Starting phenix.real_space_refine on Mon Aug 25 17:41:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g73_29795/08_2025/8g73_29795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g73_29795/08_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_29795/08_2025/8g73_29795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g73_29795/08_2025/8g73_29795.map" model { file = "/net/cci-nas-00/data/ceres_data/8g73_29795/08_2025/8g73_29795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g73_29795/08_2025/8g73_29795.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.62, per 1000 atoms: 0.20 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: 2.00 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.87 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: 5.89 Time building geometry restraints manager: 2.80 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 1306) selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1306)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 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: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.070 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (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 ARG 0.008 0.001 ARG A 509 TYR 0.073 0.002 TYR B 423 PHE 0.059 0.002 PHE D 400 TRP 0.026 0.002 TRP B 353 HIS 0.016 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00557 (29059) covalent geometry : angle 0.85666 (39544) SS BOND : bond 0.01098 ( 41) SS BOND : angle 1.65996 ( 82) hydrogen bonds : bond 0.19867 ( 1096) hydrogen bonds : angle 8.24030 ( 2994) link_BETA1-4 : bond 0.00783 ( 11) link_BETA1-4 : angle 1.90700 ( 33) link_NAG-ASN : bond 0.02897 ( 36) link_NAG-ASN : angle 6.54717 ( 108) *********************** 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 : 0.976 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: 0.5125 time to fit residues: 204.0063 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 : 0.890 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.3980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 856 ASN A 935 GLN A 954 GLN A 965 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 370 ASN D 607 GLN D 613 GLN D 655 HIS D 675 GLN ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.240103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.160523 restraints weight = 34879.537| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 4.26 r_work: 0.3489 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 29147 Z= 0.207 Angle : 0.723 17.640 39767 Z= 0.365 Chirality : 0.051 0.746 4604 Planarity : 0.006 0.059 5073 Dihedral : 7.187 89.639 4850 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 3.29 % Allowed : 13.37 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.14), residues: 3526 helix: 1.38 (0.20), residues: 704 sheet: -0.04 (0.17), residues: 874 loop : -1.18 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 466 TYR 0.037 0.002 TYR D 423 PHE 0.052 0.002 PHE B 400 TRP 0.035 0.002 TRP D 436 HIS 0.009 0.002 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00482 (29059) covalent geometry : angle 0.68842 (39544) SS BOND : bond 0.00767 ( 41) SS BOND : angle 1.10923 ( 82) hydrogen bonds : bond 0.05855 ( 1096) hydrogen bonds : angle 6.23766 ( 2994) link_BETA1-4 : bond 0.00550 ( 11) link_BETA1-4 : angle 1.87998 ( 33) link_NAG-ASN : bond 0.00884 ( 36) link_NAG-ASN : angle 4.11527 ( 108) *********************** 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 321 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 219 time to evaluate : 0.808 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: -0.0139 (mmm) cc_final: -0.0504 (mpp) REVERT: A 100 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.5698 (mt) REVERT: A 153 MET cc_start: 0.0865 (ptp) cc_final: 0.0250 (pmm) REVERT: A 177 MET cc_start: 0.1370 (mtp) cc_final: 0.1072 (mtp) REVERT: A 532 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7236 (t0) REVERT: A 646 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7195 (mtp-110) REVERT: A 779 GLN cc_start: 0.8571 (tt0) cc_final: 0.8207 (tp40) REVERT: A 790 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8576 (mtpt) REVERT: A 825 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7965 (mtpt) REVERT: A 964 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7312 (mptp) REVERT: A 1029 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8872 (tpp) REVERT: A 1038 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8555 (mttt) REVERT: A 1091 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8364 (mtt-85) REVERT: A 1125 ASN cc_start: 0.6928 (m-40) cc_final: 0.6318 (p0) REVERT: B 195 LYS cc_start: 0.6110 (mtpt) cc_final: 0.5649 (mtmm) REVERT: B 319 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7675 (mtp180) REVERT: B 422 ASN cc_start: -0.0887 (OUTLIER) cc_final: -0.1240 (t0) REVERT: B 564 GLN cc_start: 0.6903 (tp40) cc_final: 0.6636 (mm110) REVERT: B 606 ASN cc_start: 0.6916 (p0) cc_final: 0.6713 (m110) REVERT: B 613 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: B 780 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8317 (pt0) REVERT: B 858 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8132 (mt) REVERT: B 954 GLN cc_start: 0.8433 (mt0) cc_final: 0.8218 (mt0) REVERT: B 1045 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7948 (tmtt) REVERT: B 1125 ASN cc_start: 0.7129 (m-40) cc_final: 0.6712 (p0) REVERT: D 153 MET cc_start: 0.0443 (ttt) cc_final: -0.0682 (mtp) REVERT: D 190 ARG cc_start: 0.6246 (mpp80) cc_final: 0.5780 (mtp85) REVERT: D 319 ARG cc_start: 0.7496 (ptp-170) cc_final: 0.7193 (mtt180) REVERT: D 820 ASP cc_start: 0.8143 (m-30) cc_final: 0.7933 (m-30) REVERT: D 949 GLN cc_start: 0.8120 (tp40) cc_final: 0.7597 (mt0) REVERT: D 994 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7811 (t0) REVERT: D 1002 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: D 1010 GLN cc_start: 0.8562 (tp40) cc_final: 0.8181 (tm-30) REVERT: D 1038 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8010 (mmtp) REVERT: F 34 MET cc_start: 0.2747 (OUTLIER) cc_final: 0.1464 (ttt) outliers start: 102 outliers final: 37 residues processed: 294 average time/residue: 0.4751 time to fit residues: 169.0376 Evaluate side-chains 239 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 641 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 900 MET 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 B residue 51 THR 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 602 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1045 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 94 SER 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 D residue 1136 THR Chi-restraints excluded: chain F residue 34 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 341 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 280 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 118 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 chunk 298 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 271 GLN A 564 GLN A 856 ASN A 935 GLN A 969 ASN B 207 HIS B 245 HIS B 641 ASN B1002 GLN C 44 GLN D 613 GLN ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN D1002 GLN D1005 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.241094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.175725 restraints weight = 34864.244| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.13 r_work: 0.3537 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29147 Z= 0.128 Angle : 0.614 16.201 39767 Z= 0.307 Chirality : 0.047 0.648 4604 Planarity : 0.005 0.053 5073 Dihedral : 5.696 56.570 4816 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 3.25 % Allowed : 13.79 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.14), residues: 3526 helix: 1.66 (0.20), residues: 710 sheet: -0.00 (0.17), residues: 889 loop : -1.12 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 509 TYR 0.024 0.001 TYR A1067 PHE 0.034 0.001 PHE D 400 TRP 0.010 0.001 TRP B 353 HIS 0.006 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00295 (29059) covalent geometry : angle 0.58018 (39544) SS BOND : bond 0.00471 ( 41) SS BOND : angle 0.88888 ( 82) hydrogen bonds : bond 0.04515 ( 1096) hydrogen bonds : angle 5.82821 ( 2994) link_BETA1-4 : bond 0.00488 ( 11) link_BETA1-4 : angle 1.76700 ( 33) link_NAG-ASN : bond 0.00629 ( 36) link_NAG-ASN : angle 3.74338 ( 108) *********************** 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 310 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 209 time to evaluate : 0.898 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: -0.0011 (mmm) cc_final: -0.0382 (mpp) REVERT: E 80 LEU cc_start: 0.0409 (OUTLIER) cc_final: -0.0527 (mt) REVERT: A 100 ILE cc_start: 0.6381 (OUTLIER) cc_final: 0.5661 (mt) REVERT: A 129 LYS cc_start: 0.6665 (mttm) cc_final: 0.6063 (ptmm) REVERT: A 153 MET cc_start: 0.0966 (ptp) cc_final: 0.0120 (pmm) REVERT: A 177 MET cc_start: 0.1854 (mtp) cc_final: 0.1473 (mtp) REVERT: A 190 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5732 (mmt90) REVERT: A 200 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.5538 (m-80) REVERT: A 202 LYS cc_start: 0.7131 (mttt) cc_final: 0.6768 (mttp) REVERT: A 229 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6029 (tt) REVERT: A 271 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: A 396 TYR cc_start: 0.4654 (OUTLIER) cc_final: 0.3702 (p90) REVERT: A 530 SER cc_start: 0.7470 (OUTLIER) cc_final: 0.6729 (t) REVERT: A 536 ASN cc_start: 0.6788 (OUTLIER) cc_final: 0.6206 (t0) REVERT: A 565 PHE cc_start: 0.7596 (m-10) cc_final: 0.7296 (m-80) REVERT: A 646 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7203 (mtp-110) REVERT: A 779 GLN cc_start: 0.8515 (tt0) cc_final: 0.8243 (tp40) REVERT: A 790 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8691 (mtpt) REVERT: A 825 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8063 (mtpt) REVERT: A 964 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7430 (mptp) REVERT: A 990 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: A 1038 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8557 (mttt) REVERT: A 1091 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8298 (mtt-85) REVERT: A 1125 ASN cc_start: 0.7016 (m-40) cc_final: 0.6627 (p0) REVERT: B 195 LYS cc_start: 0.6339 (mtpt) cc_final: 0.5919 (mtmm) REVERT: B 319 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7738 (mtp180) REVERT: B 787 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: B 858 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 1045 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8009 (tmtt) REVERT: B 1125 ASN cc_start: 0.7407 (m-40) cc_final: 0.7072 (p0) REVERT: C 22 CYS cc_start: 0.1299 (OUTLIER) cc_final: 0.0018 (p) REVERT: D 45 SER cc_start: 0.7981 (p) cc_final: 0.7744 (t) REVERT: D 153 MET cc_start: 0.0316 (ttt) cc_final: -0.0664 (mtp) REVERT: D 190 ARG cc_start: 0.6355 (mpp80) cc_final: 0.5970 (mtp85) REVERT: D 567 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7269 (mtt180) REVERT: D 949 GLN cc_start: 0.8075 (tp40) cc_final: 0.7617 (mt0) REVERT: D 994 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7850 (t0) REVERT: D 995 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7561 (mtp180) REVERT: D 1010 GLN cc_start: 0.8514 (tp40) cc_final: 0.8180 (tt0) REVERT: D 1014 ARG cc_start: 0.9096 (mtt180) cc_final: 0.8748 (mtt180) REVERT: D 1038 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8021 (mmtp) REVERT: F 34 MET cc_start: 0.2666 (OUTLIER) cc_final: 0.1577 (ttt) REVERT: F 51 ILE cc_start: -0.0669 (OUTLIER) cc_final: -0.0870 (mt) REVERT: F 78 VAL cc_start: -0.0323 (OUTLIER) cc_final: -0.0575 (p) outliers start: 101 outliers final: 35 residues processed: 283 average time/residue: 0.5083 time to fit residues: 173.0888 Evaluate side-chains 245 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS 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 83 VAL Chi-restraints excluded: chain A residue 90 VAL 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 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 396 TYR 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 536 ASN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR 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 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN 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 C residue 22 CYS 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 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 658 ASN 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 1136 THR Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 80 optimal weight: 1.9990 chunk 329 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 275 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 327 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 207 HIS B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 613 GLN B 641 ASN B 658 ASN B 901 GLN B 954 GLN D 613 GLN D 764 ASN D 804 GLN D 935 GLN D1005 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 ASN D1125 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.238901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.162778 restraints weight = 36198.133| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.86 r_work: 0.3617 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29147 Z= 0.175 Angle : 0.641 15.904 39767 Z= 0.321 Chirality : 0.048 0.626 4604 Planarity : 0.005 0.053 5073 Dihedral : 5.248 54.686 4814 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 4.35 % Allowed : 12.76 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.14), residues: 3526 helix: 1.66 (0.20), residues: 698 sheet: -0.06 (0.16), residues: 927 loop : -1.14 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.033 0.002 TYR A1067 PHE 0.028 0.002 PHE D 400 TRP 0.012 0.001 TRP A 886 HIS 0.011 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00417 (29059) covalent geometry : angle 0.61001 (39544) SS BOND : bond 0.00773 ( 41) SS BOND : angle 0.98715 ( 82) hydrogen bonds : bond 0.04952 ( 1096) hydrogen bonds : angle 5.75809 ( 2994) link_BETA1-4 : bond 0.00411 ( 11) link_BETA1-4 : angle 1.81612 ( 33) link_NAG-ASN : bond 0.00688 ( 36) link_NAG-ASN : angle 3.65743 ( 108) *********************** 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 331 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 196 time to evaluate : 0.783 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: -0.0291 (mmm) cc_final: -0.0610 (mpp) REVERT: E 80 LEU cc_start: 0.0718 (OUTLIER) cc_final: -0.0298 (mt) REVERT: A 100 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.5864 (mt) REVERT: A 129 LYS cc_start: 0.6540 (mttm) cc_final: 0.5966 (ptmm) REVERT: A 177 MET cc_start: 0.2102 (OUTLIER) cc_final: 0.1781 (mtp) REVERT: A 200 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.5476 (m-80) REVERT: A 202 LYS cc_start: 0.6972 (mttt) cc_final: 0.6625 (mttp) REVERT: A 332 ILE cc_start: 0.5509 (OUTLIER) cc_final: 0.5149 (mp) REVERT: A 396 TYR cc_start: 0.4494 (OUTLIER) cc_final: 0.3647 (p90) REVERT: A 529 LYS cc_start: 0.7130 (mmmm) cc_final: 0.6897 (tppt) REVERT: A 530 SER cc_start: 0.7367 (OUTLIER) cc_final: 0.6738 (t) REVERT: A 565 PHE cc_start: 0.7730 (m-10) cc_final: 0.7462 (m-80) REVERT: A 646 ARG cc_start: 0.7523 (mtt180) cc_final: 0.7211 (mtp-110) REVERT: A 779 GLN cc_start: 0.8507 (tt0) cc_final: 0.8203 (tp40) REVERT: A 780 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8331 (mt-10) REVERT: A 790 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8704 (mtpt) REVERT: A 825 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7965 (mtpt) REVERT: A 964 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7695 (mptp) REVERT: A 1038 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8495 (mttt) REVERT: A 1091 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8276 (mtt-85) REVERT: B 195 LYS cc_start: 0.6302 (mtpt) cc_final: 0.5860 (mtmm) REVERT: B 211 ASN cc_start: 0.2999 (OUTLIER) cc_final: 0.2374 (m-40) REVERT: B 319 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7737 (mtp180) REVERT: B 780 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8360 (tt0) REVERT: B 787 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: B 821 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8057 (tt) REVERT: B 858 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8424 (mt) REVERT: B 1045 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8040 (tmtt) REVERT: B 1125 ASN cc_start: 0.7733 (m-40) cc_final: 0.7486 (p0) REVERT: C 22 CYS cc_start: 0.1396 (OUTLIER) cc_final: 0.0097 (p) REVERT: C 54 ILE cc_start: 0.1424 (OUTLIER) cc_final: 0.1149 (mm) REVERT: D 45 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7801 (t) REVERT: D 153 MET cc_start: 0.0319 (ttt) cc_final: -0.0622 (mtp) REVERT: D 748 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5922 (pm20) REVERT: D 916 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8457 (tt) REVERT: D 949 GLN cc_start: 0.8073 (tp40) cc_final: 0.7385 (mt0) REVERT: D 994 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7886 (t0) REVERT: D 1010 GLN cc_start: 0.8531 (tp40) cc_final: 0.8106 (tm-30) REVERT: D 1038 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8033 (mmtp) REVERT: D 1067 TYR cc_start: 0.6311 (m-80) cc_final: 0.6079 (m-80) REVERT: D 1113 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8498 (mm110) REVERT: F 34 MET cc_start: 0.2759 (OUTLIER) cc_final: 0.1457 (ttt) REVERT: F 54 ILE cc_start: 0.2434 (OUTLIER) cc_final: 0.2217 (pt) REVERT: F 78 VAL cc_start: -0.0503 (OUTLIER) cc_final: -0.0710 (p) outliers start: 135 outliers final: 52 residues processed: 304 average time/residue: 0.5381 time to fit residues: 196.7512 Evaluate side-chains 259 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain A residue 200 TYR 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 396 TYR 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 534 VAL Chi-restraints excluded: chain A residue 551 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 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 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 277 LEU 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 656 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 821 LEU 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 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 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 587 ILE 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 814 LYS Chi-restraints excluded: chain D residue 900 MET 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 D residue 1136 THR 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 37 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 119 optimal weight: 0.0050 chunk 240 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 142 optimal weight: 0.2980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN E 76 ASN A 121 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 613 GLN B 641 ASN B 954 GLN D 804 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.240813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165542 restraints weight = 36301.590| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.61 r_work: 0.3678 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29147 Z= 0.111 Angle : 0.578 14.265 39767 Z= 0.287 Chirality : 0.045 0.576 4604 Planarity : 0.004 0.055 5073 Dihedral : 4.841 52.163 4812 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.80 % Rotamer: Outliers : 3.38 % Allowed : 13.95 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.14), residues: 3526 helix: 1.89 (0.20), residues: 700 sheet: -0.04 (0.16), residues: 943 loop : -1.10 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 66 TYR 0.026 0.001 TYR B1067 PHE 0.025 0.001 PHE D 400 TRP 0.010 0.001 TRP D 64 HIS 0.007 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00255 (29059) covalent geometry : angle 0.54741 (39544) SS BOND : bond 0.00532 ( 41) SS BOND : angle 0.80189 ( 82) hydrogen bonds : bond 0.03979 ( 1096) hydrogen bonds : angle 5.53972 ( 2994) link_BETA1-4 : bond 0.00462 ( 11) link_BETA1-4 : angle 1.59793 ( 33) link_NAG-ASN : bond 0.00630 ( 36) link_NAG-ASN : angle 3.48234 ( 108) *********************** 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 309 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 204 time to evaluate : 1.064 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: -0.0209 (mmm) cc_final: -0.0529 (mpp) REVERT: A 100 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.5830 (mt) REVERT: A 129 LYS cc_start: 0.6637 (mttm) cc_final: 0.6049 (ptmm) REVERT: A 177 MET cc_start: 0.2116 (OUTLIER) cc_final: 0.1670 (mtp) REVERT: A 200 TYR cc_start: 0.6687 (OUTLIER) cc_final: 0.5546 (m-80) REVERT: A 202 LYS cc_start: 0.6940 (mttt) cc_final: 0.6646 (mttp) REVERT: A 361 CYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6421 (p) REVERT: A 389 ASP cc_start: 0.7279 (m-30) cc_final: 0.7049 (m-30) REVERT: A 529 LYS cc_start: 0.7119 (mmmm) cc_final: 0.6779 (mmmm) REVERT: A 565 PHE cc_start: 0.7701 (m-10) cc_final: 0.7474 (m-80) REVERT: A 567 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6430 (mtt90) REVERT: A 646 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7039 (mtp-110) REVERT: A 790 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8709 (mtpt) REVERT: A 825 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7950 (mtpt) REVERT: A 964 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7678 (mptp) REVERT: A 1038 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8508 (mttt) REVERT: A 1091 ARG cc_start: 0.8505 (mtt180) cc_final: 0.8212 (mtt-85) REVERT: B 195 LYS cc_start: 0.6328 (mtpt) cc_final: 0.5888 (mtmm) REVERT: B 211 ASN cc_start: 0.2952 (OUTLIER) cc_final: 0.2365 (m-40) REVERT: B 229 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.5807 (tt) REVERT: B 319 ARG cc_start: 0.8122 (ttm170) cc_final: 0.7644 (mtp180) REVERT: B 787 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: B 1045 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7988 (tmtt) REVERT: B 1125 ASN cc_start: 0.7767 (m-40) cc_final: 0.7513 (p0) REVERT: C 22 CYS cc_start: 0.1347 (OUTLIER) cc_final: 0.0324 (p) REVERT: C 54 ILE cc_start: 0.1511 (OUTLIER) cc_final: 0.1192 (mm) REVERT: C 100 LYS cc_start: 0.3271 (OUTLIER) cc_final: 0.2950 (tptt) REVERT: D 45 SER cc_start: 0.8129 (OUTLIER) cc_final: 0.7809 (t) REVERT: D 153 MET cc_start: 0.0187 (ttt) cc_final: -0.0729 (mtp) REVERT: D 190 ARG cc_start: 0.6233 (mpp80) cc_final: 0.5855 (mtp180) REVERT: D 748 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5880 (pm20) REVERT: D 814 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.6877 (pptt) REVERT: D 916 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8381 (tt) REVERT: D 949 GLN cc_start: 0.8027 (tp40) cc_final: 0.7302 (mt0) REVERT: D 994 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7890 (t70) REVERT: D 1010 GLN cc_start: 0.8470 (tp40) cc_final: 0.7969 (tm-30) REVERT: D 1038 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7978 (mmtp) REVERT: D 1125 ASN cc_start: 0.7446 (m-40) cc_final: 0.7193 (t0) REVERT: F 34 MET cc_start: 0.2578 (OUTLIER) cc_final: 0.1375 (ttt) REVERT: F 54 ILE cc_start: 0.2549 (OUTLIER) cc_final: 0.2325 (pt) REVERT: F 78 VAL cc_start: -0.0490 (OUTLIER) cc_final: -0.0762 (p) outliers start: 105 outliers final: 39 residues processed: 281 average time/residue: 0.5002 time to fit residues: 169.2843 Evaluate side-chains 248 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 78 VAL 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 177 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 361 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 902 MET 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 211 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 603 ASN 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 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 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 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 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 587 ILE 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 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 1038 LYS Chi-restraints excluded: chain D residue 1067 TYR 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 52 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 281 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 87 optimal weight: 0.0170 chunk 170 optimal weight: 0.9990 chunk 341 optimal weight: 4.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1119 ASN B 207 HIS B 613 GLN B 641 ASN B 954 GLN B 957 GLN D 563 GLN D 935 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.239051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.162758 restraints weight = 36023.029| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.57 r_work: 0.3630 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29147 Z= 0.146 Angle : 0.606 14.515 39767 Z= 0.302 Chirality : 0.047 0.569 4604 Planarity : 0.004 0.055 5073 Dihedral : 4.876 51.414 4812 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.49 % Favored : 96.40 % Rotamer: Outliers : 3.54 % Allowed : 14.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.14), residues: 3526 helix: 1.81 (0.20), residues: 701 sheet: 0.05 (0.16), residues: 928 loop : -1.11 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.030 0.001 TYR D1067 PHE 0.024 0.002 PHE D 192 TRP 0.014 0.001 TRP B 353 HIS 0.007 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00347 (29059) covalent geometry : angle 0.57490 (39544) SS BOND : bond 0.00611 ( 41) SS BOND : angle 1.12686 ( 82) hydrogen bonds : bond 0.04462 ( 1096) hydrogen bonds : angle 5.55698 ( 2994) link_BETA1-4 : bond 0.00378 ( 11) link_BETA1-4 : angle 1.63759 ( 33) link_NAG-ASN : bond 0.00612 ( 36) link_NAG-ASN : angle 3.49371 ( 108) *********************** 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 291 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 181 time to evaluate : 0.892 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: -0.0307 (mmm) cc_final: -0.1879 (pmm) REVERT: A 129 LYS cc_start: 0.6659 (mttm) cc_final: 0.6051 (ptmm) REVERT: A 153 MET cc_start: 0.1293 (tpt) cc_final: 0.0582 (tpp) REVERT: A 200 TYR cc_start: 0.6622 (OUTLIER) cc_final: 0.5461 (m-80) REVERT: A 202 LYS cc_start: 0.6956 (mttt) cc_final: 0.6632 (mttp) REVERT: A 332 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5337 (mm) REVERT: A 396 TYR cc_start: 0.4564 (OUTLIER) cc_final: 0.3892 (p90) REVERT: A 529 LYS cc_start: 0.7110 (mmmm) cc_final: 0.6900 (tppt) REVERT: A 530 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.6878 (t) REVERT: A 532 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7214 (t0) REVERT: A 565 PHE cc_start: 0.7774 (m-10) cc_final: 0.7565 (m-80) REVERT: A 567 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6432 (mtt90) REVERT: A 646 ARG cc_start: 0.7401 (mtt180) cc_final: 0.7060 (mtp-110) REVERT: A 790 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8718 (mtpt) REVERT: A 825 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7978 (mtpt) REVERT: A 868 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 964 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7699 (mptp) REVERT: A 1038 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8495 (mtpt) REVERT: A 1091 ARG cc_start: 0.8528 (mtt180) cc_final: 0.8216 (mtt-85) REVERT: B 195 LYS cc_start: 0.6441 (mtpt) cc_final: 0.5984 (mtmm) REVERT: B 211 ASN cc_start: 0.3022 (OUTLIER) cc_final: 0.2797 (m-40) REVERT: B 319 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7708 (mtp180) REVERT: B 787 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: B 900 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8772 (ttm) REVERT: B 1045 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8097 (tmtt) REVERT: B 1125 ASN cc_start: 0.7838 (m-40) cc_final: 0.7634 (p0) REVERT: C 22 CYS cc_start: 0.1385 (OUTLIER) cc_final: 0.0303 (p) REVERT: C 54 ILE cc_start: 0.1662 (OUTLIER) cc_final: 0.1386 (mm) REVERT: C 100 LYS cc_start: 0.3197 (OUTLIER) cc_final: 0.2951 (tptt) REVERT: D 45 SER cc_start: 0.8267 (OUTLIER) cc_final: 0.7907 (t) REVERT: D 153 MET cc_start: 0.0296 (ttt) cc_final: -0.0668 (mtp) REVERT: D 190 ARG cc_start: 0.6186 (mpp80) cc_final: 0.5795 (mtp180) REVERT: D 266 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: D 814 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.6852 (pptt) REVERT: D 916 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8454 (tt) REVERT: D 949 GLN cc_start: 0.8008 (tp40) cc_final: 0.7304 (mt0) REVERT: D 994 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7902 (t70) REVERT: D 1010 GLN cc_start: 0.8490 (tp40) cc_final: 0.8094 (tm-30) REVERT: D 1038 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8023 (mmtp) REVERT: D 1113 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8481 (mm110) REVERT: F 34 MET cc_start: 0.2477 (OUTLIER) cc_final: 0.1381 (ttt) REVERT: F 78 VAL cc_start: -0.0568 (OUTLIER) cc_final: -0.0799 (p) outliers start: 110 outliers final: 52 residues processed: 263 average time/residue: 0.5174 time to fit residues: 162.5766 Evaluate side-chains 251 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 173 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 90 VAL 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 551 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR 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 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU 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 704 SER 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 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 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 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 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 587 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 734 THR 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 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 198 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 348 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 227 optimal weight: 0.7980 chunk 334 optimal weight: 3.9990 chunk 53 optimal weight: 0.0060 chunk 49 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 94 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 613 GLN B 641 ASN B 954 GLN B 957 GLN D 935 GLN D 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.238823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163736 restraints weight = 35952.842| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.61 r_work: 0.3634 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: 0.8205 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29147 Z= 0.134 Angle : 0.586 13.874 39767 Z= 0.293 Chirality : 0.046 0.553 4604 Planarity : 0.004 0.062 5073 Dihedral : 4.830 51.418 4812 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.68 % Rotamer: Outliers : 3.42 % Allowed : 14.37 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.14), residues: 3526 helix: 1.86 (0.20), residues: 701 sheet: 0.05 (0.16), residues: 936 loop : -1.09 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 577 TYR 0.028 0.001 TYR D1067 PHE 0.028 0.001 PHE D 192 TRP 0.012 0.001 TRP B 353 HIS 0.007 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00316 (29059) covalent geometry : angle 0.55651 (39544) SS BOND : bond 0.00540 ( 41) SS BOND : angle 0.92660 ( 82) hydrogen bonds : bond 0.04296 ( 1096) hydrogen bonds : angle 5.48671 ( 2994) link_BETA1-4 : bond 0.00404 ( 11) link_BETA1-4 : angle 1.57352 ( 33) link_NAG-ASN : bond 0.00573 ( 36) link_NAG-ASN : angle 3.43681 ( 108) *********************** 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 283 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 177 time to evaluate : 1.108 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: -0.0336 (mmm) cc_final: -0.1851 (pmm) REVERT: A 129 LYS cc_start: 0.6660 (mttm) cc_final: 0.6054 (ptmm) REVERT: A 200 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.6236 (t80) REVERT: A 202 LYS cc_start: 0.6955 (mttt) cc_final: 0.6442 (mttp) REVERT: A 332 ILE cc_start: 0.5586 (OUTLIER) cc_final: 0.5309 (mm) REVERT: A 396 TYR cc_start: 0.4611 (OUTLIER) cc_final: 0.3953 (p90) REVERT: A 529 LYS cc_start: 0.7087 (mmmm) cc_final: 0.6726 (mmmm) REVERT: A 530 SER cc_start: 0.7466 (OUTLIER) cc_final: 0.6998 (t) REVERT: A 537 LYS cc_start: 0.7166 (ttmt) cc_final: 0.6768 (ttpt) REVERT: A 565 PHE cc_start: 0.7775 (m-10) cc_final: 0.7574 (m-80) REVERT: A 567 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6414 (mtt90) REVERT: A 646 ARG cc_start: 0.7418 (mtt180) cc_final: 0.7065 (mtp-110) REVERT: A 780 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8442 (mp0) REVERT: A 790 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8688 (mtpt) REVERT: A 825 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7986 (mtpt) REVERT: A 868 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: A 964 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7712 (mptp) REVERT: A 1038 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8501 (mtpt) REVERT: B 51 THR cc_start: 0.8064 (p) cc_final: 0.7603 (t) REVERT: B 53 ASP cc_start: 0.7610 (m-30) cc_final: 0.7070 (m-30) REVERT: B 195 LYS cc_start: 0.6436 (mtpt) cc_final: 0.5956 (mtmm) REVERT: B 229 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.5850 (tt) REVERT: B 319 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7692 (mtp180) REVERT: B 539 VAL cc_start: 0.7842 (m) cc_final: 0.7470 (p) REVERT: B 787 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: B 900 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8788 (ttm) REVERT: B 935 GLN cc_start: 0.6693 (mt0) cc_final: 0.6385 (mm-40) REVERT: B 1045 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8081 (tmtt) REVERT: C 22 CYS cc_start: 0.1476 (OUTLIER) cc_final: 0.0329 (p) REVERT: C 54 ILE cc_start: 0.1675 (OUTLIER) cc_final: 0.1387 (mm) REVERT: C 100 LYS cc_start: 0.3224 (OUTLIER) cc_final: 0.2950 (tttt) REVERT: D 45 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7987 (p) REVERT: D 153 MET cc_start: 0.0211 (ttt) cc_final: -0.0783 (mtp) REVERT: D 190 ARG cc_start: 0.6263 (mpp80) cc_final: 0.5869 (mtp180) REVERT: D 266 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: D 814 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.6852 (pptt) REVERT: D 916 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8450 (tt) REVERT: D 949 GLN cc_start: 0.7994 (tp40) cc_final: 0.7263 (mt0) REVERT: D 994 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7879 (t0) REVERT: D 1010 GLN cc_start: 0.8503 (tp40) cc_final: 0.8050 (tm-30) REVERT: D 1038 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8012 (mmtp) REVERT: D 1113 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8514 (mm110) REVERT: F 34 MET cc_start: 0.2424 (OUTLIER) cc_final: 0.1309 (ttt) REVERT: F 78 VAL cc_start: -0.0536 (OUTLIER) cc_final: -0.0741 (p) outliers start: 106 outliers final: 46 residues processed: 260 average time/residue: 0.4827 time to fit residues: 151.6909 Evaluate side-chains 241 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 170 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 70 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 90 VAL 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 551 VAL 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 90 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 484 GLU 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 704 SER 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 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 36 VAL 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 336 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 734 THR 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 1113 GLN Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 255 optimal weight: 5.9990 chunk 343 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 321 optimal weight: 0.0570 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 207 HIS B 321 GLN B 658 ASN B 954 GLN B 957 GLN D 935 GLN D1125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.238050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.164304 restraints weight = 35732.540| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 4.00 r_work: 0.3576 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29147 Z= 0.152 Angle : 0.604 13.879 39767 Z= 0.301 Chirality : 0.047 0.547 4604 Planarity : 0.004 0.059 5073 Dihedral : 4.918 51.722 4812 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 3.42 % Allowed : 14.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3526 helix: 1.87 (0.20), residues: 695 sheet: 0.10 (0.17), residues: 915 loop : -1.12 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 577 TYR 0.036 0.002 TYR B1067 PHE 0.031 0.002 PHE D 192 TRP 0.013 0.001 TRP B 353 HIS 0.007 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00362 (29059) covalent geometry : angle 0.57518 (39544) SS BOND : bond 0.00734 ( 41) SS BOND : angle 0.94259 ( 82) hydrogen bonds : bond 0.04556 ( 1096) hydrogen bonds : angle 5.50555 ( 2994) link_BETA1-4 : bond 0.00398 ( 11) link_BETA1-4 : angle 1.62374 ( 33) link_NAG-ASN : bond 0.00569 ( 36) link_NAG-ASN : angle 3.39396 ( 108) *********************** 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 280 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 174 time to evaluate : 0.926 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: -0.0329 (mmm) cc_final: -0.1424 (pmm) REVERT: A 129 LYS cc_start: 0.6642 (mttm) cc_final: 0.6066 (ptmm) REVERT: A 200 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.6264 (t80) REVERT: A 202 LYS cc_start: 0.6979 (mttt) cc_final: 0.6452 (mttp) REVERT: A 332 ILE cc_start: 0.5606 (OUTLIER) cc_final: 0.5292 (mm) REVERT: A 396 TYR cc_start: 0.4708 (OUTLIER) cc_final: 0.4058 (p90) REVERT: A 529 LYS cc_start: 0.7100 (mmmm) cc_final: 0.6751 (mmmm) REVERT: A 530 SER cc_start: 0.7458 (OUTLIER) cc_final: 0.6976 (t) REVERT: A 532 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7248 (t0) REVERT: A 537 LYS cc_start: 0.7134 (ttmt) cc_final: 0.6757 (ttpt) REVERT: A 567 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6388 (mtt90) REVERT: A 646 ARG cc_start: 0.7453 (mtt180) cc_final: 0.7117 (mtp-110) REVERT: A 790 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8699 (mtpt) REVERT: A 825 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7999 (mtpt) REVERT: A 868 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: A 964 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7729 (mptp) REVERT: A 1038 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8519 (mtpt) REVERT: B 51 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7592 (t) REVERT: B 53 ASP cc_start: 0.7596 (m-30) cc_final: 0.7027 (m-30) REVERT: B 195 LYS cc_start: 0.6531 (mtpt) cc_final: 0.6054 (mtmm) REVERT: B 229 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.5879 (tt) REVERT: B 319 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7716 (mtp180) REVERT: B 787 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8162 (mp10) REVERT: B 900 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8808 (ttm) REVERT: B 1045 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8164 (tmtt) REVERT: C 22 CYS cc_start: 0.1477 (OUTLIER) cc_final: 0.0477 (p) REVERT: C 54 ILE cc_start: 0.1730 (OUTLIER) cc_final: 0.1441 (mm) REVERT: C 100 LYS cc_start: 0.3208 (OUTLIER) cc_final: 0.2954 (tptt) REVERT: D 45 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8092 (p) REVERT: D 153 MET cc_start: 0.0112 (ttt) cc_final: -0.1122 (mtm) REVERT: D 190 ARG cc_start: 0.6301 (mpp80) cc_final: 0.5905 (mtp180) REVERT: D 266 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: D 814 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.6848 (pptt) REVERT: D 949 GLN cc_start: 0.8035 (tp40) cc_final: 0.7275 (mt0) REVERT: D 973 ILE cc_start: 0.8610 (mm) cc_final: 0.8407 (mp) REVERT: D 994 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7939 (t0) REVERT: D 1010 GLN cc_start: 0.8552 (tp40) cc_final: 0.8067 (tm-30) REVERT: D 1038 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8104 (mmtp) REVERT: D 1113 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8515 (mm110) REVERT: F 34 MET cc_start: 0.2384 (OUTLIER) cc_final: 0.1181 (ttt) REVERT: F 78 VAL cc_start: -0.0441 (OUTLIER) cc_final: -0.0647 (p) outliers start: 106 outliers final: 55 residues processed: 253 average time/residue: 0.4954 time to fit residues: 150.3799 Evaluate side-chains 248 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 167 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE 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 86 ILE Chi-restraints excluded: chain A residue 90 VAL 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 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 990 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1136 THR 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 302 THR Chi-restraints excluded: chain B residue 484 GLU 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 656 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 735 SER 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 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain D residue 36 VAL 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 565 PHE Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 734 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 248 optimal weight: 9.9990 chunk 331 optimal weight: 0.5980 chunk 275 optimal weight: 0.5980 chunk 243 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 286 optimal weight: 0.2980 chunk 215 optimal weight: 0.8980 chunk 242 optimal weight: 3.9990 chunk 342 optimal weight: 0.9980 chunk 274 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 954 GLN B 957 GLN D 607 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 = 0.4679 r_free = 0.4679 target = 0.238959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.164609 restraints weight = 35901.349| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.58 r_work: 0.3629 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29147 Z= 0.107 Angle : 0.557 13.082 39767 Z= 0.278 Chirality : 0.045 0.510 4604 Planarity : 0.004 0.059 5073 Dihedral : 4.680 51.000 4812 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.12 % Favored : 96.77 % Rotamer: Outliers : 2.51 % Allowed : 15.31 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.14), residues: 3526 helix: 2.03 (0.20), residues: 697 sheet: 0.11 (0.16), residues: 916 loop : -1.07 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 577 TYR 0.018 0.001 TYR A1067 PHE 0.033 0.001 PHE D 192 TRP 0.011 0.001 TRP B 353 HIS 0.006 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00247 (29059) covalent geometry : angle 0.53055 (39544) SS BOND : bond 0.00400 ( 41) SS BOND : angle 0.71995 ( 82) hydrogen bonds : bond 0.03887 ( 1096) hydrogen bonds : angle 5.33452 ( 2994) link_BETA1-4 : bond 0.00383 ( 11) link_BETA1-4 : angle 1.47600 ( 33) link_NAG-ASN : bond 0.00559 ( 36) link_NAG-ASN : angle 3.17877 ( 108) *********************** 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 261 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 183 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: -0.0223 (mmm) cc_final: -0.1386 (pmm) REVERT: A 129 LYS cc_start: 0.6600 (mttm) cc_final: 0.6040 (ptmm) REVERT: A 200 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.6338 (t80) REVERT: A 202 LYS cc_start: 0.6935 (mttt) cc_final: 0.6449 (mttp) REVERT: A 332 ILE cc_start: 0.5588 (OUTLIER) cc_final: 0.5283 (mm) REVERT: A 529 LYS cc_start: 0.7077 (mmmm) cc_final: 0.6769 (mmmm) REVERT: A 532 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7212 (t0) REVERT: A 536 ASN cc_start: 0.6771 (OUTLIER) cc_final: 0.6094 (t0) REVERT: A 537 LYS cc_start: 0.7181 (ttmt) cc_final: 0.6916 (ttpt) REVERT: A 646 ARG cc_start: 0.7435 (mtt180) cc_final: 0.7064 (mtp-110) REVERT: A 780 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8341 (mp0) REVERT: A 790 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8721 (mtpt) REVERT: A 825 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7998 (mtpt) REVERT: A 868 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: A 964 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8003 (mtpt) REVERT: A 1038 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8465 (mtpt) REVERT: B 51 THR cc_start: 0.8060 (p) cc_final: 0.7594 (t) REVERT: B 53 ASP cc_start: 0.7580 (m-30) cc_final: 0.6965 (m-30) REVERT: B 195 LYS cc_start: 0.6541 (mtpt) cc_final: 0.6058 (mtmm) REVERT: B 229 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.5926 (tt) REVERT: B 319 ARG cc_start: 0.8114 (ttm170) cc_final: 0.7664 (mtp180) REVERT: B 787 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: B 900 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8759 (ttm) REVERT: B 1045 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7857 (ttpp) REVERT: C 22 CYS cc_start: 0.1587 (OUTLIER) cc_final: 0.0480 (p) REVERT: C 54 ILE cc_start: 0.1648 (OUTLIER) cc_final: 0.1336 (mm) REVERT: C 100 LYS cc_start: 0.3182 (OUTLIER) cc_final: 0.2919 (tptt) REVERT: D 45 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8037 (p) REVERT: D 153 MET cc_start: 0.0116 (ttt) cc_final: -0.1218 (mtm) REVERT: D 190 ARG cc_start: 0.6306 (mpp80) cc_final: 0.5891 (mtp180) REVERT: D 266 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: D 814 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.6868 (pptt) REVERT: D 949 GLN cc_start: 0.7850 (tp40) cc_final: 0.7178 (mt0) REVERT: D 994 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7942 (t70) REVERT: D 1010 GLN cc_start: 0.8502 (tp40) cc_final: 0.8032 (tm-30) REVERT: D 1038 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7967 (mmtp) REVERT: D 1113 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8501 (mm110) REVERT: F 34 MET cc_start: 0.2313 (OUTLIER) cc_final: 0.1166 (ttt) REVERT: F 78 VAL cc_start: -0.0462 (OUTLIER) cc_final: -0.0673 (p) outliers start: 78 outliers final: 45 residues processed: 240 average time/residue: 0.5266 time to fit residues: 152.2629 Evaluate side-chains 238 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 170 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 90 VAL 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 430 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 790 LYS 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 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS 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 787 GLN Chi-restraints excluded: chain B residue 900 MET 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 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 36 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 565 PHE 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 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 50 VAL 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 188 optimal weight: 0.9980 chunk 335 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 349 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 321 GLN B 658 ASN B 762 GLN B 954 GLN B 957 GLN D 935 GLN D1125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.237841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164983 restraints weight = 35611.531| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 4.14 r_work: 0.3573 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29147 Z= 0.152 Angle : 0.600 13.120 39767 Z= 0.300 Chirality : 0.047 0.511 4604 Planarity : 0.004 0.058 5073 Dihedral : 4.829 50.984 4811 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 2.67 % Allowed : 15.28 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.14), residues: 3526 helix: 1.92 (0.20), residues: 691 sheet: 0.10 (0.16), residues: 926 loop : -1.10 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1014 TYR 0.024 0.001 TYR A1138 PHE 0.034 0.002 PHE D 192 TRP 0.012 0.001 TRP B 353 HIS 0.007 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00364 (29059) covalent geometry : angle 0.57262 (39544) SS BOND : bond 0.00656 ( 41) SS BOND : angle 0.89845 ( 82) hydrogen bonds : bond 0.04455 ( 1096) hydrogen bonds : angle 5.43286 ( 2994) link_BETA1-4 : bond 0.00407 ( 11) link_BETA1-4 : angle 1.54435 ( 33) link_NAG-ASN : bond 0.00527 ( 36) link_NAG-ASN : angle 3.32497 ( 108) ********************** 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 260 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 177 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: -0.0390 (mmm) cc_final: -0.1435 (pmm) REVERT: A 129 LYS cc_start: 0.6596 (mttm) cc_final: 0.6034 (ptmm) REVERT: A 190 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5523 (mmt180) REVERT: A 200 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.6336 (t80) REVERT: A 202 LYS cc_start: 0.7002 (mttt) cc_final: 0.6409 (mttp) REVERT: A 332 ILE cc_start: 0.5666 (OUTLIER) cc_final: 0.5317 (mm) REVERT: A 396 TYR cc_start: 0.4749 (OUTLIER) cc_final: 0.4093 (p90) REVERT: A 529 LYS cc_start: 0.7096 (mmmm) cc_final: 0.6787 (mmmm) REVERT: A 532 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7260 (t0) REVERT: A 536 ASN cc_start: 0.6754 (OUTLIER) cc_final: 0.6071 (t0) REVERT: A 537 LYS cc_start: 0.7214 (ttmt) cc_final: 0.6852 (ttpt) REVERT: A 567 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6632 (mtt90) REVERT: A 646 ARG cc_start: 0.7466 (mtt180) cc_final: 0.7087 (mtp-110) REVERT: A 780 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8382 (mp0) REVERT: A 790 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8736 (mtpt) REVERT: A 825 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8002 (mtpt) REVERT: A 868 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 964 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8118 (mtpt) REVERT: A 1038 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8504 (mtpt) REVERT: B 51 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7591 (t) REVERT: B 53 ASP cc_start: 0.7599 (m-30) cc_final: 0.7012 (m-30) REVERT: B 195 LYS cc_start: 0.6589 (mtpt) cc_final: 0.6105 (mtmm) REVERT: B 229 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.5901 (tt) REVERT: B 302 THR cc_start: 0.8213 (t) cc_final: 0.7992 (p) REVERT: B 319 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7697 (mtp180) REVERT: B 787 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8191 (mp10) REVERT: B 900 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8819 (ttm) REVERT: B 1045 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8098 (tmtt) REVERT: C 22 CYS cc_start: 0.1558 (OUTLIER) cc_final: 0.0355 (p) REVERT: C 54 ILE cc_start: 0.1649 (OUTLIER) cc_final: 0.1353 (mm) REVERT: C 100 LYS cc_start: 0.3141 (OUTLIER) cc_final: 0.2900 (tptt) REVERT: D 45 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8110 (p) REVERT: D 153 MET cc_start: 0.0188 (ttt) cc_final: -0.1166 (mtm) REVERT: D 190 ARG cc_start: 0.6273 (mpp80) cc_final: 0.5889 (mtp180) REVERT: D 266 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: D 588 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8140 (m) REVERT: D 814 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.6853 (pptt) REVERT: D 949 GLN cc_start: 0.7967 (tp40) cc_final: 0.7261 (mt0) REVERT: D 983 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7111 (ttm170) REVERT: D 994 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7965 (t0) REVERT: D 1010 GLN cc_start: 0.8554 (tp40) cc_final: 0.8061 (tm-30) REVERT: D 1038 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8107 (mmtp) REVERT: D 1113 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8565 (mm110) REVERT: F 34 MET cc_start: 0.2307 (OUTLIER) cc_final: 0.1070 (ttt) outliers start: 83 outliers final: 44 residues processed: 237 average time/residue: 0.5198 time to fit residues: 147.8952 Evaluate side-chains 243 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 90 VAL 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 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 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 790 LYS 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 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1136 THR 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 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 787 GLN Chi-restraints excluded: chain B residue 900 MET 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 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 36 VAL 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 565 PHE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 734 THR 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 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 F residue 34 MET Chi-restraints excluded: chain F residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 196 optimal weight: 1.9990 chunk 279 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 321 GLN B 954 GLN B 957 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 = 0.239482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.166871 restraints weight = 35710.321| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 4.15 r_work: 0.3560 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29147 Z= 0.164 Angle : 0.619 13.142 39767 Z= 0.308 Chirality : 0.047 0.511 4604 Planarity : 0.004 0.057 5073 Dihedral : 5.116 59.583 4811 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 2.64 % Allowed : 15.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.14), residues: 3526 helix: 1.78 (0.20), residues: 696 sheet: 0.06 (0.16), residues: 922 loop : -1.09 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 646 TYR 0.024 0.001 TYR B1067 PHE 0.022 0.002 PHE A 898 TRP 0.012 0.002 TRP A 64 HIS 0.007 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00391 (29059) covalent geometry : angle 0.58943 (39544) SS BOND : bond 0.00724 ( 41) SS BOND : angle 1.34948 ( 82) hydrogen bonds : bond 0.04652 ( 1096) hydrogen bonds : angle 5.51586 ( 2994) link_BETA1-4 : bond 0.00387 ( 11) link_BETA1-4 : angle 1.62361 ( 33) link_NAG-ASN : bond 0.00695 ( 36) link_NAG-ASN : angle 3.40432 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16749.74 seconds wall clock time: 283 minutes 31.78 seconds (17011.78 seconds total)