Starting phenix.real_space_refine on Tue May 27 16:55:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g73_29795/05_2025/8g73_29795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g73_29795/05_2025/8g73_29795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g73_29795/05_2025/8g73_29795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g73_29795/05_2025/8g73_29795.map" model { file = "/net/cci-nas-00/data/ceres_data/8g73_29795/05_2025/8g73_29795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g73_29795/05_2025/8g73_29795.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1380 atoms to isotropic. 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 129 5.16 5 C 18040 2.51 5 N 4703 2.21 5 O 5548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 2.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28420 Number of models: 1 Model: "" Number of chains: 20 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8367 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "B" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "C" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "D" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "F" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 18.60, per 1000 atoms: 0.65 Number of scatterers: 28420 At special positions: 0 Unit cell: (164.25, 154.76, 205.13, 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 129 16.00 O 5548 8.00 N 4703 7.00 C 18040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " 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=2.06 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 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=1.97 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1074 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 282 " " NAG D1303 " - " ASN D 616 " " NAG D1304 " - " ASN D 657 " " NAG D1305 " - " ASN D 709 " " NAG D1306 " - " ASN D1074 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN D 717 " " NAG O 1 " - " ASN D 801 " " NAG P 1 " - " ASN D1098 " " NAG Q 1 " - " ASN D1134 " Time building additional restraints: 7.56 Conformation dependent library (CDL) restraints added in 3.6 seconds 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6638 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 62 sheets defined 22.0% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.681A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.962A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.503A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.818A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.547A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.559A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 4.008A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.848A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 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 783 removed outlier: 3.501A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.198A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.738A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.730A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.161A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.747A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.709A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.527A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.260A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.737A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.331A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 998 " --> pdb=" O ASP D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 4.111A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.236A pdb=" N GLY E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.345A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.597A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.890A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.671A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.901A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AB3, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB7, first strand: chain 'A' and resid 565 through 567 removed outlier: 7.000A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.513A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.657A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.300A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.300A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.336A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.444A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.148A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.893A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.629A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.685A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.831A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.371A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.697A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.562A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.552A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.980A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.776A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.630A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.437A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AE7, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.584A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR C 104 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.248A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.812A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 68 through 70 Processing sheet with id=AF2, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.482A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.617A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 311 through 318 removed outlier: 5.088A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 650 " --> pdb=" O PHE D 643 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AF6, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.647A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 376 through 380 Processing sheet with id=AF8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.598A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.625A pdb=" N ALA D 694 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.364A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.364A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.304A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.171A pdb=" N GLY F 10 " --> pdb=" O THR F 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.547A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR F 104 " --> pdb=" O ALA F 97 " (cutoff:3.500A) 1112 hydrogen bonds defined for protein. 2994 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: 13.76 Time building geometry restraints manager: 8.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4622 1.31 - 1.44: 8165 1.44 - 1.57: 16103 1.57 - 1.70: 1 1.70 - 1.83: 168 Bond restraints: 29059 Sorted by residual: bond pdb=" N ILE D 664 " pdb=" CA ILE D 664 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.70e-03 1.69e+04 1.87e+01 bond pdb=" C PRO A 85 " pdb=" O PRO A 85 " ideal model delta sigma weight residual 1.233 1.183 0.050 1.23e-02 6.61e+03 1.66e+01 bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.11e-02 8.12e+03 1.60e+01 bond pdb=" N VAL D 320 " pdb=" CA VAL D 320 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" N TYR D 695 " pdb=" CA TYR D 695 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.41e-02 5.03e+03 1.10e+01 ... (remaining 29054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 38371 2.38 - 4.76: 1069 4.76 - 7.14: 76 7.14 - 9.52: 26 9.52 - 11.90: 2 Bond angle restraints: 39544 Sorted by residual: angle pdb=" C ALA D 694 " pdb=" N TYR D 695 " pdb=" CA TYR D 695 " ideal model delta sigma weight residual 122.53 110.63 11.90 1.61e+00 3.86e-01 5.46e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 119.40 -8.70 1.22e+00 6.72e-01 5.08e+01 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" C PRO A 330 " ideal model delta sigma weight residual 110.55 101.05 9.50 1.63e+00 3.76e-01 3.40e+01 angle pdb=" O ASP B 586 " pdb=" C ASP B 586 " pdb=" N ILE B 587 " ideal model delta sigma weight residual 123.27 117.11 6.16 1.13e+00 7.83e-01 2.98e+01 angle pdb=" CA ALA D 694 " pdb=" C ALA D 694 " pdb=" O ALA D 694 " ideal model delta sigma weight residual 120.80 114.95 5.85 1.11e+00 8.12e-01 2.78e+01 ... (remaining 39539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 16724 22.75 - 45.50: 997 45.50 - 68.25: 147 68.25 - 91.00: 42 91.00 - 113.75: 4 Dihedral angle restraints: 17914 sinusoidal: 7576 harmonic: 10338 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.97 72.97 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.43 71.43 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -132.45 46.45 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 17911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.275: 4585 0.275 - 0.551: 16 0.551 - 0.826: 1 0.826 - 1.101: 1 1.101 - 1.377: 1 Chirality restraints: 4604 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.11e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.99e+01 ... (remaining 4601 not shown) Planarity restraints: 5109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.14e+03 pdb=" C7 NAG A1306 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " -0.118 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG B1304 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.090 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.295 2.00e-02 2.50e+03 2.45e-01 7.49e+02 pdb=" C7 NAG A1301 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.196 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.409 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.000 2.00e-02 2.50e+03 ... (remaining 5106 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 49 2.16 - 2.85: 9703 2.85 - 3.53: 37249 3.53 - 4.22: 66557 4.22 - 4.90: 113327 Nonbonded interactions: 226885 Sorted by model distance: nonbonded pdb=" CZ TYR A 351 " pdb=" OD1 ASN A 422 " model vdw 1.478 3.260 nonbonded pdb=" O SER D 373 " pdb=" CD1 TRP D 436 " model vdw 1.498 3.260 nonbonded pdb=" O ASP D 398 " pdb=" CA VAL D 511 " model vdw 1.524 3.470 nonbonded pdb=" N PHE D 400 " pdb=" O VAL D 510 " model vdw 1.564 3.120 nonbonded pdb=" CZ3 TRP D 436 " pdb=" O ASN D 437 " model vdw 1.634 3.340 ... (remaining 226880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1306)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.050 Extract box with map and model: 1.290 Check model and map are aligned: 0.250 Set scattering table: 0.250 Process input model: 69.900 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 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 : 0.006 0.129 29147 Z= 0.347 Angle : 0.925 34.008 39767 Z= 0.533 Chirality : 0.065 1.377 4604 Planarity : 0.011 0.303 5073 Dihedral : 14.230 113.751 11153 Min Nonbonded Distance : 1.478 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.77 % Favored : 96.00 % Rotamer: Outliers : 1.29 % Allowed : 13.41 % Favored : 85.30 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 3526 helix: 0.85 (0.20), residues: 682 sheet: 0.11 (0.17), residues: 842 loop : -1.15 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 353 HIS 0.016 0.001 HIS D1083 PHE 0.059 0.002 PHE D 400 TYR 0.073 0.002 TYR B 423 ARG 0.008 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.02897 ( 36) link_NAG-ASN : angle 6.54717 ( 108) link_BETA1-4 : bond 0.00783 ( 11) link_BETA1-4 : angle 1.90700 ( 33) hydrogen bonds : bond 0.19867 ( 1096) hydrogen bonds : angle 8.24030 ( 2994) SS BOND : bond 0.01098 ( 41) SS BOND : angle 1.65996 ( 82) covalent geometry : bond 0.00557 (29059) covalent geometry : angle 0.85666 (39544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 2.915 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: E 34 MET cc_start: 0.0951 (mmm) cc_final: 0.0232 (pmm) REVERT: E 47 MET cc_start: -0.0113 (mmm) cc_final: -0.0494 (tmm) REVERT: A 40 ASP cc_start: 0.7158 (m-30) cc_final: 0.6871 (m-30) REVERT: A 153 MET cc_start: 0.0999 (ptp) cc_final: 0.0492 (pmm) REVERT: A 207 HIS cc_start: 0.6185 (m170) cc_final: 0.5824 (t-90) REVERT: A 229 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5719 (tt) REVERT: A 779 GLN cc_start: 0.7557 (tt0) cc_final: 0.6910 (tp40) REVERT: A 868 GLU cc_start: 0.7057 (pp20) cc_final: 0.6184 (mm-30) REVERT: A 900 MET cc_start: 0.8469 (ttm) cc_final: 0.8220 (mtp) REVERT: A 990 GLU cc_start: 0.7958 (mt-10) cc_final: 0.6970 (mp0) REVERT: A 1038 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7811 (ttmt) REVERT: A 1091 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7624 (mtt-85) REVERT: A 1141 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6690 (tp) REVERT: B 153 MET cc_start: 0.0666 (ptt) cc_final: -0.0188 (mtp) REVERT: B 177 MET cc_start: 0.0743 (mmp) cc_final: 0.0442 (mmm) REVERT: B 211 ASN cc_start: 0.3091 (OUTLIER) cc_final: 0.2379 (m-40) REVERT: B 564 GLN cc_start: 0.6026 (OUTLIER) cc_final: 0.5810 (mm110) REVERT: B 606 ASN cc_start: 0.6433 (p0) cc_final: 0.5967 (m110) REVERT: B 747 THR cc_start: 0.7613 (m) cc_final: 0.7399 (t) REVERT: B 780 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7155 (pt0) REVERT: B 787 GLN cc_start: 0.7611 (mt0) cc_final: 0.7374 (tt0) REVERT: B 912 THR cc_start: 0.8797 (m) cc_final: 0.8498 (p) REVERT: B 963 VAL cc_start: 0.7332 (t) cc_final: 0.7040 (p) REVERT: B 995 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7488 (mtp180) REVERT: B 1125 ASN cc_start: 0.5897 (m-40) cc_final: 0.4978 (p0) REVERT: C 47 MET cc_start: 0.0779 (ttp) cc_final: 0.0492 (mpt) REVERT: C 82 MET cc_start: -0.1760 (mmp) cc_final: -0.2361 (ptm) REVERT: D 190 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.5371 (mtp85) REVERT: D 319 ARG cc_start: 0.7520 (ptp-170) cc_final: 0.7275 (mtp180) REVERT: D 675 GLN cc_start: 0.5916 (mt0) cc_final: 0.5630 (tt0) REVERT: D 780 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7254 (pt0) REVERT: D 820 ASP cc_start: 0.6688 (m-30) cc_final: 0.6389 (m-30) REVERT: D 1005 GLN cc_start: 0.7797 (mt0) cc_final: 0.7502 (mt0) REVERT: D 1010 GLN cc_start: 0.7274 (tp40) cc_final: 0.6554 (pt0) REVERT: D 1017 GLU cc_start: 0.7516 (tt0) cc_final: 0.7299 (tt0) REVERT: D 1038 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7291 (mmtp) REVERT: F 34 MET cc_start: 0.3157 (ttt) cc_final: 0.2936 (ttt) outliers start: 40 outliers final: 20 residues processed: 332 average time/residue: 1.1360 time to fit residues: 454.2473 Evaluate side-chains 224 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 643 PHE Chi-restraints excluded: chain D residue 659 SER Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.3980 chunk 268 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 277 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN A 49 HIS A 69 HIS A 121 ASN A 188 ASN A 354 ASN A 422 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 935 GLN A 954 GLN A 965 GLN A1002 GLN A1101 HIS A1113 GLN B 69 HIS B 188 ASN B 207 HIS B 245 HIS B 314 GLN B 607 GLN B 613 GLN B 641 ASN B 764 ASN B 804 GLN B1002 GLN B1048 HIS B1101 HIS B1113 GLN C 32 ASN D 69 HIS D 121 ASN D 607 GLN D 613 GLN D 655 HIS D 675 GLN ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN D 955 ASN D1002 GLN D1048 HIS D1071 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 ASN F 32 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.239288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163025 restraints weight = 36434.053| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.69 r_work: 0.3633 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 29147 Z= 0.245 Angle : 0.778 17.759 39767 Z= 0.392 Chirality : 0.054 0.767 4604 Planarity : 0.006 0.063 5073 Dihedral : 7.194 86.005 4850 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 3.80 % Allowed : 13.05 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3526 helix: 1.26 (0.20), residues: 700 sheet: -0.06 (0.17), residues: 877 loop : -1.25 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 436 HIS 0.011 0.002 HIS D1088 PHE 0.053 0.003 PHE B 400 TYR 0.052 0.003 TYR A1067 ARG 0.009 0.001 ARG E 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00994 ( 36) link_NAG-ASN : angle 4.19575 ( 108) link_BETA1-4 : bond 0.00791 ( 11) link_BETA1-4 : angle 2.10082 ( 33) hydrogen bonds : bond 0.05861 ( 1096) hydrogen bonds : angle 6.22774 ( 2994) SS BOND : bond 0.00992 ( 41) SS BOND : angle 1.22421 ( 82) covalent geometry : bond 0.00575 (29059) covalent geometry : angle 0.74433 (39544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 228 time to evaluate : 2.949 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: E 34 MET cc_start: -0.0230 (mmm) cc_final: -0.0556 (mpp) REVERT: A 100 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.5826 (mt) REVERT: A 129 LYS cc_start: 0.6532 (mttm) cc_final: 0.5969 (ptmm) REVERT: A 153 MET cc_start: 0.0862 (ptp) cc_final: 0.0272 (pmm) REVERT: A 177 MET cc_start: 0.1846 (mtp) cc_final: 0.0886 (mtp) REVERT: A 190 ARG cc_start: 0.5894 (OUTLIER) cc_final: 0.4224 (mmt180) REVERT: A 200 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.5606 (m-80) REVERT: A 530 SER cc_start: 0.7415 (OUTLIER) cc_final: 0.6694 (t) REVERT: A 532 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.7285 (t0) REVERT: A 565 PHE cc_start: 0.7476 (m-10) cc_final: 0.7188 (m-80) REVERT: A 596 SER cc_start: 0.8812 (t) cc_final: 0.8531 (m) REVERT: A 779 GLN cc_start: 0.8479 (tt0) cc_final: 0.8108 (tp40) REVERT: A 790 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8492 (mtpt) REVERT: A 825 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7950 (mtpt) REVERT: A 964 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7630 (mptp) REVERT: A 1029 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8949 (tpp) REVERT: A 1038 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8475 (mtpt) REVERT: A 1091 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8281 (mtt-85) REVERT: A 1125 ASN cc_start: 0.7041 (m-40) cc_final: 0.6680 (p0) REVERT: B 195 LYS cc_start: 0.6215 (mtpt) cc_final: 0.5752 (mtmm) REVERT: B 319 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7721 (mtp180) REVERT: B 422 ASN cc_start: -0.0758 (OUTLIER) cc_final: -0.1173 (t0) REVERT: B 564 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6488 (mm110) REVERT: B 858 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 935 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6592 (mm110) REVERT: B 990 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7046 (mt-10) REVERT: B 994 ASP cc_start: 0.8419 (m-30) cc_final: 0.8172 (m-30) REVERT: B 995 ARG cc_start: 0.8260 (mtt180) cc_final: 0.8029 (mtp180) REVERT: B 1045 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8001 (tmtt) REVERT: B 1125 ASN cc_start: 0.7324 (m-40) cc_final: 0.7026 (p0) REVERT: C 22 CYS cc_start: 0.1072 (OUTLIER) cc_final: -0.0227 (p) REVERT: D 190 ARG cc_start: 0.6247 (mpp80) cc_final: 0.5808 (mtp85) REVERT: D 734 THR cc_start: 0.8476 (m) cc_final: 0.8242 (p) REVERT: D 780 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8461 (pt0) REVERT: D 994 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7839 (t0) REVERT: D 1002 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: D 1010 GLN cc_start: 0.8547 (tp40) cc_final: 0.8055 (tm-30) REVERT: D 1038 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8028 (mmtp) REVERT: F 34 MET cc_start: 0.2843 (OUTLIER) cc_final: 0.1592 (ttt) REVERT: F 78 VAL cc_start: -0.0446 (OUTLIER) cc_final: -0.0689 (p) outliers start: 118 outliers final: 43 residues processed: 316 average time/residue: 1.0862 time to fit residues: 419.8880 Evaluate side-chains 254 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1002 GLN Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 126 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 236 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 422 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 954 GLN A1005 GLN A1119 ASN B 207 HIS B 245 HIS B 641 ASN B 901 GLN B 954 GLN B1002 GLN C 44 GLN D 121 ASN D 370 ASN D 762 GLN ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1125 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.239750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.164960 restraints weight = 36419.193| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.91 r_work: 0.3670 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29147 Z= 0.150 Angle : 0.639 16.929 39767 Z= 0.319 Chirality : 0.047 0.676 4604 Planarity : 0.005 0.057 5073 Dihedral : 5.918 56.569 4820 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 3.51 % Allowed : 13.76 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3526 helix: 1.54 (0.20), residues: 704 sheet: -0.05 (0.16), residues: 898 loop : -1.17 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.008 0.001 HIS D1083 PHE 0.036 0.002 PHE D 400 TYR 0.036 0.002 TYR A1067 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 36) link_NAG-ASN : angle 3.85443 ( 108) link_BETA1-4 : bond 0.00486 ( 11) link_BETA1-4 : angle 1.85784 ( 33) hydrogen bonds : bond 0.04921 ( 1096) hydrogen bonds : angle 5.91349 ( 2994) SS BOND : bond 0.00778 ( 41) SS BOND : angle 0.97039 ( 82) covalent geometry : bond 0.00353 (29059) covalent geometry : angle 0.60425 (39544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 203 time to evaluate : 2.945 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: E 34 MET cc_start: -0.0234 (mmm) cc_final: -0.0557 (mpp) REVERT: E 80 LEU cc_start: 0.0298 (OUTLIER) cc_final: -0.0396 (tp) REVERT: A 100 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.5802 (mt) REVERT: A 177 MET cc_start: 0.1814 (mtp) cc_final: 0.0871 (mtp) REVERT: A 190 ARG cc_start: 0.5865 (OUTLIER) cc_final: 0.4374 (mmt180) REVERT: A 200 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.5600 (m-80) REVERT: A 202 LYS cc_start: 0.7002 (mttt) cc_final: 0.6609 (mttp) REVERT: A 396 TYR cc_start: 0.4465 (OUTLIER) cc_final: 0.3572 (p90) REVERT: A 422 ASN cc_start: 0.2780 (OUTLIER) cc_final: 0.2573 (m110) REVERT: A 536 ASN cc_start: 0.6751 (OUTLIER) cc_final: 0.6130 (t0) REVERT: A 565 PHE cc_start: 0.7653 (m-10) cc_final: 0.7389 (m-80) REVERT: A 779 GLN cc_start: 0.8479 (tt0) cc_final: 0.8143 (tp40) REVERT: A 790 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8708 (mtpt) REVERT: A 825 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7968 (mtpt) REVERT: A 868 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: A 964 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7674 (mptp) REVERT: A 990 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: A 1029 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8803 (tpp) REVERT: A 1038 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8513 (mttt) REVERT: A 1091 ARG cc_start: 0.8573 (mtt180) cc_final: 0.8284 (mtt-85) REVERT: B 195 LYS cc_start: 0.6255 (mtpt) cc_final: 0.5811 (mtmm) REVERT: B 211 ASN cc_start: 0.3013 (OUTLIER) cc_final: 0.2399 (m-40) REVERT: B 319 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7708 (mtp180) REVERT: B 422 ASN cc_start: -0.0948 (OUTLIER) cc_final: -0.1193 (t0) REVERT: B 564 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6791 (mm110) REVERT: B 787 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: B 858 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8348 (mt) REVERT: B 994 ASP cc_start: 0.8475 (m-30) cc_final: 0.8042 (t70) REVERT: B 1045 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7963 (tmtt) REVERT: B 1125 ASN cc_start: 0.7640 (m-40) cc_final: 0.7388 (p0) REVERT: D 45 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7715 (t) REVERT: D 47 VAL cc_start: 0.7140 (p) cc_final: 0.6916 (m) REVERT: D 153 MET cc_start: 0.0363 (ttt) cc_final: -0.0639 (mtp) REVERT: D 190 ARG cc_start: 0.6265 (mpp80) cc_final: 0.5865 (mtp85) REVERT: D 814 LYS cc_start: 0.7917 (mmtp) cc_final: 0.6854 (pptt) REVERT: D 994 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7932 (t0) REVERT: D 1010 GLN cc_start: 0.8528 (tp40) cc_final: 0.8042 (tm-30) REVERT: D 1038 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8028 (mmtp) REVERT: D 1113 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8517 (mm110) REVERT: F 34 MET cc_start: 0.2649 (OUTLIER) cc_final: 0.1358 (ttt) REVERT: F 95 CYS cc_start: 0.1435 (OUTLIER) cc_final: 0.0880 (m) outliers start: 109 outliers final: 43 residues processed: 283 average time/residue: 1.1650 time to fit residues: 398.9097 Evaluate side-chains 253 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 28 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 274 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 339 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 422 ASN A 501 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 954 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 245 HIS B 606 ASN B 613 GLN B 641 ASN B 658 ASN B 954 GLN D 121 ASN D 563 GLN D 613 GLN D 762 GLN D 764 ASN D 804 GLN D 935 GLN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.237930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.164795 restraints weight = 36398.352| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 3.97 r_work: 0.3596 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29147 Z= 0.187 Angle : 0.658 16.474 39767 Z= 0.329 Chirality : 0.048 0.651 4604 Planarity : 0.005 0.057 5073 Dihedral : 5.483 51.662 4816 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 4.42 % Allowed : 13.44 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3526 helix: 1.58 (0.20), residues: 698 sheet: -0.11 (0.16), residues: 912 loop : -1.22 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 104 HIS 0.011 0.001 HIS D1083 PHE 0.029 0.002 PHE B 400 TYR 0.037 0.002 TYR A1067 ARG 0.004 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 36) link_NAG-ASN : angle 3.77238 ( 108) link_BETA1-4 : bond 0.00446 ( 11) link_BETA1-4 : angle 1.88676 ( 33) hydrogen bonds : bond 0.05084 ( 1096) hydrogen bonds : angle 5.83996 ( 2994) SS BOND : bond 0.00789 ( 41) SS BOND : angle 1.06894 ( 82) covalent geometry : bond 0.00449 (29059) covalent geometry : angle 0.62588 (39544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 196 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: -0.0307 (mmm) cc_final: -0.0614 (mpp) REVERT: E 80 LEU cc_start: 0.0356 (OUTLIER) cc_final: -0.0489 (tp) REVERT: A 100 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.5984 (mt) REVERT: A 129 LYS cc_start: 0.6539 (mttm) cc_final: 0.5966 (ptmm) REVERT: A 153 MET cc_start: 0.1446 (OUTLIER) cc_final: 0.1072 (tpp) REVERT: A 200 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.5594 (m-80) REVERT: A 202 LYS cc_start: 0.7026 (mttt) cc_final: 0.6680 (mttp) REVERT: A 332 ILE cc_start: 0.5552 (OUTLIER) cc_final: 0.5195 (mp) REVERT: A 334 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6465 (p0) REVERT: A 396 TYR cc_start: 0.4541 (OUTLIER) cc_final: 0.3645 (p90) REVERT: A 532 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7279 (t0) REVERT: A 537 LYS cc_start: 0.7034 (ttmt) cc_final: 0.6645 (ttpt) REVERT: A 565 PHE cc_start: 0.7750 (m-10) cc_final: 0.7497 (m-80) REVERT: A 567 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6408 (mtt90) REVERT: A 779 GLN cc_start: 0.8545 (tt0) cc_final: 0.8231 (tp40) REVERT: A 790 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8685 (mtpt) REVERT: A 825 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7982 (mtpt) REVERT: A 964 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7749 (mptp) REVERT: A 1029 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8834 (tpp) REVERT: A 1038 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8512 (mttt) REVERT: A 1091 ARG cc_start: 0.8576 (mtt180) cc_final: 0.8245 (mtt-85) REVERT: A 1141 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7067 (tp) REVERT: B 195 LYS cc_start: 0.6377 (mtpt) cc_final: 0.5926 (mtmm) REVERT: B 211 ASN cc_start: 0.3042 (OUTLIER) cc_final: 0.2434 (m-40) REVERT: B 229 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.5743 (tt) REVERT: B 422 ASN cc_start: -0.0947 (OUTLIER) cc_final: -0.1172 (t0) REVERT: B 780 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: B 787 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: B 900 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8797 (ttm) REVERT: B 1045 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8174 (tmtt) REVERT: B 1125 ASN cc_start: 0.7845 (m-40) cc_final: 0.7579 (p0) REVERT: C 22 CYS cc_start: 0.1334 (OUTLIER) cc_final: 0.0189 (p) REVERT: C 54 ILE cc_start: 0.1385 (OUTLIER) cc_final: 0.1180 (mt) REVERT: D 45 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7843 (t) REVERT: D 47 VAL cc_start: 0.7291 (p) cc_final: 0.7074 (m) REVERT: D 153 MET cc_start: 0.0362 (ttt) cc_final: -0.0694 (mtp) REVERT: D 190 ARG cc_start: 0.6258 (mpp80) cc_final: 0.5803 (mtp85) REVERT: D 916 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8539 (tt) REVERT: D 994 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7943 (t0) REVERT: D 1010 GLN cc_start: 0.8568 (tp40) cc_final: 0.8107 (tm-30) REVERT: D 1038 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8093 (mmtp) REVERT: D 1113 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8520 (mm110) REVERT: F 34 MET cc_start: 0.2792 (OUTLIER) cc_final: 0.1468 (ttt) REVERT: F 54 ILE cc_start: 0.2565 (OUTLIER) cc_final: 0.2347 (pt) REVERT: F 78 VAL cc_start: -0.0396 (OUTLIER) cc_final: -0.0670 (p) outliers start: 137 outliers final: 51 residues processed: 299 average time/residue: 1.0756 time to fit residues: 392.3652 Evaluate side-chains 264 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 182 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 51 optimal weight: 0.0060 chunk 186 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 298 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1119 ASN B 30 ASN B 207 HIS B 564 GLN B 641 ASN B 954 GLN D1002 GLN ** D1088 HIS ** 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 = 0.4677 r_free = 0.4677 target = 0.238653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.163786 restraints weight = 36122.494| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 4.14 r_work: 0.3609 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29147 Z= 0.136 Angle : 0.611 15.128 39767 Z= 0.304 Chirality : 0.047 0.607 4604 Planarity : 0.004 0.056 5073 Dihedral : 5.127 51.840 4812 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.51 % Rotamer: Outliers : 3.93 % Allowed : 13.83 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3526 helix: 1.77 (0.20), residues: 692 sheet: -0.09 (0.16), residues: 925 loop : -1.16 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.008 0.001 HIS D1083 PHE 0.049 0.002 PHE B 400 TYR 0.026 0.001 TYR B1067 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 36) link_NAG-ASN : angle 3.67628 ( 108) link_BETA1-4 : bond 0.00440 ( 11) link_BETA1-4 : angle 1.73911 ( 33) hydrogen bonds : bond 0.04451 ( 1096) hydrogen bonds : angle 5.67926 ( 2994) SS BOND : bond 0.00531 ( 41) SS BOND : angle 0.93732 ( 82) covalent geometry : bond 0.00317 (29059) covalent geometry : angle 0.57770 (39544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 190 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: -0.0325 (mmm) cc_final: -0.0632 (mpp) REVERT: E 80 LEU cc_start: 0.0427 (OUTLIER) cc_final: -0.0460 (tp) REVERT: A 100 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.5969 (mt) REVERT: A 129 LYS cc_start: 0.6525 (mttm) cc_final: 0.5941 (ptmm) REVERT: A 153 MET cc_start: 0.1087 (OUTLIER) cc_final: -0.0359 (mpp) REVERT: A 200 TYR cc_start: 0.6745 (OUTLIER) cc_final: 0.5616 (m-80) REVERT: A 202 LYS cc_start: 0.6983 (mttt) cc_final: 0.6644 (mttp) REVERT: A 332 ILE cc_start: 0.5519 (OUTLIER) cc_final: 0.5147 (mp) REVERT: A 396 TYR cc_start: 0.4448 (OUTLIER) cc_final: 0.3587 (p90) REVERT: A 529 LYS cc_start: 0.7120 (mmmm) cc_final: 0.6836 (tppt) REVERT: A 530 SER cc_start: 0.7329 (OUTLIER) cc_final: 0.6757 (t) REVERT: A 537 LYS cc_start: 0.7087 (ttmt) cc_final: 0.6719 (ttpt) REVERT: A 565 PHE cc_start: 0.7755 (m-10) cc_final: 0.7537 (m-80) REVERT: A 567 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6378 (mtt90) REVERT: A 655 HIS cc_start: 0.7474 (t70) cc_final: 0.7023 (t70) REVERT: A 656 VAL cc_start: 0.7747 (t) cc_final: 0.7326 (m) REVERT: A 780 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8321 (mt-10) REVERT: A 790 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8715 (mtpt) REVERT: A 825 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7963 (mtpt) REVERT: A 868 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: A 964 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7726 (mptp) REVERT: A 1038 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8518 (mttt) REVERT: B 195 LYS cc_start: 0.6317 (mtpt) cc_final: 0.5859 (mtmm) REVERT: B 211 ASN cc_start: 0.3044 (OUTLIER) cc_final: 0.2816 (m-40) REVERT: B 229 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.5782 (tt) REVERT: B 654 GLU cc_start: 0.7588 (tt0) cc_final: 0.7378 (tm-30) REVERT: B 780 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: B 787 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: B 858 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8568 (mt) REVERT: B 1045 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8086 (tmtt) REVERT: B 1125 ASN cc_start: 0.7852 (m-40) cc_final: 0.7628 (p0) REVERT: C 22 CYS cc_start: 0.1411 (OUTLIER) cc_final: 0.0155 (p) REVERT: C 54 ILE cc_start: 0.1583 (OUTLIER) cc_final: 0.1302 (mm) REVERT: D 40 ASP cc_start: 0.6579 (m-30) cc_final: 0.6374 (p0) REVERT: D 45 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.7813 (t) REVERT: D 47 VAL cc_start: 0.7308 (p) cc_final: 0.7101 (m) REVERT: D 153 MET cc_start: 0.0345 (ttt) cc_final: -0.0768 (mtp) REVERT: D 266 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: D 302 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8792 (t) REVERT: D 814 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.6883 (pptt) REVERT: D 916 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8478 (tt) REVERT: D 994 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7922 (t0) REVERT: D 1010 GLN cc_start: 0.8543 (tp40) cc_final: 0.8041 (tm-30) REVERT: D 1038 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8065 (mmtp) REVERT: D 1113 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8491 (mm110) REVERT: F 34 MET cc_start: 0.2574 (OUTLIER) cc_final: 0.1406 (ttt) REVERT: F 54 ILE cc_start: 0.2591 (OUTLIER) cc_final: 0.2391 (pt) REVERT: F 78 VAL cc_start: -0.0536 (OUTLIER) cc_final: -0.0752 (p) outliers start: 122 outliers final: 46 residues processed: 283 average time/residue: 1.1156 time to fit residues: 388.6139 Evaluate side-chains 257 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 180 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 329 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 278 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 321 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 954 GLN D 607 GLN D 935 GLN D 955 ASN D1005 GLN D1125 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.236936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162422 restraints weight = 35898.836| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.83 r_work: 0.3566 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29147 Z= 0.177 Angle : 0.641 15.285 39767 Z= 0.320 Chirality : 0.048 0.598 4604 Planarity : 0.004 0.056 5073 Dihedral : 5.214 52.218 4812 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.11 % Rotamer: Outliers : 3.93 % Allowed : 13.76 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3526 helix: 1.66 (0.20), residues: 696 sheet: -0.08 (0.16), residues: 944 loop : -1.16 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 353 HIS 0.008 0.001 HIS D1083 PHE 0.040 0.002 PHE B 400 TYR 0.039 0.002 TYR D1067 ARG 0.004 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 36) link_NAG-ASN : angle 3.70048 ( 108) link_BETA1-4 : bond 0.00429 ( 11) link_BETA1-4 : angle 1.80230 ( 33) hydrogen bonds : bond 0.04933 ( 1096) hydrogen bonds : angle 5.70855 ( 2994) SS BOND : bond 0.00817 ( 41) SS BOND : angle 1.16602 ( 82) covalent geometry : bond 0.00419 (29059) covalent geometry : angle 0.60823 (39544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 194 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: -0.0334 (mmm) cc_final: -0.0627 (mpp) REVERT: A 129 LYS cc_start: 0.6602 (mttm) cc_final: 0.6030 (ptmm) REVERT: A 153 MET cc_start: 0.0863 (OUTLIER) cc_final: -0.0585 (mpp) REVERT: A 200 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.5549 (m-80) REVERT: A 202 LYS cc_start: 0.6959 (mttt) cc_final: 0.6654 (mttp) REVERT: A 332 ILE cc_start: 0.5666 (OUTLIER) cc_final: 0.5367 (mm) REVERT: A 396 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.3658 (p90) REVERT: A 529 LYS cc_start: 0.7158 (mmmm) cc_final: 0.6917 (tppt) REVERT: A 530 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.6886 (t) REVERT: A 532 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7246 (t0) REVERT: A 537 LYS cc_start: 0.7199 (ttmt) cc_final: 0.6874 (ttpt) REVERT: A 567 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6387 (mtt90) REVERT: A 613 GLN cc_start: 0.8611 (mp10) cc_final: 0.8254 (mt0) REVERT: A 790 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8714 (mtpt) REVERT: A 825 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8026 (mtpt) REVERT: A 868 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: A 964 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7732 (mptp) REVERT: A 1038 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8527 (mtpt) REVERT: B 195 LYS cc_start: 0.6534 (mtpt) cc_final: 0.6055 (mtmm) REVERT: B 229 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.5865 (tt) REVERT: B 654 GLU cc_start: 0.7685 (tt0) cc_final: 0.7475 (tm-30) REVERT: B 780 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: B 787 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: B 1045 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8219 (tmtt) REVERT: C 22 CYS cc_start: 0.1470 (OUTLIER) cc_final: 0.0161 (p) REVERT: C 54 ILE cc_start: 0.1641 (OUTLIER) cc_final: 0.1340 (mm) REVERT: D 45 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.7897 (p) REVERT: D 47 VAL cc_start: 0.7400 (p) cc_final: 0.7185 (m) REVERT: D 153 MET cc_start: 0.0263 (ttt) cc_final: -0.1124 (mtm) REVERT: D 190 ARG cc_start: 0.6288 (mpp80) cc_final: 0.5938 (mtp180) REVERT: D 266 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6800 (m-80) REVERT: D 814 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.6852 (pptt) REVERT: D 916 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8565 (tt) REVERT: D 949 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7412 (mt0) REVERT: D 950 ASP cc_start: 0.8186 (m-30) cc_final: 0.7976 (m-30) REVERT: D 994 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8008 (t0) REVERT: D 1010 GLN cc_start: 0.8579 (tp40) cc_final: 0.8130 (tm-30) REVERT: D 1038 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8099 (mmtp) REVERT: D 1113 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8504 (mm110) REVERT: F 34 MET cc_start: 0.2495 (OUTLIER) cc_final: 0.1204 (ttt) REVERT: F 78 VAL cc_start: -0.0485 (OUTLIER) cc_final: -0.0713 (p) outliers start: 122 outliers final: 57 residues processed: 281 average time/residue: 1.1038 time to fit residues: 378.5887 Evaluate side-chains 268 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 185 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 939 SER Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 45 optimal weight: 9.9990 chunk 87 optimal weight: 0.0070 chunk 4 optimal weight: 20.0000 chunk 195 optimal weight: 4.9990 chunk 308 optimal weight: 2.9990 chunk 303 optimal weight: 0.0370 chunk 9 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 342 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 207 HIS B 321 GLN B 954 GLN D 935 GLN D1005 GLN D1125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.238112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.163825 restraints weight = 35954.725| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.83 r_work: 0.3603 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29147 Z= 0.125 Angle : 0.591 13.683 39767 Z= 0.296 Chirality : 0.046 0.554 4604 Planarity : 0.004 0.055 5073 Dihedral : 4.994 52.364 4812 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 3.51 % Allowed : 14.24 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3526 helix: 1.89 (0.20), residues: 696 sheet: -0.03 (0.16), residues: 934 loop : -1.10 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.007 0.001 HIS D1083 PHE 0.035 0.001 PHE B 400 TYR 0.026 0.001 TYR D1067 ARG 0.003 0.000 ARG E 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 36) link_NAG-ASN : angle 3.36925 ( 108) link_BETA1-4 : bond 0.00471 ( 11) link_BETA1-4 : angle 1.63446 ( 33) hydrogen bonds : bond 0.04233 ( 1096) hydrogen bonds : angle 5.53692 ( 2994) SS BOND : bond 0.00478 ( 41) SS BOND : angle 1.27379 ( 82) covalent geometry : bond 0.00290 (29059) covalent geometry : angle 0.56147 (39544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 192 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: -0.0330 (mmm) cc_final: -0.0612 (mpp) REVERT: E 80 LEU cc_start: 0.0061 (OUTLIER) cc_final: -0.0396 (tp) REVERT: E 82 MET cc_start: 0.0910 (tpp) cc_final: 0.0549 (ptp) REVERT: A 100 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6130 (mt) REVERT: A 153 MET cc_start: 0.0908 (OUTLIER) cc_final: -0.0693 (mpp) REVERT: A 190 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5505 (mmt180) REVERT: A 200 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6313 (t80) REVERT: A 202 LYS cc_start: 0.6940 (mttt) cc_final: 0.6393 (mttp) REVERT: A 332 ILE cc_start: 0.5555 (OUTLIER) cc_final: 0.5307 (mm) REVERT: A 396 TYR cc_start: 0.4469 (OUTLIER) cc_final: 0.3677 (p90) REVERT: A 529 LYS cc_start: 0.7127 (mmmm) cc_final: 0.6904 (tppt) REVERT: A 530 SER cc_start: 0.7402 (OUTLIER) cc_final: 0.6850 (t) REVERT: A 532 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7237 (t0) REVERT: A 537 LYS cc_start: 0.7132 (ttmt) cc_final: 0.6816 (ttpt) REVERT: A 613 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: A 790 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8720 (mtpt) REVERT: A 825 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7989 (mtpt) REVERT: A 868 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 964 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7706 (mptp) REVERT: A 1038 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8465 (mtpt) REVERT: B 51 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7591 (t) REVERT: B 53 ASP cc_start: 0.7645 (m-30) cc_final: 0.7059 (m-30) REVERT: B 195 LYS cc_start: 0.6530 (mtpt) cc_final: 0.6049 (mtmm) REVERT: B 229 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.5916 (tt) REVERT: B 613 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8625 (mt0) REVERT: B 654 GLU cc_start: 0.7666 (tt0) cc_final: 0.7446 (tm-30) REVERT: B 780 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: B 787 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: B 900 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8799 (ttm) REVERT: B 1045 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8172 (tmtt) REVERT: C 22 CYS cc_start: 0.1437 (OUTLIER) cc_final: 0.0287 (p) REVERT: C 54 ILE cc_start: 0.1585 (OUTLIER) cc_final: 0.1319 (mm) REVERT: C 100 LYS cc_start: 0.3179 (OUTLIER) cc_final: 0.2908 (tptt) REVERT: D 45 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7848 (p) REVERT: D 47 VAL cc_start: 0.7348 (p) cc_final: 0.7148 (m) REVERT: D 153 MET cc_start: 0.0151 (ttt) cc_final: -0.1287 (mtm) REVERT: D 190 ARG cc_start: 0.6288 (mpp80) cc_final: 0.6044 (mtp180) REVERT: D 266 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6776 (m-80) REVERT: D 814 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.6845 (pptt) REVERT: D 916 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8472 (tt) REVERT: D 949 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7410 (mt0) REVERT: D 950 ASP cc_start: 0.8130 (m-30) cc_final: 0.7910 (m-30) REVERT: D 994 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7909 (t0) REVERT: D 1005 GLN cc_start: 0.8669 (mt0) cc_final: 0.8391 (mt0) REVERT: D 1010 GLN cc_start: 0.8507 (tp40) cc_final: 0.8029 (tm-30) REVERT: D 1038 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8042 (mmtp) REVERT: D 1113 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8475 (mm110) REVERT: F 34 MET cc_start: 0.2472 (OUTLIER) cc_final: 0.1260 (ttt) REVERT: F 78 VAL cc_start: -0.0491 (OUTLIER) cc_final: -0.0702 (p) REVERT: F 86 ILE cc_start: 0.0824 (OUTLIER) cc_final: 0.0620 (mt) outliers start: 109 outliers final: 49 residues processed: 270 average time/residue: 1.0981 time to fit residues: 365.2828 Evaluate side-chains 266 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 183 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 86 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 323 optimal weight: 4.9990 chunk 236 optimal weight: 0.0770 chunk 178 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 84 optimal weight: 0.0870 chunk 133 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 304 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 179 optimal weight: 0.5980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 321 GLN B 954 GLN B1125 ASN D 935 GLN D1125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.239552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.170326 restraints weight = 36223.419| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.60 r_work: 0.3623 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29147 Z= 0.102 Angle : 0.568 13.131 39767 Z= 0.283 Chirality : 0.045 0.514 4604 Planarity : 0.004 0.054 5073 Dihedral : 4.772 51.536 4812 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 2.58 % Allowed : 15.28 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3526 helix: 2.03 (0.20), residues: 700 sheet: -0.00 (0.16), residues: 940 loop : -1.08 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 152 HIS 0.006 0.001 HIS D1083 PHE 0.033 0.001 PHE D 192 TYR 0.028 0.001 TYR B 144 ARG 0.002 0.000 ARG D 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 36) link_NAG-ASN : angle 3.46309 ( 108) link_BETA1-4 : bond 0.00443 ( 11) link_BETA1-4 : angle 1.46803 ( 33) hydrogen bonds : bond 0.03728 ( 1096) hydrogen bonds : angle 5.41148 ( 2994) SS BOND : bond 0.00289 ( 41) SS BOND : angle 0.94572 ( 82) covalent geometry : bond 0.00230 (29059) covalent geometry : angle 0.53709 (39544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 202 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: -0.0225 (mmm) cc_final: -0.1360 (pmm) REVERT: E 80 LEU cc_start: 0.0046 (OUTLIER) cc_final: -0.0181 (tp) REVERT: E 82 MET cc_start: 0.1016 (tpp) cc_final: 0.0159 (mtt) REVERT: A 129 LYS cc_start: 0.6580 (mttm) cc_final: 0.6030 (ptmm) REVERT: A 153 MET cc_start: 0.0974 (OUTLIER) cc_final: -0.0662 (mpp) REVERT: A 190 ARG cc_start: 0.5763 (OUTLIER) cc_final: 0.5530 (mmt180) REVERT: A 200 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.6424 (t80) REVERT: A 202 LYS cc_start: 0.6996 (mttt) cc_final: 0.6537 (mttp) REVERT: A 529 LYS cc_start: 0.7114 (mmmm) cc_final: 0.6902 (tppt) REVERT: A 530 SER cc_start: 0.7437 (OUTLIER) cc_final: 0.6932 (t) REVERT: A 537 LYS cc_start: 0.7176 (ttmt) cc_final: 0.6911 (ttpt) REVERT: A 656 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7203 (m) REVERT: A 825 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8017 (mtpt) REVERT: A 868 GLU cc_start: 0.8109 (pp20) cc_final: 0.7573 (mp0) REVERT: A 964 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: A 1038 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8465 (mtpt) REVERT: B 51 THR cc_start: 0.8088 (p) cc_final: 0.7603 (t) REVERT: B 53 ASP cc_start: 0.7693 (m-30) cc_final: 0.7079 (m-30) REVERT: B 195 LYS cc_start: 0.6530 (mtpt) cc_final: 0.6048 (mtmm) REVERT: B 229 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.5974 (tt) REVERT: B 539 VAL cc_start: 0.7671 (m) cc_final: 0.7350 (p) REVERT: B 780 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: B 787 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: B 1045 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7904 (ttpp) REVERT: C 22 CYS cc_start: 0.1458 (OUTLIER) cc_final: 0.0403 (p) REVERT: C 54 ILE cc_start: 0.1648 (OUTLIER) cc_final: 0.1359 (mm) REVERT: C 100 LYS cc_start: 0.3168 (OUTLIER) cc_final: 0.2895 (tptt) REVERT: D 45 SER cc_start: 0.8344 (p) cc_final: 0.7927 (p) REVERT: D 153 MET cc_start: 0.0178 (ttt) cc_final: -0.1176 (mtm) REVERT: D 190 ARG cc_start: 0.6267 (mpp80) cc_final: 0.6014 (mtp180) REVERT: D 266 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: D 814 LYS cc_start: 0.7877 (mmtp) cc_final: 0.6836 (pptt) REVERT: D 949 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7408 (mt0) REVERT: D 950 ASP cc_start: 0.8094 (m-30) cc_final: 0.7862 (m-30) REVERT: D 994 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8034 (t70) REVERT: D 1005 GLN cc_start: 0.8683 (mt0) cc_final: 0.8463 (mt0) REVERT: D 1010 GLN cc_start: 0.8545 (tp40) cc_final: 0.8058 (tm-30) REVERT: D 1038 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7981 (mmtp) REVERT: D 1113 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8507 (mm110) REVERT: F 34 MET cc_start: 0.2298 (OUTLIER) cc_final: 0.1219 (ttt) REVERT: F 78 VAL cc_start: -0.0549 (OUTLIER) cc_final: -0.0753 (p) outliers start: 80 outliers final: 37 residues processed: 259 average time/residue: 1.1226 time to fit residues: 353.9232 Evaluate side-chains 242 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 233 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 296 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 282 optimal weight: 20.0000 chunk 249 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 954 GLN D 935 GLN D1125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.237465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.163529 restraints weight = 35900.221| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.90 r_work: 0.3576 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29147 Z= 0.145 Angle : 0.609 13.182 39767 Z= 0.304 Chirality : 0.047 0.516 4604 Planarity : 0.004 0.053 5073 Dihedral : 4.886 51.015 4811 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.63 % Favored : 96.26 % Rotamer: Outliers : 2.61 % Allowed : 15.44 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3526 helix: 1.91 (0.20), residues: 697 sheet: 0.03 (0.16), residues: 925 loop : -1.08 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 152 HIS 0.007 0.001 HIS D1083 PHE 0.032 0.002 PHE D 192 TYR 0.045 0.001 TYR D1067 ARG 0.005 0.000 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 36) link_NAG-ASN : angle 3.52274 ( 108) link_BETA1-4 : bond 0.00373 ( 11) link_BETA1-4 : angle 1.55434 ( 33) hydrogen bonds : bond 0.04464 ( 1096) hydrogen bonds : angle 5.50380 ( 2994) SS BOND : bond 0.00643 ( 41) SS BOND : angle 1.13683 ( 82) covalent geometry : bond 0.00344 (29059) covalent geometry : angle 0.57820 (39544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 188 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: -0.0242 (mmm) cc_final: -0.0531 (mpp) REVERT: E 80 LEU cc_start: 0.0202 (OUTLIER) cc_final: -0.0069 (tp) REVERT: E 82 MET cc_start: 0.0921 (tpp) cc_final: 0.0029 (mtt) REVERT: A 129 LYS cc_start: 0.6475 (mttm) cc_final: 0.5992 (ptmm) REVERT: A 153 MET cc_start: 0.0879 (OUTLIER) cc_final: -0.0718 (mpp) REVERT: A 190 ARG cc_start: 0.5788 (OUTLIER) cc_final: 0.5573 (mmt180) REVERT: A 200 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6433 (t80) REVERT: A 202 LYS cc_start: 0.7005 (mttt) cc_final: 0.6519 (mttp) REVERT: A 332 ILE cc_start: 0.5587 (OUTLIER) cc_final: 0.5267 (mm) REVERT: A 396 TYR cc_start: 0.4665 (OUTLIER) cc_final: 0.3940 (p90) REVERT: A 529 LYS cc_start: 0.7108 (mmmm) cc_final: 0.6899 (tppt) REVERT: A 530 SER cc_start: 0.7442 (OUTLIER) cc_final: 0.6920 (t) REVERT: A 537 LYS cc_start: 0.7194 (ttmt) cc_final: 0.6854 (ttpt) REVERT: A 567 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6580 (mtt90) REVERT: A 825 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8024 (mtpt) REVERT: A 868 GLU cc_start: 0.8115 (pp20) cc_final: 0.7584 (mp0) REVERT: A 964 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8131 (mtpt) REVERT: A 1038 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8495 (mtpt) REVERT: B 51 THR cc_start: 0.8100 (p) cc_final: 0.7606 (t) REVERT: B 53 ASP cc_start: 0.7610 (m-30) cc_final: 0.7014 (m-30) REVERT: B 153 MET cc_start: 0.2940 (tpt) cc_final: 0.2105 (ttt) REVERT: B 195 LYS cc_start: 0.6576 (mtpt) cc_final: 0.6087 (mtmm) REVERT: B 780 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: B 787 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: B 900 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8802 (ttm) REVERT: B 1045 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8186 (tmtt) REVERT: C 22 CYS cc_start: 0.1471 (OUTLIER) cc_final: 0.0414 (p) REVERT: C 54 ILE cc_start: 0.1544 (OUTLIER) cc_final: 0.1264 (mm) REVERT: C 100 LYS cc_start: 0.3186 (OUTLIER) cc_final: 0.2894 (tptt) REVERT: D 45 SER cc_start: 0.8407 (p) cc_final: 0.8077 (p) REVERT: D 153 MET cc_start: 0.0192 (ttt) cc_final: -0.1265 (mtm) REVERT: D 190 ARG cc_start: 0.6255 (mpp80) cc_final: 0.5996 (mtp180) REVERT: D 266 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: D 814 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.6843 (pptt) REVERT: D 949 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7446 (mt0) REVERT: D 950 ASP cc_start: 0.8132 (m-30) cc_final: 0.7899 (m-30) REVERT: D 983 ARG cc_start: 0.7379 (mtp85) cc_final: 0.7137 (ttm170) REVERT: D 994 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7922 (t0) REVERT: D 1010 GLN cc_start: 0.8550 (tp40) cc_final: 0.8048 (tm-30) REVERT: D 1038 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8045 (mmtp) REVERT: D 1113 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8516 (mm110) REVERT: F 34 MET cc_start: 0.2263 (OUTLIER) cc_final: 0.1079 (ttt) REVERT: F 78 VAL cc_start: -0.0463 (OUTLIER) cc_final: -0.0680 (p) outliers start: 81 outliers final: 46 residues processed: 245 average time/residue: 1.2062 time to fit residues: 360.9862 Evaluate side-chains 252 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 182 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 207 optimal weight: 0.0070 chunk 234 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 207 HIS B 321 GLN B 762 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN D 935 GLN D 949 GLN D1125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.237159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.163898 restraints weight = 36007.939| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.74 r_work: 0.3631 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29147 Z= 0.190 Angle : 0.650 13.458 39767 Z= 0.325 Chirality : 0.048 0.525 4604 Planarity : 0.004 0.053 5073 Dihedral : 5.311 58.698 4811 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.00 % Favored : 95.89 % Rotamer: Outliers : 2.61 % Allowed : 15.47 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3526 helix: 1.68 (0.20), residues: 699 sheet: -0.02 (0.16), residues: 934 loop : -1.08 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 353 HIS 0.007 0.001 HIS D1083 PHE 0.027 0.002 PHE B 400 TYR 0.046 0.002 TYR D1067 ARG 0.006 0.000 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 36) link_NAG-ASN : angle 3.48139 ( 108) link_BETA1-4 : bond 0.00402 ( 11) link_BETA1-4 : angle 1.71388 ( 33) hydrogen bonds : bond 0.04943 ( 1096) hydrogen bonds : angle 5.64469 ( 2994) SS BOND : bond 0.00826 ( 41) SS BOND : angle 1.28794 ( 82) covalent geometry : bond 0.00456 (29059) covalent geometry : angle 0.62147 (39544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 189 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: -0.0126 (mmm) cc_final: -0.0431 (mpp) REVERT: E 80 LEU cc_start: 0.0079 (OUTLIER) cc_final: -0.0240 (tp) REVERT: E 82 MET cc_start: 0.1026 (tpp) cc_final: 0.0091 (mtt) REVERT: A 129 LYS cc_start: 0.6513 (mttm) cc_final: 0.6025 (ptmm) REVERT: A 153 MET cc_start: 0.0656 (OUTLIER) cc_final: -0.0737 (mpp) REVERT: A 200 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6511 (t80) REVERT: A 202 LYS cc_start: 0.7038 (mttt) cc_final: 0.6540 (mttp) REVERT: A 332 ILE cc_start: 0.5643 (OUTLIER) cc_final: 0.5295 (mm) REVERT: A 396 TYR cc_start: 0.4767 (OUTLIER) cc_final: 0.4014 (p90) REVERT: A 529 LYS cc_start: 0.7127 (mmmm) cc_final: 0.6777 (mmmm) REVERT: A 530 SER cc_start: 0.7490 (OUTLIER) cc_final: 0.7017 (t) REVERT: A 532 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7280 (t0) REVERT: A 537 LYS cc_start: 0.7319 (ttmt) cc_final: 0.6966 (ttpt) REVERT: A 567 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6484 (mtt90) REVERT: A 825 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8017 (mtpt) REVERT: A 868 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: A 964 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7742 (mptp) REVERT: A 1038 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8520 (mtpt) REVERT: B 51 THR cc_start: 0.8112 (p) cc_final: 0.7539 (t) REVERT: B 53 ASP cc_start: 0.7554 (m-30) cc_final: 0.6839 (m-30) REVERT: B 153 MET cc_start: 0.2867 (tpt) cc_final: 0.1758 (ttm) REVERT: B 195 LYS cc_start: 0.6579 (mtpt) cc_final: 0.6083 (mtmm) REVERT: B 780 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: B 787 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: B 1045 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8179 (tmtt) REVERT: C 22 CYS cc_start: 0.1663 (OUTLIER) cc_final: 0.0522 (p) REVERT: C 54 ILE cc_start: 0.1587 (OUTLIER) cc_final: 0.1310 (mm) REVERT: C 100 LYS cc_start: 0.3267 (OUTLIER) cc_final: 0.2945 (tptt) REVERT: D 45 SER cc_start: 0.8417 (p) cc_final: 0.8078 (p) REVERT: D 153 MET cc_start: 0.0264 (ttt) cc_final: -0.1253 (mtm) REVERT: D 190 ARG cc_start: 0.6360 (mpp80) cc_final: 0.5939 (mtp180) REVERT: D 266 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: D 814 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.6895 (pptt) REVERT: D 950 ASP cc_start: 0.8240 (m-30) cc_final: 0.8026 (m-30) REVERT: D 983 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7172 (ttm170) REVERT: D 994 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7939 (t0) REVERT: D 1010 GLN cc_start: 0.8530 (tp40) cc_final: 0.8126 (tm-30) REVERT: D 1038 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8068 (mmtp) REVERT: D 1113 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8472 (mm110) REVERT: F 34 MET cc_start: 0.2461 (OUTLIER) cc_final: 0.0870 (ttt) REVERT: F 78 VAL cc_start: -0.0483 (OUTLIER) cc_final: -0.0724 (p) outliers start: 81 outliers final: 47 residues processed: 243 average time/residue: 1.1650 time to fit residues: 342.3612 Evaluate side-chains 255 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 184 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 213 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 277 optimal weight: 20.0000 chunk 306 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN A 99 ASN A 655 HIS B 207 HIS B 271 GLN B 321 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN D 935 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.237610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.164878 restraints weight = 36088.628| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.81 r_work: 0.3628 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29147 Z= 0.161 Angle : 0.617 13.103 39767 Z= 0.309 Chirality : 0.047 0.514 4604 Planarity : 0.004 0.054 5073 Dihedral : 5.225 58.690 4811 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 2.61 % Allowed : 15.69 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3526 helix: 1.70 (0.20), residues: 700 sheet: -0.02 (0.16), residues: 933 loop : -1.08 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 353 HIS 0.007 0.001 HIS D1083 PHE 0.032 0.002 PHE D 192 TYR 0.036 0.001 TYR A1067 ARG 0.005 0.000 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 36) link_NAG-ASN : angle 3.38097 ( 108) link_BETA1-4 : bond 0.00406 ( 11) link_BETA1-4 : angle 1.66675 ( 33) hydrogen bonds : bond 0.04659 ( 1096) hydrogen bonds : angle 5.56964 ( 2994) SS BOND : bond 0.00696 ( 41) SS BOND : angle 1.16802 ( 82) covalent geometry : bond 0.00385 (29059) covalent geometry : angle 0.58880 (39544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34401.76 seconds wall clock time: 590 minutes 59.16 seconds (35459.16 seconds total)