Starting phenix.real_space_refine on Thu Mar 5 09:36:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t5o_25699/03_2026/7t5o_25699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t5o_25699/03_2026/7t5o_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_25699/03_2026/7t5o_25699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t5o_25699/03_2026/7t5o_25699.map" model { file = "/net/cci-nas-00/data/ceres_data/7t5o_25699/03_2026/7t5o_25699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t5o_25699/03_2026/7t5o_25699.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.18, per 1000 atoms: 0.24 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: 1.64 Conformation dependent library (CDL) restraints added in 1.4 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: 0.84 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: 4.76 Time building geometry restraints manager: 2.32 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: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.840 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.018 0.001 ARG L 19 TYR 0.061 0.003 TYR C 369 PHE 0.061 0.004 PHE A 906 TRP 0.036 0.003 TRP H 50 HIS 0.016 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00742 (21736) covalent geometry : angle 1.38316 (29585) SS BOND : bond 0.00951 ( 35) SS BOND : angle 2.43374 ( 70) hydrogen bonds : bond 0.21085 ( 680) hydrogen bonds : angle 9.80958 ( 1926) *********************** 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 : 0.546 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: 0.1454 time to fit residues: 78.9055 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 : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.212338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.178098 restraints weight = 39808.902| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 3.68 r_work: 0.4454 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21771 Z= 0.169 Angle : 0.701 12.734 29655 Z= 0.366 Chirality : 0.046 0.214 3378 Planarity : 0.006 0.055 3841 Dihedral : 5.763 22.829 2944 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.47 % Allowed : 7.75 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.15), residues: 2730 helix: -1.68 (0.17), residues: 624 sheet: -0.31 (0.25), residues: 441 loop : -1.46 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 19 TYR 0.025 0.002 TYR C 505 PHE 0.034 0.002 PHE C 906 TRP 0.015 0.002 TRP A 886 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00372 (21736) covalent geometry : angle 0.69699 (29585) SS BOND : bond 0.00531 ( 35) SS BOND : angle 1.61611 ( 70) hydrogen bonds : bond 0.05819 ( 680) hydrogen bonds : angle 7.13156 ( 1926) *********************** 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 303 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 268 time to evaluate : 0.884 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: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6129 (m-80) REVERT: B 54 LEU cc_start: 0.5034 (mm) cc_final: 0.4630 (pp) REVERT: B 800 PHE cc_start: 0.6089 (m-10) cc_final: 0.5887 (m-80) REVERT: B 888 PHE cc_start: 0.3860 (t80) cc_final: 0.3650 (t80) REVERT: B 927 PHE cc_start: 0.6279 (t80) cc_final: 0.5043 (t80) REVERT: C 440 ASN cc_start: 0.7927 (t0) cc_final: 0.7721 (p0) REVERT: C 703 ASN cc_start: 0.6574 (m-40) cc_final: 0.6342 (m-40) outliers start: 35 outliers final: 21 residues processed: 291 average time/residue: 0.1424 time to fit residues: 64.4353 Evaluate side-chains 243 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 625 HIS Chi-restraints excluded: chain C residue 636 TYR 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 212 optimal weight: 8.9990 chunk 95 optimal weight: 0.0060 chunk 31 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1064 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 755 GLN C 644 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.211054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.176887 restraints weight = 39741.727| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 3.65 r_work: 0.4434 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 21771 Z= 0.149 Angle : 0.641 12.312 29655 Z= 0.333 Chirality : 0.045 0.172 3378 Planarity : 0.005 0.064 3841 Dihedral : 5.302 25.498 2944 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.02 % Allowed : 10.11 % Favored : 87.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.15), residues: 2730 helix: -0.98 (0.19), residues: 611 sheet: -0.26 (0.25), residues: 424 loop : -1.32 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 53 TYR 0.025 0.001 TYR B 505 PHE 0.031 0.002 PHE C 906 TRP 0.013 0.001 TRP A 886 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00330 (21736) covalent geometry : angle 0.63620 (29585) SS BOND : bond 0.00425 ( 35) SS BOND : angle 1.76506 ( 70) hydrogen bonds : bond 0.05540 ( 680) hydrogen bonds : angle 6.56933 ( 1926) *********************** 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 294 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.6146 (m-80) REVERT: B 54 LEU cc_start: 0.5024 (mm) cc_final: 0.4379 (pp) REVERT: B 330 PRO cc_start: 0.8421 (Cg_exo) cc_final: 0.8119 (Cg_endo) REVERT: B 888 PHE cc_start: 0.3854 (t80) cc_final: 0.3466 (t80) REVERT: B 927 PHE cc_start: 0.6216 (t80) cc_final: 0.5130 (t80) REVERT: C 440 ASN cc_start: 0.8011 (t0) cc_final: 0.7791 (p0) REVERT: C 456 PHE cc_start: 0.8330 (m-80) cc_final: 0.7793 (m-80) REVERT: H 76 MET cc_start: 0.7045 (mmm) cc_final: 0.6289 (ptt) REVERT: L 49 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8095 (m-30) outliers start: 48 outliers final: 30 residues processed: 279 average time/residue: 0.1370 time to fit residues: 60.0336 Evaluate side-chains 243 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 898 PHE 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 645 THR 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 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1064 HIS Chi-restraints excluded: chain H residue 65 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 198 optimal weight: 0.0980 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 0.0870 chunk 176 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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** ** B1106 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 = 0.4991 r_free = 0.4991 target = 0.211461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.176724 restraints weight = 39799.440| |-----------------------------------------------------------------------------| r_work (start): 0.4605 rms_B_bonded: 3.72 r_work: 0.4420 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21771 Z= 0.131 Angle : 0.609 14.707 29655 Z= 0.316 Chirality : 0.044 0.198 3378 Planarity : 0.005 0.064 3841 Dihedral : 5.087 20.380 2944 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.11 % Allowed : 11.72 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2730 helix: -0.61 (0.20), residues: 617 sheet: -0.33 (0.26), residues: 424 loop : -1.27 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 19 TYR 0.028 0.001 TYR C 495 PHE 0.023 0.002 PHE C 906 TRP 0.036 0.001 TRP B 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00287 (21736) covalent geometry : angle 0.60469 (29585) SS BOND : bond 0.00353 ( 35) SS BOND : angle 1.63987 ( 70) hydrogen bonds : bond 0.05154 ( 680) hydrogen bonds : angle 6.27732 ( 1926) *********************** 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 284 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 888 PHE cc_start: 0.3778 (t80) cc_final: 0.3453 (t80) REVERT: B 927 PHE cc_start: 0.6027 (t80) cc_final: 0.5199 (t80) REVERT: B 969 ASN cc_start: 0.8161 (p0) cc_final: 0.7952 (p0) REVERT: C 440 ASN cc_start: 0.7944 (t0) cc_final: 0.7737 (p0) REVERT: C 759 PHE cc_start: 0.6421 (OUTLIER) cc_final: 0.6187 (m-10) REVERT: C 774 GLN cc_start: 0.6403 (mt0) cc_final: 0.6192 (mm-40) REVERT: C 912 THR cc_start: 0.2803 (OUTLIER) cc_final: 0.2558 (t) REVERT: H 76 MET cc_start: 0.7004 (mmm) cc_final: 0.6373 (ptt) REVERT: H 89 GLU cc_start: 0.6844 (mp0) cc_final: 0.6638 (mp0) REVERT: L 19 ARG cc_start: 0.7778 (mmm160) cc_final: 0.7445 (mmm160) REVERT: L 49 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: L 72 LEU cc_start: 0.5313 (tp) cc_final: 0.5106 (tp) outliers start: 50 outliers final: 29 residues processed: 269 average time/residue: 0.1373 time to fit residues: 57.9785 Evaluate side-chains 244 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 898 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 315 THR Chi-restraints excluded: chain B residue 645 THR 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 992 GLN Chi-restraints excluded: chain B residue 1101 HIS 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 636 TYR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 984 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 5 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 907 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 628 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1011 GLN C 388 ASN C 542 ASN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.205468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.170806 restraints weight = 39441.345| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 3.19 r_work: 0.4344 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 21771 Z= 0.193 Angle : 0.697 13.213 29655 Z= 0.363 Chirality : 0.047 0.180 3378 Planarity : 0.005 0.062 3841 Dihedral : 5.330 22.391 2944 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.82 % Allowed : 12.31 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.16), residues: 2730 helix: -0.79 (0.20), residues: 618 sheet: -0.31 (0.24), residues: 467 loop : -1.33 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1107 TYR 0.034 0.002 TYR C 495 PHE 0.040 0.002 PHE C 906 TRP 0.037 0.002 TRP B 436 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00442 (21736) covalent geometry : angle 0.69021 (29585) SS BOND : bond 0.00503 ( 35) SS BOND : angle 2.06737 ( 70) hydrogen bonds : bond 0.05897 ( 680) hydrogen bonds : angle 6.54867 ( 1926) *********************** 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 288 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 864 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6396 (tp) REVERT: A 896 ILE cc_start: 0.5520 (OUTLIER) cc_final: 0.5012 (tp) REVERT: B 330 PRO cc_start: 0.8462 (Cg_exo) cc_final: 0.8177 (Cg_endo) REVERT: B 436 TRP cc_start: 0.5357 (p-90) cc_final: 0.4292 (p-90) REVERT: B 437 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7315 (t0) REVERT: B 457 ARG cc_start: 0.5180 (mmm160) cc_final: 0.4382 (mmp-170) REVERT: B 868 GLU cc_start: 0.6641 (mp0) cc_final: 0.6365 (mp0) REVERT: B 1111 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6693 (pt0) REVERT: C 299 THR cc_start: 0.3121 (m) cc_final: 0.1947 (p) REVERT: C 464 PHE cc_start: 0.6574 (m-80) cc_final: 0.6159 (m-80) REVERT: C 726 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5873 (mm) REVERT: C 873 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6767 (m-80) REVERT: H 76 MET cc_start: 0.7037 (mmm) cc_final: 0.5977 (ptt) REVERT: H 89 GLU cc_start: 0.6950 (mp0) cc_final: 0.6740 (mp0) REVERT: L 76 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7641 (ptp-170) REVERT: L 138 CYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6632 (t) REVERT: L 193 ARG cc_start: 0.7005 (mpp80) cc_final: 0.6172 (mpp80) outliers start: 67 outliers final: 41 residues processed: 268 average time/residue: 0.1300 time to fit residues: 55.4996 Evaluate side-chains 247 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 736 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 896 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 55 PHE 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 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 974 SER 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 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 495 TYR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS 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 984 LEU 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 7 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 95 optimal weight: 0.0570 chunk 42 optimal weight: 7.9990 chunk 40 optimal weight: 0.0570 chunk 207 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1002 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.208351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.174002 restraints weight = 39418.716| |-----------------------------------------------------------------------------| r_work (start): 0.4572 rms_B_bonded: 3.12 r_work: 0.4405 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21771 Z= 0.135 Angle : 0.615 10.209 29655 Z= 0.319 Chirality : 0.045 0.234 3378 Planarity : 0.004 0.058 3841 Dihedral : 5.061 21.521 2944 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.32 % Allowed : 13.49 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.16), residues: 2730 helix: -0.51 (0.20), residues: 625 sheet: -0.33 (0.26), residues: 413 loop : -1.24 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 19 TYR 0.033 0.001 TYR C 453 PHE 0.035 0.002 PHE B 927 TRP 0.025 0.001 TRP B 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00296 (21736) covalent geometry : angle 0.61057 (29585) SS BOND : bond 0.00364 ( 35) SS BOND : angle 1.55423 ( 70) hydrogen bonds : bond 0.05191 ( 680) hydrogen bonds : angle 6.22350 ( 1926) *********************** 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 279 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 330 PRO cc_start: 0.8511 (Cg_exo) cc_final: 0.8269 (Cg_endo) REVERT: B 436 TRP cc_start: 0.5459 (p-90) cc_final: 0.4456 (p-90) REVERT: B 437 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7337 (t0) REVERT: B 1111 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6729 (pt0) REVERT: C 194 PHE cc_start: 0.4096 (OUTLIER) cc_final: 0.1614 (p90) REVERT: C 299 THR cc_start: 0.3350 (m) cc_final: 0.2098 (p) REVERT: C 369 TYR cc_start: 0.5234 (OUTLIER) cc_final: 0.4665 (t80) REVERT: C 464 PHE cc_start: 0.6552 (m-80) cc_final: 0.6135 (m-80) REVERT: C 740 MET cc_start: 0.4643 (mmm) cc_final: 0.3533 (ptm) REVERT: C 794 ILE cc_start: 0.3893 (OUTLIER) cc_final: 0.3279 (tt) REVERT: H 32 TYR cc_start: 0.5998 (OUTLIER) cc_final: 0.5430 (t80) REVERT: H 76 MET cc_start: 0.7027 (mmm) cc_final: 0.6161 (ptt) REVERT: H 89 GLU cc_start: 0.6916 (mp0) cc_final: 0.6693 (mp0) REVERT: L 138 CYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6546 (t) outliers start: 55 outliers final: 34 residues processed: 264 average time/residue: 0.1350 time to fit residues: 56.7885 Evaluate side-chains 247 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 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 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 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 495 TYR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 170 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 784 GLN A 907 ASN ** A1002 GLN ** 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 414 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** 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 = 0.4870 r_free = 0.4870 target = 0.199765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.164654 restraints weight = 39521.271| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 3.18 r_work: 0.4271 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.133 21771 Z= 0.297 Angle : 0.802 15.888 29655 Z= 0.421 Chirality : 0.051 0.403 3378 Planarity : 0.006 0.064 3841 Dihedral : 5.807 26.771 2944 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.54 % Allowed : 13.19 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.15), residues: 2730 helix: -0.98 (0.20), residues: 611 sheet: -0.49 (0.25), residues: 456 loop : -1.56 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1107 TYR 0.037 0.003 TYR C 204 PHE 0.043 0.003 PHE C 906 TRP 0.027 0.002 TRP L 90 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00691 (21736) covalent geometry : angle 0.79718 (29585) SS BOND : bond 0.00626 ( 35) SS BOND : angle 2.04561 ( 70) hydrogen bonds : bond 0.06760 ( 680) hydrogen bonds : angle 7.01282 ( 1926) *********************** 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 306 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 222 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 735 SER cc_start: 0.8295 (m) cc_final: 0.7647 (p) REVERT: A 869 MET cc_start: 0.6801 (ttm) cc_final: 0.6569 (ttm) REVERT: A 896 ILE cc_start: 0.5702 (OUTLIER) cc_final: 0.5078 (tp) REVERT: B 329 PHE cc_start: 0.6195 (m-80) cc_final: 0.5311 (t80) REVERT: B 330 PRO cc_start: 0.8599 (Cg_exo) cc_final: 0.8352 (Cg_endo) REVERT: B 436 TRP cc_start: 0.5206 (p-90) cc_final: 0.4202 (p-90) REVERT: B 437 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.7341 (t0) REVERT: B 457 ARG cc_start: 0.5477 (mmm160) cc_final: 0.4630 (mmp-170) REVERT: B 850 ILE cc_start: 0.4528 (OUTLIER) cc_final: 0.4286 (mt) REVERT: B 1111 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6956 (pt0) REVERT: C 194 PHE cc_start: 0.4170 (OUTLIER) cc_final: 0.1780 (p90) REVERT: C 299 THR cc_start: 0.2888 (m) cc_final: 0.1609 (p) REVERT: C 464 PHE cc_start: 0.6775 (m-80) cc_final: 0.6197 (m-80) REVERT: C 794 ILE cc_start: 0.4086 (OUTLIER) cc_final: 0.3448 (tt) REVERT: C 873 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6977 (m-10) REVERT: H 32 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.5423 (t80) REVERT: H 46 GLU cc_start: 0.6252 (mm-30) cc_final: 0.6001 (mm-30) REVERT: L 49 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8516 (t0) REVERT: L 53 ARG cc_start: 0.7107 (ptp-110) cc_final: 0.6894 (ptp-110) REVERT: L 76 ARG cc_start: 0.8371 (mtm180) cc_final: 0.7947 (ptp-170) REVERT: L 138 CYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6576 (t) outliers start: 84 outliers final: 49 residues processed: 278 average time/residue: 0.1317 time to fit residues: 58.4424 Evaluate side-chains 262 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 204 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 818 ILE Chi-restraints excluded: chain A residue 896 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 55 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 655 HIS 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 878 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 1009 THR Chi-restraints excluded: chain B residue 1094 VAL 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 495 TYR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS 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 911 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 993 ILE 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 158 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 69 THR Chi-restraints excluded: chain L residue 121 LEU 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 228 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 206 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 201 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 628 GLN ** 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 965 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.205282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.168254 restraints weight = 39253.015| |-----------------------------------------------------------------------------| r_work (start): 0.4488 rms_B_bonded: 3.80 r_work: 0.4329 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21771 Z= 0.149 Angle : 0.658 10.852 29655 Z= 0.342 Chirality : 0.046 0.277 3378 Planarity : 0.005 0.061 3841 Dihedral : 5.356 22.541 2944 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.49 % Allowed : 15.21 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2730 helix: -0.66 (0.20), residues: 625 sheet: -0.44 (0.27), residues: 395 loop : -1.46 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 53 TYR 0.034 0.002 TYR C1007 PHE 0.025 0.002 PHE B 800 TRP 0.018 0.001 TRP B 436 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00334 (21736) covalent geometry : angle 0.65210 (29585) SS BOND : bond 0.00420 ( 35) SS BOND : angle 1.85050 ( 70) hydrogen bonds : bond 0.05477 ( 680) hydrogen bonds : angle 6.48830 ( 1926) *********************** 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 274 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 PRO cc_start: 0.8633 (Cg_exo) cc_final: 0.8430 (Cg_endo) REVERT: B 436 TRP cc_start: 0.5290 (p-90) cc_final: 0.4281 (p-90) REVERT: B 437 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.7460 (t0) REVERT: B 457 ARG cc_start: 0.5512 (mmm160) cc_final: 0.4797 (mmm160) REVERT: B 789 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5997 (m-80) REVERT: B 1005 GLN cc_start: 0.7376 (tp40) cc_final: 0.7027 (tt0) REVERT: B 1111 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6767 (pt0) REVERT: C 194 PHE cc_start: 0.4145 (OUTLIER) cc_final: 0.1008 (p90) REVERT: C 299 THR cc_start: 0.3036 (m) cc_final: 0.1702 (p) REVERT: C 304 LYS cc_start: 0.5734 (mmtm) cc_final: 0.4831 (mttm) REVERT: C 464 PHE cc_start: 0.6752 (m-80) cc_final: 0.6231 (m-80) REVERT: C 740 MET cc_start: 0.4801 (mmm) cc_final: 0.3725 (ttp) REVERT: C 794 ILE cc_start: 0.4133 (OUTLIER) cc_final: 0.3585 (tt) REVERT: C 1050 MET cc_start: 0.6553 (ptm) cc_final: 0.6330 (ptp) REVERT: H 32 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.5430 (t80) REVERT: H 48 MET cc_start: 0.6610 (mtp) cc_final: 0.6381 (mtp) REVERT: H 77 SER cc_start: 0.7264 (OUTLIER) cc_final: 0.6517 (p) REVERT: H 89 GLU cc_start: 0.6802 (mp0) cc_final: 0.6600 (mp0) REVERT: L 138 CYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6422 (t) REVERT: L 193 ARG cc_start: 0.6777 (mpp80) cc_final: 0.5943 (mpp80) outliers start: 59 outliers final: 40 residues processed: 257 average time/residue: 0.1350 time to fit residues: 54.9274 Evaluate side-chains 249 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 818 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 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 525 CYS 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 789 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 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 495 TYR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 933 LYS 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 77 SER 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 121 LEU 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 256 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 103 optimal weight: 0.3980 chunk 177 optimal weight: 10.0000 chunk 66 optimal weight: 0.0870 chunk 23 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 628 GLN ** 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** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.201338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.166022 restraints weight = 39371.795| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 3.16 r_work: 0.4271 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 21771 Z= 0.215 Angle : 0.725 13.389 29655 Z= 0.379 Chirality : 0.048 0.364 3378 Planarity : 0.005 0.063 3841 Dihedral : 5.540 24.165 2944 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.65 % Allowed : 15.09 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.16), residues: 2730 helix: -0.81 (0.20), residues: 629 sheet: -0.39 (0.25), residues: 440 loop : -1.53 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 53 TYR 0.032 0.002 TYR C 453 PHE 0.033 0.002 PHE C 906 TRP 0.020 0.002 TRP L 90 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00493 (21736) covalent geometry : angle 0.71949 (29585) SS BOND : bond 0.00526 ( 35) SS BOND : angle 1.91776 ( 70) hydrogen bonds : bond 0.06054 ( 680) hydrogen bonds : angle 6.71694 ( 1926) *********************** 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 271 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 735 SER cc_start: 0.8271 (m) cc_final: 0.7638 (p) REVERT: B 329 PHE cc_start: 0.6074 (m-80) cc_final: 0.5332 (t80) REVERT: B 330 PRO cc_start: 0.8700 (Cg_exo) cc_final: 0.8467 (Cg_endo) REVERT: B 436 TRP cc_start: 0.5065 (p-90) cc_final: 0.4156 (p-90) REVERT: B 437 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.7392 (t0) REVERT: B 457 ARG cc_start: 0.5472 (mmm160) cc_final: 0.4885 (mmm160) REVERT: B 1005 GLN cc_start: 0.7224 (tp40) cc_final: 0.6938 (tt0) REVERT: C 194 PHE cc_start: 0.3970 (OUTLIER) cc_final: 0.1632 (p90) REVERT: C 299 THR cc_start: 0.2840 (m) cc_final: 0.1518 (p) REVERT: C 464 PHE cc_start: 0.6728 (m-80) cc_final: 0.6163 (m-80) REVERT: C 740 MET cc_start: 0.5007 (mmm) cc_final: 0.3926 (ttp) REVERT: C 794 ILE cc_start: 0.4348 (OUTLIER) cc_final: 0.3758 (tt) REVERT: H 32 TYR cc_start: 0.5896 (OUTLIER) cc_final: 0.5283 (t80) REVERT: H 77 SER cc_start: 0.7118 (OUTLIER) cc_final: 0.6389 (p) REVERT: L 76 ARG cc_start: 0.8309 (mtm180) cc_final: 0.7902 (ptp-170) REVERT: L 138 CYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6641 (t) outliers start: 63 outliers final: 48 residues processed: 254 average time/residue: 0.1375 time to fit residues: 55.2575 Evaluate side-chains 253 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 805 ILE 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 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 525 CYS 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 850 ILE 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 1132 ILE 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 595 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR 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 H residue 32 TYR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 77 SER 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 30 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 121 LEU 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 268 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 256 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 15 optimal weight: 0.0370 chunk 52 optimal weight: 0.5980 chunk 137 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** 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 = 0.4928 r_free = 0.4928 target = 0.205271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.168838 restraints weight = 39515.969| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 3.80 r_work: 0.4309 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21771 Z= 0.149 Angle : 0.669 11.948 29655 Z= 0.346 Chirality : 0.046 0.342 3378 Planarity : 0.005 0.069 3841 Dihedral : 5.268 22.114 2944 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.19 % Allowed : 15.89 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.16), residues: 2730 helix: -0.65 (0.20), residues: 632 sheet: -0.49 (0.26), residues: 405 loop : -1.43 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 19 TYR 0.042 0.002 TYR C 453 PHE 0.023 0.002 PHE C 374 TRP 0.017 0.001 TRP B 436 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00332 (21736) covalent geometry : angle 0.66468 (29585) SS BOND : bond 0.00395 ( 35) SS BOND : angle 1.69625 ( 70) hydrogen bonds : bond 0.05376 ( 680) hydrogen bonds : angle 6.43847 ( 1926) ********************** 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 266 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 735 SER cc_start: 0.8230 (m) cc_final: 0.7632 (p) REVERT: B 329 PHE cc_start: 0.5985 (m-80) cc_final: 0.5204 (t80) REVERT: B 436 TRP cc_start: 0.5447 (p-90) cc_final: 0.4508 (p-90) REVERT: B 437 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.7383 (t0) REVERT: B 457 ARG cc_start: 0.5617 (mmm160) cc_final: 0.5029 (mmm160) REVERT: B 1005 GLN cc_start: 0.7352 (tp40) cc_final: 0.7001 (tt0) REVERT: B 1111 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7333 (mm-30) REVERT: C 194 PHE cc_start: 0.3987 (OUTLIER) cc_final: 0.1789 (p90) REVERT: C 299 THR cc_start: 0.3007 (m) cc_final: 0.1703 (p) REVERT: C 464 PHE cc_start: 0.6777 (m-80) cc_final: 0.6213 (m-80) REVERT: C 740 MET cc_start: 0.5237 (mmm) cc_final: 0.4189 (ttp) REVERT: C 794 ILE cc_start: 0.4089 (OUTLIER) cc_final: 0.3585 (tt) REVERT: C 906 PHE cc_start: 0.5692 (OUTLIER) cc_final: 0.3925 (t80) REVERT: H 32 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.5348 (t80) REVERT: L 76 ARG cc_start: 0.8269 (mtm180) cc_final: 0.7875 (ptp-170) REVERT: L 138 CYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6349 (t) outliers start: 52 outliers final: 40 residues processed: 253 average time/residue: 0.1380 time to fit residues: 54.8376 Evaluate side-chains 248 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 818 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 387 LEU 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 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1132 ILE 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 595 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 933 LYS 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 158 THR Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 121 LEU 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 151 optimal weight: 0.0050 chunk 126 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 15 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 204 optimal weight: 0.0970 chunk 197 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 231 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 overall best weight: 0.2510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1002 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** 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** C1010 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.209207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.173250 restraints weight = 39245.077| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 3.91 r_work: 0.4388 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21771 Z= 0.125 Angle : 0.638 10.656 29655 Z= 0.328 Chirality : 0.045 0.310 3378 Planarity : 0.005 0.067 3841 Dihedral : 4.922 23.119 2944 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.81 % Allowed : 16.43 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.16), residues: 2730 helix: -0.42 (0.20), residues: 637 sheet: -0.33 (0.25), residues: 469 loop : -1.34 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 19 TYR 0.031 0.001 TYR B 505 PHE 0.027 0.001 PHE B 888 TRP 0.017 0.001 TRP B 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00275 (21736) covalent geometry : angle 0.63493 (29585) SS BOND : bond 0.00350 ( 35) SS BOND : angle 1.47404 ( 70) hydrogen bonds : bond 0.04721 ( 680) hydrogen bonds : angle 6.04348 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6267.70 seconds wall clock time: 107 minutes 41.32 seconds (6461.32 seconds total)