00951 ( 35) SS BOND : angle 2.43374 ( 70) covalent geometry : bond 0.00742 (21736) covalent geometry : angle 1.38316 (29585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.6714 (ptm) cc_final: 0.6456 (ptm) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.3339 time to fit residues: 180.4216 Evaluate side-chains 238 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 140 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 314 GLN B 331 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1011 GLN C 487 ASN C 675 GLN C 926 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1036 GLN H 65 GLN H 178 GLN ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 201 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.212592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.177710 restraints weight = 39530.262| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 3.40 r_work: 0.4472 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21771 Z= 0.164 Angle : 0.690 12.620 29655 Z= 0.361 Chirality : 0.046 0.210 3378 Planarity : 0.006 0.054 3841 Dihedral : 5.739 22.799 2944 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.43 % Allowed : 7.71 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2730 helix: -1.63 (0.18), residues: 624 sheet: -0.32 (0.25), residues: 441 loop : -1.46 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 886 HIS 0.004 0.001 HIS B1058 PHE 0.033 0.002 PHE C 906 TYR 0.025 0.002 TYR A 756 ARG 0.007 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.05771 ( 680) hydrogen bonds : angle 7.08440 ( 1926) SS BOND : bond 0.00604 ( 35) SS BOND : angle 1.63817 ( 70) covalent geometry : bond 0.00354 (21736) covalent geometry : angle 0.68656 (29585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.6119 (m-80) REVERT: B 54 LEU cc_start: 0.5026 (mm) cc_final: 0.4631 (pp) REVERT: B 888 PHE cc_start: 0.3851 (t80) cc_final: 0.3643 (t80) REVERT: B 927 PHE cc_start: 0.6265 (t80) cc_final: 0.5029 (t80) REVERT: C 440 ASN cc_start: 0.7902 (t0) cc_final: 0.7700 (p0) REVERT: C 703 ASN cc_start: 0.6553 (m-40) cc_final: 0.6326 (m-40) outliers start: 34 outliers final: 20 residues processed: 293 average time/residue: 0.3321 time to fit residues: 151.4219 Evaluate side-chains 240 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 112 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 121 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 613 GLN B 655 HIS C 196 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN H 6 GLN H 65 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.206337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.171937 restraints weight = 39459.974| |-----------------------------------------------------------------------------| r_work (start): 0.4534 rms_B_bonded: 3.20 r_work: 0.4361 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 21771 Z= 0.203 Angle : 0.723 14.352 29655 Z= 0.378 Chirality : 0.048 0.178 3378 Planarity : 0.005 0.061 3841 Dihedral : 5.606 27.139 2944 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.61 % Allowed : 10.20 % Favored : 87.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 2730 helix: -1.20 (0.19), residues: 613 sheet: -0.35 (0.25), residues: 425 loop : -1.41 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.006 0.001 HIS C1064 PHE 0.040 0.002 PHE C 906 TYR 0.029 0.002 TYR C1067 ARG 0.007 0.001 ARG B1107 Details of bonding type rmsd hydrogen bonds : bond 0.06237 ( 680) hydrogen bonds : angle 6.91684 ( 1926) SS BOND : bond 0.00593 ( 35) SS BOND : angle 2.12725 ( 70) covalent geometry : bond 0.00460 (21736) covalent geometry : angle 0.71673 (29585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: B 868 GLU cc_start: 0.6705 (mp0) cc_final: 0.6476 (mp0) REVERT: B 927 PHE cc_start: 0.6137 (t80) cc_final: 0.5463 (t80) REVERT: B 1111 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6896 (pt0) REVERT: C 299 THR cc_start: 0.3145 (m) cc_final: 0.2046 (p) REVERT: C 873 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: L 76 ARG cc_start: 0.7964 (mtm180) cc_final: 0.7576 (ptp-170) outliers start: 62 outliers final: 37 residues processed: 278 average time/residue: 0.3167 time to fit residues: 139.5019 Evaluate side-chains 244 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 159 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 262 optimal weight: 0.0670 chunk 13 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B1011 GLN C 644 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.206209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.170998 restraints weight = 40049.494| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 3.73 r_work: 0.4315 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21771 Z= 0.174 Angle : 0.666 12.563 29655 Z= 0.346 Chirality : 0.046 0.232 3378 Planarity : 0.005 0.069 3841 Dihedral : 5.420 22.794 2944 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.57 % Allowed : 12.90 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 2730 helix: -0.87 (0.19), residues: 617 sheet: -0.56 (0.25), residues: 426 loop : -1.36 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 436 HIS 0.005 0.001 HIS C1064 PHE 0.032 0.002 PHE C 906 TYR 0.021 0.002 TYR C1067 ARG 0.006 0.000 ARG B1107 Details of bonding type rmsd hydrogen bonds : bond 0.05779 ( 680) hydrogen bonds : angle 6.63759 ( 1926) SS BOND : bond 0.00428 ( 35) SS BOND : angle 1.76074 ( 70) covalent geometry : bond 0.00387 (21736) covalent geometry : angle 0.66121 (29585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: A 896 ILE cc_start: 0.5525 (OUTLIER) cc_final: 0.5103 (tp) REVERT: A 962 LEU cc_start: 0.8069 (tp) cc_final: 0.7813 (mt) REVERT: B 516 GLU cc_start: 0.7479 (tp30) cc_final: 0.7092 (tp30) REVERT: B 1111 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6849 (pt0) REVERT: C 299 THR cc_start: 0.3004 (m) cc_final: 0.1740 (p) REVERT: C 464 PHE cc_start: 0.6698 (m-80) cc_final: 0.6242 (m-80) REVERT: C 983 ARG cc_start: 0.2094 (mtp180) cc_final: 0.1050 (mtt180) REVERT: H 99 MET cc_start: 0.5438 (mtm) cc_final: 0.5170 (mtm) REVERT: L 138 CYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6497 (t) outliers start: 61 outliers final: 36 residues processed: 275 average time/residue: 0.3226 time to fit residues: 137.9794 Evaluate side-chains 252 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1064 HIS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 138 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 230 optimal weight: 9.9990 chunk 152 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 628 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 542 ASN ** C 928 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 = 0.4941 r_free = 0.4941 target = 0.206324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.170667 restraints weight = 39443.295| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 3.35 r_work: 0.4376 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21771 Z= 0.156 Angle : 0.646 11.158 29655 Z= 0.335 Chirality : 0.046 0.315 3378 Planarity : 0.005 0.065 3841 Dihedral : 5.282 21.430 2944 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.78 % Allowed : 13.49 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.16), residues: 2730 helix: -0.71 (0.20), residues: 622 sheet: -0.44 (0.25), residues: 443 loop : -1.35 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.005 0.001 HIS B1048 PHE 0.034 0.002 PHE B 927 TYR 0.042 0.002 TYR C 453 ARG 0.007 0.000 ARG B 319 Details of bonding type rmsd hydrogen bonds : bond 0.05568 ( 680) hydrogen bonds : angle 6.47683 ( 1926) SS BOND : bond 0.00443 ( 35) SS BOND : angle 1.77159 ( 70) covalent geometry : bond 0.00349 (21736) covalent geometry : angle 0.64084 (29585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.6213 (m-80) REVERT: A 896 ILE cc_start: 0.5361 (OUTLIER) cc_final: 0.4864 (tp) REVERT: B 330 PRO cc_start: 0.8488 (Cg_exo) cc_final: 0.8198 (Cg_endo) REVERT: B 437 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7223 (t0) REVERT: B 1111 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6891 (pt0) REVERT: C 194 PHE cc_start: 0.4081 (OUTLIER) cc_final: 0.1625 (p90) REVERT: C 299 THR cc_start: 0.2763 (m) cc_final: 0.1485 (p) REVERT: C 369 TYR cc_start: 0.5357 (OUTLIER) cc_final: 0.4654 (t80) REVERT: C 464 PHE cc_start: 0.6588 (m-80) cc_final: 0.6123 (m-80) REVERT: C 794 ILE cc_start: 0.3963 (OUTLIER) cc_final: 0.3337 (tt) REVERT: H 32 TYR cc_start: 0.6091 (OUTLIER) cc_final: 0.5480 (t80) REVERT: L 76 ARG cc_start: 0.8102 (mtm180) cc_final: 0.7688 (ptp-170) REVERT: L 138 CYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6523 (t) outliers start: 66 outliers final: 42 residues processed: 266 average time/residue: 0.3629 time to fit residues: 153.5388 Evaluate side-chains 255 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1064 HIS Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 138 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 15 optimal weight: 0.0370 chunk 42 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 170 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 192 optimal weight: 0.2980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.209033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.172578 restraints weight = 39285.756| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 3.58 r_work: 0.4398 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21771 Z= 0.126 Angle : 0.606 8.773 29655 Z= 0.314 Chirality : 0.044 0.325 3378 Planarity : 0.005 0.060 3841 Dihedral : 5.013 20.275 2944 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.40 % Allowed : 14.54 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.16), residues: 2730 helix: -0.59 (0.20), residues: 636 sheet: -0.42 (0.26), residues: 399 loop : -1.33 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 PHE 0.036 0.001 PHE C 497 TYR 0.037 0.001 TYR C 505 ARG 0.005 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 680) hydrogen bonds : angle 6.15998 ( 1926) SS BOND : bond 0.00334 ( 35) SS BOND : angle 1.43188 ( 70) covalent geometry : bond 0.00273 (21736) covalent geometry : angle 0.60299 (29585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6205 (m-80) REVERT: B 330 PRO cc_start: 0.8574 (Cg_exo) cc_final: 0.8340 (Cg_endo) REVERT: B 1029 MET cc_start: 0.4446 (OUTLIER) cc_final: 0.3836 (tmm) REVERT: B 1111 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6795 (pt0) REVERT: B 1132 ILE cc_start: 0.5050 (tt) cc_final: 0.4632 (mm) REVERT: C 194 PHE cc_start: 0.3955 (OUTLIER) cc_final: 0.1517 (p90) REVERT: C 299 THR cc_start: 0.2554 (m) cc_final: 0.1272 (p) REVERT: C 304 LYS cc_start: 0.5579 (mmtm) cc_final: 0.4396 (mmtt) REVERT: C 464 PHE cc_start: 0.6658 (m-80) cc_final: 0.6241 (m-80) REVERT: C 740 MET cc_start: 0.4775 (mmm) cc_final: 0.3545 (ttp) REVERT: C 794 ILE cc_start: 0.3902 (OUTLIER) cc_final: 0.3340 (tt) REVERT: H 32 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5729 (t80) REVERT: H 76 MET cc_start: 0.7122 (mmm) cc_final: 0.6199 (ptt) REVERT: L 138 CYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6307 (t) outliers start: 57 outliers final: 34 residues processed: 266 average time/residue: 0.3197 time to fit residues: 133.3852 Evaluate side-chains 248 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1064 HIS Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain L residue 138 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 177 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 61 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 250 optimal weight: 0.0870 chunk 185 optimal weight: 0.0670 chunk 213 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.207346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.171953 restraints weight = 39224.990| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 3.69 r_work: 0.4379 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21771 Z= 0.139 Angle : 0.616 9.985 29655 Z= 0.319 Chirality : 0.045 0.219 3378 Planarity : 0.005 0.060 3841 Dihedral : 4.969 20.044 2944 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.65 % Allowed : 14.54 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2730 helix: -0.40 (0.20), residues: 629 sheet: -0.21 (0.25), residues: 440 loop : -1.37 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 436 HIS 0.005 0.001 HIS A1048 PHE 0.038 0.002 PHE B 927 TYR 0.026 0.001 TYR C 505 ARG 0.008 0.001 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 680) hydrogen bonds : angle 6.10166 ( 1926) SS BOND : bond 0.00386 ( 35) SS BOND : angle 1.40363 ( 70) covalent geometry : bond 0.00309 (21736) covalent geometry : angle 0.61305 (29585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: B 330 PRO cc_start: 0.8553 (Cg_exo) cc_final: 0.8333 (Cg_endo) REVERT: B 437 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7219 (t0) REVERT: B 1111 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6846 (pt0) REVERT: C 194 PHE cc_start: 0.4058 (OUTLIER) cc_final: 0.1648 (p90) REVERT: C 299 THR cc_start: 0.2664 (m) cc_final: 0.1343 (p) REVERT: C 304 LYS cc_start: 0.5779 (mmtm) cc_final: 0.4310 (mttm) REVERT: C 369 TYR cc_start: 0.5294 (OUTLIER) cc_final: 0.4674 (t80) REVERT: C 464 PHE cc_start: 0.6672 (m-80) cc_final: 0.6220 (m-80) REVERT: C 740 MET cc_start: 0.4979 (mmm) cc_final: 0.3766 (ttp) REVERT: C 794 ILE cc_start: 0.4047 (OUTLIER) cc_final: 0.3496 (tt) REVERT: H 32 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5718 (t80) REVERT: H 48 MET cc_start: 0.6812 (mtp) cc_final: 0.6538 (mtp) REVERT: H 76 MET cc_start: 0.7153 (mmm) cc_final: 0.6217 (ptt) REVERT: H 99 MET cc_start: 0.6281 (ptp) cc_final: 0.5543 (ptp) REVERT: L 76 ARG cc_start: 0.8222 (mtm180) cc_final: 0.7931 (ptp-170) REVERT: L 138 CYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6293 (t) outliers start: 63 outliers final: 42 residues processed: 260 average time/residue: 0.3256 time to fit residues: 133.7164 Evaluate side-chains 255 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1064 HIS Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 138 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 267 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 196 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 388 ASN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.202047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.166841 restraints weight = 39381.530| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 3.62 r_work: 0.4293 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 21771 Z= 0.221 Angle : 0.721 13.520 29655 Z= 0.377 Chirality : 0.048 0.331 3378 Planarity : 0.005 0.065 3841 Dihedral : 5.486 24.537 2944 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.03 % Allowed : 14.96 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2730 helix: -0.72 (0.20), residues: 625 sheet: -0.47 (0.26), residues: 424 loop : -1.49 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 90 HIS 0.006 0.001 HIS C1064 PHE 0.038 0.002 PHE C 906 TYR 0.028 0.002 TYR B 505 ARG 0.007 0.001 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.06085 ( 680) hydrogen bonds : angle 6.63753 ( 1926) SS BOND : bond 0.00534 ( 35) SS BOND : angle 1.87321 ( 70) covalent geometry : bond 0.00506 (21736) covalent geometry : angle 0.71623 (29585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 735 SER cc_start: 0.8270 (m) cc_final: 0.7639 (p) REVERT: A 759 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: A 964 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7521 (mttp) REVERT: B 329 PHE cc_start: 0.6101 (m-80) cc_final: 0.5310 (t80) REVERT: B 330 PRO cc_start: 0.8683 (Cg_exo) cc_final: 0.8427 (Cg_endo) REVERT: B 437 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7179 (t0) REVERT: B 1111 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6756 (pt0) REVERT: C 194 PHE cc_start: 0.4059 (OUTLIER) cc_final: 0.1740 (p90) REVERT: C 299 THR cc_start: 0.2771 (m) cc_final: 0.1445 (p) REVERT: C 464 PHE cc_start: 0.6783 (m-80) cc_final: 0.6268 (m-80) REVERT: C 740 MET cc_start: 0.5061 (mmm) cc_final: 0.4020 (ttp) REVERT: C 794 ILE cc_start: 0.4176 (OUTLIER) cc_final: 0.3589 (tt) REVERT: C 873 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6776 (m-10) REVERT: H 32 TYR cc_start: 0.6235 (OUTLIER) cc_final: 0.5585 (t80) REVERT: H 99 MET cc_start: 0.6490 (ptp) cc_final: 0.5661 (ptt) REVERT: H 191 VAL cc_start: 0.7501 (m) cc_final: 0.7299 (p) REVERT: L 138 CYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6324 (t) REVERT: L 144 TYR cc_start: 0.7270 (t80) cc_final: 0.6926 (t80) outliers start: 72 outliers final: 49 residues processed: 266 average time/residue: 0.3256 time to fit residues: 136.3261 Evaluate side-chains 253 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 138 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 218 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.206791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.168799 restraints weight = 39184.382| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 3.81 r_work: 0.4350 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21771 Z= 0.140 Angle : 0.650 11.684 29655 Z= 0.336 Chirality : 0.045 0.311 3378 Planarity : 0.005 0.067 3841 Dihedral : 5.142 21.556 2944 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.28 % Allowed : 16.27 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2730 helix: -0.51 (0.20), residues: 631 sheet: -0.28 (0.26), residues: 431 loop : -1.43 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 436 HIS 0.005 0.001 HIS A1048 PHE 0.021 0.002 PHE C 374 TYR 0.029 0.001 TYR B 505 ARG 0.008 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.05239 ( 680) hydrogen bonds : angle 6.27543 ( 1926) SS BOND : bond 0.00388 ( 35) SS BOND : angle 1.54025 ( 70) covalent geometry : bond 0.00311 (21736) covalent geometry : angle 0.64598 (29585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6442 (m-80) REVERT: B 330 PRO cc_start: 0.8679 (Cg_exo) cc_final: 0.8460 (Cg_endo) REVERT: B 1132 ILE cc_start: 0.5148 (tt) cc_final: 0.4921 (tt) REVERT: C 194 PHE cc_start: 0.3945 (OUTLIER) cc_final: 0.0991 (p90) REVERT: C 299 THR cc_start: 0.2682 (m) cc_final: 0.1372 (p) REVERT: C 304 LYS cc_start: 0.5885 (mmtm) cc_final: 0.4324 (mtpp) REVERT: C 464 PHE cc_start: 0.6660 (m-80) cc_final: 0.6148 (m-80) REVERT: C 740 MET cc_start: 0.5022 (mmm) cc_final: 0.4193 (ttp) REVERT: C 794 ILE cc_start: 0.4098 (OUTLIER) cc_final: 0.3622 (tt) REVERT: C 873 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.6696 (m-10) REVERT: C 881 THR cc_start: 0.7338 (p) cc_final: 0.6978 (p) REVERT: C 1050 MET cc_start: 0.6352 (ptm) cc_final: 0.6083 (ptp) REVERT: H 32 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5438 (t80) REVERT: H 48 MET cc_start: 0.6719 (mtp) cc_final: 0.6485 (mtp) REVERT: H 99 MET cc_start: 0.6353 (ptp) cc_final: 0.5506 (ptt) REVERT: L 76 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7839 (ptp90) REVERT: L 138 CYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6515 (t) outliers start: 54 outliers final: 43 residues processed: 244 average time/residue: 0.3236 time to fit residues: 124.7121 Evaluate side-chains 249 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 138 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 239 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 241 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.204010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.168907 restraints weight = 39331.815| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 3.67 r_work: 0.4319 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21771 Z= 0.180 Angle : 0.691 11.530 29655 Z= 0.357 Chirality : 0.047 0.337 3378 Planarity : 0.005 0.071 3841 Dihedral : 5.243 22.229 2944 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.23 % Allowed : 16.48 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2730 helix: -0.57 (0.20), residues: 627 sheet: -0.42 (0.26), residues: 422 loop : -1.44 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 436 HIS 0.005 0.001 HIS A1048 PHE 0.028 0.002 PHE C 906 TYR 0.027 0.002 TYR B 505 ARG 0.010 0.001 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.05544 ( 680) hydrogen bonds : angle 6.40991 ( 1926) SS BOND : bond 0.00470 ( 35) SS BOND : angle 1.65080 ( 70) covalent geometry : bond 0.00413 (21736) covalent geometry : angle 0.68665 (29585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.6408 (m-80) REVERT: B 329 PHE cc_start: 0.6039 (m-80) cc_final: 0.5299 (t80) REVERT: B 330 PRO cc_start: 0.8753 (Cg_exo) cc_final: 0.8530 (Cg_endo) REVERT: B 1132 ILE cc_start: 0.5246 (tt) cc_final: 0.4936 (tt) REVERT: C 194 PHE cc_start: 0.3980 (OUTLIER) cc_final: 0.1743 (p90) REVERT: C 299 THR cc_start: 0.2707 (m) cc_final: 0.1347 (p) REVERT: C 464 PHE cc_start: 0.6775 (m-80) cc_final: 0.6207 (m-80) REVERT: C 497 PHE cc_start: 0.4289 (m-10) cc_final: 0.3861 (m-80) REVERT: C 740 MET cc_start: 0.4986 (mmm) cc_final: 0.4163 (ttp) REVERT: C 794 ILE cc_start: 0.4090 (OUTLIER) cc_final: 0.3565 (tt) REVERT: C 873 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6787 (m-10) REVERT: H 32 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.5415 (t80) REVERT: H 99 MET cc_start: 0.6327 (ptp) cc_final: 0.5484 (ptt) REVERT: L 138 CYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6400 (t) outliers start: 53 outliers final: 45 residues processed: 242 average time/residue: 0.3351 time to fit residues: 128.5154 Evaluate side-chains 244 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 138 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 195 optimal weight: 0.7980 chunk 9 optimal weight: 0.0030 chunk 15 optimal weight: 0.0470 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 183 optimal weight: 0.0980 chunk 193 optimal weight: 3.9990 chunk 258 optimal weight: 0.2980 overall best weight: 0.2488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1011 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.212331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.183805 restraints weight = 41582.993| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 2.77 r_work: 0.4463 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21771 Z= 0.123 Angle : 0.629 11.139 29655 Z= 0.324 Chirality : 0.045 0.245 3378 Planarity : 0.004 0.069 3841 Dihedral : 4.898 20.375 2944 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.11 % Allowed : 16.39 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.16), residues: 2730 helix: -0.31 (0.20), residues: 632 sheet: -0.32 (0.25), residues: 472 loop : -1.34 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 436 HIS 0.006 0.001 HIS A1048 PHE 0.022 0.001 PHE A 759 TYR 0.029 0.001 TYR B 505 ARG 0.009 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 680) hydrogen bonds : angle 6.01648 ( 1926) SS BOND : bond 0.00350 ( 35) SS BOND : angle 1.40105 ( 70) covalent geometry : bond 0.00271 (21736) covalent geometry : angle 0.62625 (29585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14757.56 seconds wall clock time: 255 minutes 30.63 seconds (15330.63 seconds total)