Starting phenix.real_space_refine on Sat Mar 7 00:25:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hld_34874/03_2026/8hld_34874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hld_34874/03_2026/8hld_34874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hld_34874/03_2026/8hld_34874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hld_34874/03_2026/8hld_34874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hld_34874/03_2026/8hld_34874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hld_34874/03_2026/8hld_34874.map" } resolution = 2.8 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 22819 2.51 5 N 5904 2.21 5 O 7158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36031 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8382 Classifications: {'peptide': 1072} Link IDs: {'PTRANS': 57, 'TRANS': 1014} Chain breaks: 4 Chain: "B" Number of atoms: 8376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8376 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "C" Number of atoms: 8376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8376 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 14, 'TRANS': 207} Chain: "L" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1561 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 17, 'TRANS': 191} Chain: "I" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 14, 'TRANS': 207} Chain: "M" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1561 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 17, 'TRANS': 191} Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 14, 'TRANS': 207} Chain: "N" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1561 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 17, 'TRANS': 191} Chain: "D" 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: "E" 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: "F" 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: "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: "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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: "b" 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: "c" 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: "d" 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: "e" 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: "f" 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: "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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 9.02, per 1000 atoms: 0.25 Number of scatterers: 36031 At special positions: 0 Unit cell: (231.531, 230.444, 221.748, 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 150 16.00 O 7158 8.00 N 5904 7.00 C 22819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.79 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.46 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.12 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=2.14 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.72 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.53 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.12 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=2.31 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.64 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.17 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.12 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.71 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 193 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 203 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 87 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 193 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 147 " - pdb=" SG CYS J 203 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 87 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 193 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1408 " - " NAG B1409 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " 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-ASN " NAG A1401 " - " ASN A 17 " " NAG A1402 " - " ASN A 61 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 282 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 616 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG B1401 " - " ASN B 17 " " NAG B1402 " - " ASN B 61 " " NAG B1403 " - " ASN B 149 " " NAG B1404 " - " ASN B 282 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 616 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B1074 " " NAG C1401 " - " ASN C 17 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 149 " " NAG C1404 " - " ASN C 282 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 343 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1074 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " " NAG T 1 " - " ASN B 122 " " NAG U 1 " - " ASN B 165 " " NAG V 1 " - " ASN B 234 " " NAG W 1 " - " ASN B 331 " " NAG X 1 " - " ASN B 343 " " NAG Y 1 " - " ASN B 709 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG b 1 " - " ASN B1098 " " NAG c 1 " - " ASN B1134 " " NAG d 1 " - " ASN C 122 " " NAG e 1 " - " ASN C 165 " " NAG f 1 " - " ASN C 234 " " NAG g 1 " - " ASN C 331 " " NAG h 1 " - " ASN C 343 " " NAG i 1 " - " ASN C 709 " " NAG j 1 " - " ASN C 717 " " NAG k 1 " - " ASN C 801 " " NAG l 1 " - " ASN C1074 " " NAG m 1 " - " ASN C1098 " " NAG n 1 " - " ASN C1134 " Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.9 seconds 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8384 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 81 sheets defined 17.9% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.774A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.578A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.565A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.700A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.623A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 28 through 31 removed outlier: 3.607A pdb=" N ARG H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 31' Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'I' and resid 28 through 31 removed outlier: 3.607A pdb=" N ARG I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 31' Processing helix chain 'I' and resid 194 through 196 No H-bonds generated for 'chain 'I' and resid 194 through 196' Processing helix chain 'M' and resid 121 through 127 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'J' and resid 28 through 31 removed outlier: 3.606A pdb=" N ARG J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 31' Processing helix chain 'J' and resid 194 through 196 No H-bonds generated for 'chain 'J' and resid 194 through 196' Processing helix chain 'N' and resid 121 through 127 Processing helix chain 'N' and resid 181 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.536A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.093A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.834A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.633A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 155 removed outlier: 6.840A pdb=" N TYR A 144 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.970A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.339A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.863A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.872A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.536A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.835A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.633A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 151 through 155 removed outlier: 6.840A pdb=" N TYR B 144 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.520A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.544A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.555A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.158A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.536A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 49 through 55 removed outlier: 4.638A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.633A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 151 through 155 removed outlier: 6.839A pdb=" N TYR C 144 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU C 154 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY C 142 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.585A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.531A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.848A pdb=" N GLN H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N CYS H 96 " --> pdb=" O GLN H 112 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 127 through 131 removed outlier: 5.007A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 127 through 131 removed outlier: 5.007A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 157 through 161 Processing sheet with id=AF9, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AG1, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.970A pdb=" N THR L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.455A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE L 31 " --> pdb=" O TRP L 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 114 through 118 Processing sheet with id=AG4, first strand: chain 'L' and resid 114 through 118 Processing sheet with id=AG5, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.440A pdb=" N TRP L 148 " --> pdb=" O VAL L 155 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'I' and resid 11 through 12 removed outlier: 5.848A pdb=" N GLN I 112 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N CYS I 96 " --> pdb=" O GLN I 112 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 127 through 131 removed outlier: 5.007A pdb=" N ALA I 144 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 191 " --> pdb=" O ALA I 144 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY I 146 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 189 " --> pdb=" O GLY I 146 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU I 148 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 187 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 150 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU I 185 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 127 through 131 removed outlier: 5.007A pdb=" N ALA I 144 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 191 " --> pdb=" O ALA I 144 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY I 146 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 189 " --> pdb=" O GLY I 146 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU I 148 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 187 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 150 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU I 185 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 157 through 161 Processing sheet with id=AH2, first strand: chain 'M' and resid 9 through 12 Processing sheet with id=AH3, first strand: chain 'M' and resid 18 through 23 removed outlier: 3.969A pdb=" N THR M 69 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 44 through 47 removed outlier: 6.456A pdb=" N TRP M 34 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE M 31 " --> pdb=" O TRP M 90 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AH6, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AH7, first strand: chain 'M' and resid 154 through 155 removed outlier: 4.440A pdb=" N TRP M 148 " --> pdb=" O VAL M 155 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AH9, first strand: chain 'J' and resid 11 through 12 removed outlier: 5.848A pdb=" N GLN J 112 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N CYS J 96 " --> pdb=" O GLN J 112 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 127 through 131 removed outlier: 5.007A pdb=" N ALA J 144 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL J 191 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY J 146 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL J 189 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU J 148 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 187 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 150 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU J 185 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 127 through 131 removed outlier: 5.007A pdb=" N ALA J 144 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL J 191 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY J 146 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL J 189 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU J 148 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 187 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 150 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU J 185 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 157 through 161 Processing sheet with id=AI4, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AI5, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.970A pdb=" N THR N 69 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 44 through 47 removed outlier: 6.456A pdb=" N TRP N 34 " --> pdb=" O VAL N 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE N 31 " --> pdb=" O TRP N 90 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AI8, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AI9, first strand: chain 'N' and resid 154 through 155 removed outlier: 4.440A pdb=" N TRP N 148 " --> pdb=" O VAL N 155 " (cutoff:3.500A) 1420 hydrogen bonds defined for protein. 3783 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: 12.54 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7917 1.33 - 1.45: 9414 1.45 - 1.58: 19357 1.58 - 1.70: 0 1.70 - 1.83: 189 Bond restraints: 36877 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.24e+01 bond pdb=" N PRO A 39 " pdb=" CD PRO A 39 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.263 0.068 1.59e-02 3.96e+03 1.83e+01 bond pdb=" N PRO B 322 " pdb=" CD PRO B 322 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.71e+01 bond pdb=" N PRO B 561 " pdb=" CD PRO B 561 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.68e+01 ... (remaining 36872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 49108 2.77 - 5.53: 997 5.53 - 8.30: 124 8.30 - 11.07: 12 11.07 - 13.84: 4 Bond angle restraints: 50245 Sorted by residual: angle pdb=" N PHE C 565 " pdb=" CA PHE C 565 " pdb=" C PHE C 565 " ideal model delta sigma weight residual 108.86 116.78 -7.92 1.41e+00 5.03e-01 3.15e+01 angle pdb=" N PHE B 565 " pdb=" CA PHE B 565 " pdb=" C PHE B 565 " ideal model delta sigma weight residual 108.86 116.76 -7.90 1.41e+00 5.03e-01 3.14e+01 angle pdb=" C TYR A 38 " pdb=" N PRO A 39 " pdb=" CA PRO A 39 " ideal model delta sigma weight residual 119.84 114.22 5.62 1.25e+00 6.40e-01 2.02e+01 angle pdb=" C LEU C 560 " pdb=" N PRO C 561 " pdb=" CA PRO C 561 " ideal model delta sigma weight residual 119.84 114.30 5.54 1.25e+00 6.40e-01 1.96e+01 angle pdb=" C LEU B 560 " pdb=" N PRO B 561 " pdb=" CA PRO B 561 " ideal model delta sigma weight residual 119.84 114.32 5.52 1.25e+00 6.40e-01 1.95e+01 ... (remaining 50240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 20277 17.93 - 35.87: 2020 35.87 - 53.80: 580 53.80 - 71.73: 177 71.73 - 89.67: 56 Dihedral angle restraints: 23110 sinusoidal: 10045 harmonic: 13065 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.05 71.95 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.06 71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 23107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 5906 0.330 - 0.660: 11 0.660 - 0.990: 3 0.990 - 1.320: 2 1.320 - 1.650: 2 Chirality restraints: 5924 Sorted by residual: chirality pdb=" C1 NAG B1409 " pdb=" O4 NAG B1408 " pdb=" C2 NAG B1409 " pdb=" O5 NAG B1409 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 NAG n 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG n 1 " pdb=" O5 NAG n 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.81e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.92 -1.48 2.00e-01 2.50e+01 5.48e+01 ... (remaining 5921 not shown) Planarity restraints: 6435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.174 2.00e-02 2.50e+03 2.09e-01 5.44e+02 pdb=" CG ASN B 331 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.344 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " 0.253 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.096 2.00e-02 2.50e+03 1.16e-01 1.68e+02 pdb=" CG ASN A 331 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.196 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.82e-02 4.24e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG A1408 " -0.067 2.00e-02 2.50e+03 ... (remaining 6432 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 255 2.50 - 3.10: 25394 3.10 - 3.70: 51604 3.70 - 4.30: 76131 4.30 - 4.90: 129845 Nonbonded interactions: 283229 Sorted by model distance: nonbonded pdb=" O LEU C 335 " pdb=" O CYS C 336 " model vdw 1.902 3.040 nonbonded pdb=" O LYS C 529 " pdb=" OG SER C 530 " model vdw 1.928 3.040 nonbonded pdb=" O ILE B 332 " pdb=" OG1 THR B 333 " model vdw 1.931 3.040 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.983 3.120 ... (remaining 283224 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 939 or resid 944 through 1407)) selection = (chain 'B' and resid 14 through 1407) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.880 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 : 0.012 0.503 37017 Z= 0.535 Angle : 1.269 56.240 50611 Z= 0.651 Chirality : 0.075 1.650 5924 Planarity : 0.008 0.104 6381 Dihedral : 16.397 89.667 14564 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 1.88 % Allowed : 9.29 % Favored : 88.82 % Rotamer: Outliers : 9.10 % Allowed : 13.76 % Favored : 77.14 % 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 are not related in a simple way. whole: -3.31 (0.11), residues: 4465 helix: -2.42 (0.16), residues: 703 sheet: -0.88 (0.12), residues: 1454 loop : -3.09 (0.11), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.032 0.003 TYR M 48 PHE 0.058 0.003 PHE H 103 TRP 0.023 0.003 TRP A 886 HIS 0.015 0.002 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.01049 (36877) covalent geometry : angle 1.00182 (50245) SS BOND : bond 0.13543 ( 54) SS BOND : angle 13.01566 ( 108) hydrogen bonds : bond 0.17025 ( 1318) hydrogen bonds : angle 7.58435 ( 3783) link_BETA1-4 : bond 0.03594 ( 32) link_BETA1-4 : angle 4.55885 ( 96) link_NAG-ASN : bond 0.01993 ( 54) link_NAG-ASN : angle 8.16351 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 356 poor density : 465 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6328 (t0) cc_final: 0.5580 (t0) REVERT: A 117 LEU cc_start: 0.7482 (tp) cc_final: 0.6812 (mp) REVERT: A 177 MET cc_start: 0.3318 (pmm) cc_final: 0.2604 (mpt) REVERT: A 324 GLU cc_start: 0.5065 (OUTLIER) cc_final: 0.4405 (pt0) REVERT: A 389 ASP cc_start: 0.5739 (OUTLIER) cc_final: 0.3371 (t70) REVERT: A 532 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7222 (m-40) REVERT: A 582 LEU cc_start: 0.7528 (mt) cc_final: 0.7316 (mp) REVERT: A 738 CYS cc_start: 0.5858 (OUTLIER) cc_final: 0.5638 (t) REVERT: A 1039 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8216 (mtm-85) REVERT: B 278 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6896 (tttm) REVERT: B 298 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: B 324 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: B 335 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5580 (tt) REVERT: B 353 TRP cc_start: 0.6796 (p-90) cc_final: 0.6483 (p90) REVERT: C 273 ARG cc_start: 0.4853 (mmm160) cc_final: 0.4305 (mmt-90) REVERT: C 528 LYS cc_start: 0.4884 (OUTLIER) cc_final: 0.3718 (mmtp) REVERT: C 856 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7446 (p0) REVERT: C 978 ASN cc_start: 0.8537 (m-40) cc_final: 0.8318 (m-40) REVERT: H 13 LYS cc_start: 0.4524 (mtmm) cc_final: 0.4191 (tptp) REVERT: H 124 LYS cc_start: 0.2781 (OUTLIER) cc_final: 0.2459 (tppt) REVERT: H 167 THR cc_start: 0.4551 (OUTLIER) cc_final: 0.4336 (p) REVERT: H 171 HIS cc_start: 0.2771 (OUTLIER) cc_final: 0.2460 (t-170) REVERT: L 180 LEU cc_start: -0.0737 (OUTLIER) cc_final: -0.0994 (tp) REVERT: L 181 THR cc_start: 0.1633 (OUTLIER) cc_final: 0.1391 (p) REVERT: I 163 SER cc_start: 0.4482 (OUTLIER) cc_final: 0.3808 (p) REVERT: I 202 ILE cc_start: 0.3217 (OUTLIER) cc_final: 0.2932 (mt) REVERT: M 181 THR cc_start: 0.2707 (OUTLIER) cc_final: 0.2431 (p) REVERT: J 70 MET cc_start: 0.4219 (mtt) cc_final: 0.3438 (mtm) REVERT: J 163 SER cc_start: 0.2986 (OUTLIER) cc_final: 0.2645 (m) REVERT: J 167 THR cc_start: 0.2342 (OUTLIER) cc_final: 0.2091 (t) outliers start: 356 outliers final: 73 residues processed: 768 average time/residue: 0.4905 time to fit residues: 480.0442 Evaluate side-chains 328 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 234 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain N residue 114 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 30.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 115 GLN A 185 ASN A 245 HIS A 360 ASN A 422 ASN A 450 ASN A 498 GLN A 644 GLN A 658 ASN A 804 GLN A 824 ASN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1058 HIS A1101 HIS B 14 GLN B 30 ASN B 81 ASN B 146 HIS B 185 ASN B 218 GLN B 314 GLN B 317 ASN B 360 ASN B 422 ASN B 440 ASN B 498 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 655 HIS B 755 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 992 GLN B1002 GLN B1054 GLN C 115 GLN C 185 ASN C 218 GLN C 394 ASN C 422 ASN C 440 ASN C 544 ASN C 613 GLN C 644 GLN C 658 ASN C 675 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 992 GLN C1071 GLN C1101 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN L 188 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN M 37 GLN M 68 ASN M 188 HIS M 194 GLN ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 68 ASN N 128 ASN N 188 HIS N 194 GLN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.218176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.168633 restraints weight = 60125.866| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.74 r_work: 0.3327 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.152 37017 Z= 0.454 Angle : 1.030 18.869 50611 Z= 0.509 Chirality : 0.064 0.721 5924 Planarity : 0.008 0.074 6381 Dihedral : 10.308 118.178 6777 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.76 % Favored : 91.00 % Rotamer: Outliers : 6.70 % Allowed : 17.60 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.12), residues: 4465 helix: -1.17 (0.18), residues: 709 sheet: -0.30 (0.13), residues: 1420 loop : -2.66 (0.11), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 357 TYR 0.045 0.003 TYR C 28 PHE 0.046 0.004 PHE H 103 TRP 0.023 0.003 TRP I 106 HIS 0.009 0.003 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.01110 (36877) covalent geometry : angle 0.98662 (50245) SS BOND : bond 0.01143 ( 54) SS BOND : angle 2.94794 ( 108) hydrogen bonds : bond 0.07414 ( 1318) hydrogen bonds : angle 6.42391 ( 3783) link_BETA1-4 : bond 0.01061 ( 32) link_BETA1-4 : angle 3.10203 ( 96) link_NAG-ASN : bond 0.01080 ( 54) link_NAG-ASN : angle 4.27886 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 267 time to evaluate : 1.312 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: A 66 HIS cc_start: 0.6558 (m-70) cc_final: 0.6182 (t70) REVERT: A 271 GLN cc_start: 0.8132 (mt0) cc_final: 0.7643 (tm-30) REVERT: A 306 PHE cc_start: 0.8716 (m-80) cc_final: 0.8515 (m-80) REVERT: A 389 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.4720 (t70) REVERT: A 569 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7583 (mt) REVERT: A 745 ASP cc_start: 0.8204 (p0) cc_final: 0.7914 (p0) REVERT: B 177 MET cc_start: 0.5383 (pmm) cc_final: 0.2935 (tpt) REVERT: B 298 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: B 400 PHE cc_start: 0.8114 (p90) cc_final: 0.7653 (p90) REVERT: C 99 ASN cc_start: 0.6846 (t0) cc_final: 0.6204 (t0) REVERT: C 153 MET cc_start: 0.5786 (OUTLIER) cc_final: 0.5514 (pmm) REVERT: C 170 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6991 (t80) REVERT: C 190 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7123 (mmm-85) REVERT: C 314 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8420 (mt0) REVERT: C 336 CYS cc_start: 0.3566 (OUTLIER) cc_final: 0.3055 (t) REVERT: C 417 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7254 (mtmm) REVERT: C 528 LYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5354 (mmtp) REVERT: C 541 PHE cc_start: 0.6911 (p90) cc_final: 0.6707 (p90) REVERT: H 13 LYS cc_start: 0.4837 (mtmm) cc_final: 0.4168 (tptt) REVERT: H 124 LYS cc_start: 0.2926 (OUTLIER) cc_final: 0.2579 (tppt) REVERT: H 131 LEU cc_start: 0.2070 (mp) cc_final: 0.1708 (mm) REVERT: H 148 LEU cc_start: 0.1460 (tt) cc_final: 0.1172 (mp) REVERT: H 167 THR cc_start: 0.4750 (OUTLIER) cc_final: 0.4511 (p) REVERT: H 171 HIS cc_start: 0.2858 (OUTLIER) cc_final: 0.2577 (t-170) REVERT: L 30 LYS cc_start: 0.1523 (mptt) cc_final: 0.1301 (mptt) REVERT: L 181 THR cc_start: 0.1589 (OUTLIER) cc_final: 0.1339 (p) REVERT: I 70 MET cc_start: 0.3717 (OUTLIER) cc_final: 0.3049 (tpt) REVERT: I 171 HIS cc_start: 0.1169 (OUTLIER) cc_final: 0.0806 (m170) REVERT: I 202 ILE cc_start: 0.3539 (OUTLIER) cc_final: 0.3250 (mt) REVERT: M 181 THR cc_start: 0.2348 (OUTLIER) cc_final: 0.2139 (p) REVERT: J 70 MET cc_start: 0.4356 (mtt) cc_final: 0.3668 (mtm) REVERT: J 137 SER cc_start: -0.1087 (OUTLIER) cc_final: -0.1558 (t) REVERT: J 167 THR cc_start: 0.2302 (OUTLIER) cc_final: 0.1979 (t) REVERT: J 180 SER cc_start: -0.1339 (OUTLIER) cc_final: -0.1654 (t) REVERT: N 1 LEU cc_start: 0.5095 (OUTLIER) cc_final: 0.4875 (pp) REVERT: N 41 GLN cc_start: 0.3283 (mp10) cc_final: 0.2336 (mm-40) REVERT: N 175 SER cc_start: 0.0888 (OUTLIER) cc_final: 0.0261 (t) outliers start: 262 outliers final: 107 residues processed: 498 average time/residue: 0.4762 time to fit residues: 306.0013 Evaluate side-chains 331 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 202 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1057 PRO Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 275 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 252 optimal weight: 9.9990 chunk 412 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 265 optimal weight: 0.5980 chunk 289 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 245 HIS A 613 GLN A 949 GLN A 992 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 498 GLN C 675 GLN C 804 GLN C 935 GLN H 6 GLN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.215607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.165584 restraints weight = 61800.481| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.82 r_work: 0.3395 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37017 Z= 0.143 Angle : 0.744 13.236 50611 Z= 0.362 Chirality : 0.050 0.814 5924 Planarity : 0.005 0.074 6381 Dihedral : 8.681 85.695 6695 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.76 % Favored : 93.03 % Rotamer: Outliers : 4.48 % Allowed : 19.69 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 4465 helix: 0.23 (0.19), residues: 703 sheet: 0.10 (0.14), residues: 1419 loop : -2.31 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 190 TYR 0.022 0.001 TYR B 170 PHE 0.049 0.002 PHE H 103 TRP 0.017 0.001 TRP N 34 HIS 0.005 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00321 (36877) covalent geometry : angle 0.70900 (50245) SS BOND : bond 0.00545 ( 54) SS BOND : angle 2.15043 ( 108) hydrogen bonds : bond 0.04570 ( 1318) hydrogen bonds : angle 5.73402 ( 3783) link_BETA1-4 : bond 0.00822 ( 32) link_BETA1-4 : angle 2.62565 ( 96) link_NAG-ASN : bond 0.00529 ( 54) link_NAG-ASN : angle 3.14962 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 233 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 CYS cc_start: 0.3448 (OUTLIER) cc_final: 0.2244 (m) REVERT: A 66 HIS cc_start: 0.6610 (m-70) cc_final: 0.6065 (t-90) REVERT: A 152 TRP cc_start: 0.6327 (t60) cc_final: 0.5555 (t60) REVERT: A 245 HIS cc_start: 0.5899 (OUTLIER) cc_final: 0.5350 (t70) REVERT: A 389 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.4172 (t70) REVERT: A 569 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7607 (mt) REVERT: A 745 ASP cc_start: 0.7946 (p0) cc_final: 0.7672 (p0) REVERT: A 1136 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9070 (p) REVERT: B 177 MET cc_start: 0.5141 (pmm) cc_final: 0.2884 (tpp) REVERT: B 314 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8164 (mm-40) REVERT: B 400 PHE cc_start: 0.7956 (p90) cc_final: 0.7320 (p90) REVERT: B 517 LEU cc_start: -0.1534 (OUTLIER) cc_final: -0.2330 (pp) REVERT: C 99 ASN cc_start: 0.6952 (t0) cc_final: 0.6222 (t0) REVERT: C 153 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5640 (pmm) REVERT: C 417 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7328 (mptt) REVERT: C 517 LEU cc_start: 0.0087 (OUTLIER) cc_final: -0.0524 (pt) REVERT: C 528 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.6287 (mmmt) REVERT: C 565 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.5990 (p90) REVERT: C 614 ASP cc_start: 0.8528 (p0) cc_final: 0.8328 (m-30) REVERT: C 675 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6541 (mt0) REVERT: C 985 ASP cc_start: 0.7421 (p0) cc_final: 0.7172 (p0) REVERT: H 13 LYS cc_start: 0.4812 (mtmm) cc_final: 0.4081 (tptp) REVERT: H 70 MET cc_start: 0.1442 (mtt) cc_final: 0.0891 (mpt) REVERT: H 167 THR cc_start: 0.4731 (OUTLIER) cc_final: 0.4503 (p) REVERT: H 171 HIS cc_start: 0.3042 (OUTLIER) cc_final: 0.2726 (t-170) REVERT: L 203 GLU cc_start: 0.4561 (OUTLIER) cc_final: 0.3564 (mp0) REVERT: I 70 MET cc_start: 0.3600 (OUTLIER) cc_final: 0.3027 (tpt) REVERT: I 171 HIS cc_start: 0.1191 (OUTLIER) cc_final: 0.0830 (m90) REVERT: I 202 ILE cc_start: 0.3561 (OUTLIER) cc_final: 0.3230 (mt) REVERT: J 70 MET cc_start: 0.4104 (mtt) cc_final: 0.3322 (mtm) REVERT: J 137 SER cc_start: -0.1051 (OUTLIER) cc_final: -0.1504 (t) REVERT: J 167 THR cc_start: 0.2106 (OUTLIER) cc_final: 0.1835 (t) REVERT: N 34 TRP cc_start: 0.1428 (m100) cc_final: 0.0847 (t-100) REVERT: N 41 GLN cc_start: 0.3648 (mp10) cc_final: 0.2657 (mm-40) outliers start: 175 outliers final: 82 residues processed: 390 average time/residue: 0.4779 time to fit residues: 241.5024 Evaluate side-chains 302 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 199 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 171 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 312 optimal weight: 3.9990 chunk 289 optimal weight: 0.0370 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 302 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 286 optimal weight: 7.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS B 207 HIS ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 178 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.215187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.165561 restraints weight = 61410.210| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.85 r_work: 0.3383 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37017 Z= 0.157 Angle : 0.734 13.985 50611 Z= 0.355 Chirality : 0.050 0.707 5924 Planarity : 0.005 0.072 6381 Dihedral : 8.111 87.108 6675 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.08 % Favored : 92.77 % Rotamer: Outliers : 4.73 % Allowed : 19.77 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.12), residues: 4465 helix: 0.74 (0.20), residues: 698 sheet: 0.26 (0.14), residues: 1421 loop : -2.08 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.024 0.001 TYR A 170 PHE 0.045 0.002 PHE H 103 TRP 0.010 0.001 TRP A 353 HIS 0.024 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00369 (36877) covalent geometry : angle 0.70100 (50245) SS BOND : bond 0.00642 ( 54) SS BOND : angle 2.13905 ( 108) hydrogen bonds : bond 0.04600 ( 1318) hydrogen bonds : angle 5.55600 ( 3783) link_BETA1-4 : bond 0.00744 ( 32) link_BETA1-4 : angle 2.56442 ( 96) link_NAG-ASN : bond 0.00487 ( 54) link_NAG-ASN : angle 3.00741 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 217 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.5103 (mtt180) REVERT: A 66 HIS cc_start: 0.6774 (m-70) cc_final: 0.6101 (t-90) REVERT: A 152 TRP cc_start: 0.6313 (t60) cc_final: 0.5487 (t60) REVERT: A 326 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6387 (pp) REVERT: A 544 ASN cc_start: 0.7710 (p0) cc_final: 0.7366 (m-40) REVERT: A 569 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7619 (mt) REVERT: A 1136 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9075 (p) REVERT: B 177 MET cc_start: 0.4994 (pmm) cc_final: 0.3037 (tpp) REVERT: B 314 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8037 (mm-40) REVERT: B 324 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: B 400 PHE cc_start: 0.7864 (p90) cc_final: 0.7138 (p90) REVERT: B 465 GLU cc_start: 0.7495 (tt0) cc_final: 0.7244 (tm-30) REVERT: B 517 LEU cc_start: -0.1398 (OUTLIER) cc_final: -0.2033 (pp) REVERT: C 99 ASN cc_start: 0.6788 (t0) cc_final: 0.5970 (t0) REVERT: C 153 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5581 (pmm) REVERT: C 417 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7242 (mmtp) REVERT: C 420 ASP cc_start: 0.6672 (m-30) cc_final: 0.6391 (p0) REVERT: C 493 GLN cc_start: 0.5633 (OUTLIER) cc_final: 0.5153 (tm130) REVERT: C 528 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.6288 (mmmt) REVERT: C 558 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6790 (mtpm) REVERT: H 13 LYS cc_start: 0.5099 (mtmm) cc_final: 0.4349 (tptp) REVERT: H 124 LYS cc_start: 0.2876 (OUTLIER) cc_final: 0.2631 (tppt) REVERT: H 148 LEU cc_start: 0.1747 (tt) cc_final: 0.1247 (pt) REVERT: H 167 THR cc_start: 0.5249 (OUTLIER) cc_final: 0.5036 (p) REVERT: H 171 HIS cc_start: 0.3198 (OUTLIER) cc_final: 0.2856 (t-170) REVERT: L 203 GLU cc_start: 0.4864 (OUTLIER) cc_final: 0.3927 (mp0) REVERT: I 171 HIS cc_start: 0.1070 (OUTLIER) cc_final: 0.0727 (m90) REVERT: I 202 ILE cc_start: 0.3625 (OUTLIER) cc_final: 0.3191 (mt) REVERT: M 162 THR cc_start: 0.1060 (OUTLIER) cc_final: 0.0786 (p) REVERT: J 70 MET cc_start: 0.4128 (mtt) cc_final: 0.3385 (mtm) REVERT: J 136 LYS cc_start: 0.0738 (OUTLIER) cc_final: 0.0531 (pmtt) REVERT: J 137 SER cc_start: -0.1027 (OUTLIER) cc_final: -0.1286 (t) REVERT: J 167 THR cc_start: 0.2090 (OUTLIER) cc_final: 0.1840 (t) REVERT: N 34 TRP cc_start: 0.1455 (m100) cc_final: 0.0812 (t-100) REVERT: N 41 GLN cc_start: 0.4042 (mp10) cc_final: 0.2841 (mm-40) outliers start: 185 outliers final: 103 residues processed: 387 average time/residue: 0.4806 time to fit residues: 238.1824 Evaluate side-chains 321 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 196 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 171 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 51 optimal weight: 20.0000 chunk 354 optimal weight: 10.0000 chunk 276 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 107 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 320 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 334 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS B 14 GLN B 207 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 360 ASN C 675 GLN H 204 ASN L 37 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 88 GLN ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 204 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.221427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.173187 restraints weight = 61437.203| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.93 r_work: 0.3424 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37017 Z= 0.126 Angle : 0.694 13.591 50611 Z= 0.334 Chirality : 0.048 0.637 5924 Planarity : 0.004 0.071 6381 Dihedral : 7.602 88.692 6670 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.85 % Favored : 93.01 % Rotamer: Outliers : 4.22 % Allowed : 20.10 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.12), residues: 4465 helix: 1.14 (0.20), residues: 700 sheet: 0.41 (0.14), residues: 1397 loop : -1.93 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.022 0.001 TYR B 170 PHE 0.041 0.001 PHE H 103 TRP 0.009 0.001 TRP L 185 HIS 0.011 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00284 (36877) covalent geometry : angle 0.66300 (50245) SS BOND : bond 0.00484 ( 54) SS BOND : angle 1.84172 ( 108) hydrogen bonds : bond 0.03999 ( 1318) hydrogen bonds : angle 5.33729 ( 3783) link_BETA1-4 : bond 0.00752 ( 32) link_BETA1-4 : angle 2.48580 ( 96) link_NAG-ASN : bond 0.00430 ( 54) link_NAG-ASN : angle 2.84299 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 220 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 CYS cc_start: 0.2876 (OUTLIER) cc_final: 0.2190 (m) REVERT: A 66 HIS cc_start: 0.6785 (m-70) cc_final: 0.6109 (t-90) REVERT: A 152 TRP cc_start: 0.6316 (t60) cc_final: 0.5491 (t60) REVERT: A 245 HIS cc_start: 0.5705 (OUTLIER) cc_final: 0.5138 (t70) REVERT: A 326 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6349 (pp) REVERT: A 1017 GLU cc_start: 0.8738 (tt0) cc_final: 0.8381 (pt0) REVERT: A 1136 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9064 (p) REVERT: B 177 MET cc_start: 0.5183 (pmm) cc_final: 0.3123 (tpp) REVERT: B 314 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8053 (mm-40) REVERT: B 324 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: B 420 ASP cc_start: 0.5173 (t0) cc_final: 0.4182 (m-30) REVERT: B 508 TYR cc_start: 0.6343 (m-80) cc_final: 0.5625 (m-80) REVERT: B 569 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6835 (pp) REVERT: B 957 GLN cc_start: 0.8617 (tt0) cc_final: 0.8370 (pt0) REVERT: B 1113 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8651 (mt0) REVERT: C 99 ASN cc_start: 0.6649 (t0) cc_final: 0.5892 (t0) REVERT: C 400 PHE cc_start: 0.8157 (p90) cc_final: 0.7266 (p90) REVERT: C 417 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7462 (mptm) REVERT: C 493 GLN cc_start: 0.5623 (OUTLIER) cc_final: 0.5235 (tm130) REVERT: C 558 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6745 (mtpm) REVERT: H 6 GLN cc_start: 0.4501 (OUTLIER) cc_final: 0.3682 (mm110) REVERT: H 13 LYS cc_start: 0.5189 (mtmm) cc_final: 0.4489 (tptp) REVERT: H 124 LYS cc_start: 0.2837 (OUTLIER) cc_final: 0.2598 (tppt) REVERT: H 171 HIS cc_start: 0.3043 (OUTLIER) cc_final: 0.2828 (t-170) REVERT: L 203 GLU cc_start: 0.4759 (OUTLIER) cc_final: 0.3979 (mp0) REVERT: I 171 HIS cc_start: 0.1016 (OUTLIER) cc_final: 0.0670 (m90) REVERT: M 162 THR cc_start: 0.0773 (OUTLIER) cc_final: 0.0424 (p) REVERT: J 70 MET cc_start: 0.4160 (mtt) cc_final: 0.3598 (mtm) REVERT: N 34 TRP cc_start: 0.1449 (m100) cc_final: 0.0817 (t-100) REVERT: N 41 GLN cc_start: 0.4069 (mp10) cc_final: 0.2832 (mm-40) outliers start: 165 outliers final: 90 residues processed: 372 average time/residue: 0.4783 time to fit residues: 229.5109 Evaluate side-chains 300 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 193 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 171 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 0 optimal weight: 40.0000 chunk 270 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 402 optimal weight: 30.0000 chunk 217 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 283 optimal weight: 8.9990 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 245 HIS A 271 GLN A 675 GLN B 14 GLN B 207 HIS B 245 HIS B 271 GLN B 280 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 675 GLN B 935 GLN C 87 ASN C 360 ASN C 675 GLN C 751 ASN H 204 ASN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.214784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.163304 restraints weight = 59876.056| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.83 r_work: 0.3335 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 37017 Z= 0.319 Angle : 0.865 17.665 50611 Z= 0.421 Chirality : 0.057 0.785 5924 Planarity : 0.006 0.064 6381 Dihedral : 8.259 89.731 6657 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.86 % Favored : 92.00 % Rotamer: Outliers : 5.50 % Allowed : 19.62 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.12), residues: 4465 helix: 0.40 (0.20), residues: 706 sheet: 0.29 (0.14), residues: 1365 loop : -2.03 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1000 TYR 0.030 0.002 TYR C 28 PHE 0.031 0.003 PHE H 103 TRP 0.018 0.002 TRP L 34 HIS 0.018 0.002 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00783 (36877) covalent geometry : angle 0.82912 (50245) SS BOND : bond 0.00760 ( 54) SS BOND : angle 2.41449 ( 108) hydrogen bonds : bond 0.06228 ( 1318) hydrogen bonds : angle 5.78959 ( 3783) link_BETA1-4 : bond 0.00653 ( 32) link_BETA1-4 : angle 2.74980 ( 96) link_NAG-ASN : bond 0.00659 ( 54) link_NAG-ASN : angle 3.50055 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 207 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6728 (m-70) cc_final: 0.6119 (t-90) REVERT: A 152 TRP cc_start: 0.6256 (t60) cc_final: 0.5462 (t60) REVERT: A 271 GLN cc_start: 0.8166 (mt0) cc_final: 0.7711 (tm-30) REVERT: A 326 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6526 (pp) REVERT: A 329 PHE cc_start: 0.6834 (m-80) cc_final: 0.6482 (m-80) REVERT: A 389 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.4810 (t70) REVERT: A 532 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7929 (m110) REVERT: A 569 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7795 (mp) REVERT: A 745 ASP cc_start: 0.8072 (p0) cc_final: 0.7867 (p0) REVERT: B 33 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7919 (m) REVERT: B 177 MET cc_start: 0.5268 (pmm) cc_final: 0.3191 (tpt) REVERT: B 237 ARG cc_start: 0.7278 (mtp180) cc_final: 0.7004 (mmm-85) REVERT: B 298 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: B 376 THR cc_start: 0.4323 (OUTLIER) cc_final: 0.3355 (p) REVERT: B 394 ASN cc_start: 0.7716 (m-40) cc_final: 0.6789 (p0) REVERT: B 423 TYR cc_start: 0.7532 (t80) cc_final: 0.7296 (t80) REVERT: B 508 TYR cc_start: 0.6255 (m-80) cc_final: 0.5418 (m-80) REVERT: B 517 LEU cc_start: -0.0974 (OUTLIER) cc_final: -0.1626 (pp) REVERT: B 564 GLN cc_start: 0.6818 (mt0) cc_final: 0.6562 (mp10) REVERT: B 569 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6762 (pp) REVERT: B 613 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8771 (mt0) REVERT: C 324 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: C 417 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7445 (mptm) REVERT: C 493 GLN cc_start: 0.5559 (OUTLIER) cc_final: 0.5144 (tm130) REVERT: C 558 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7027 (mtpm) REVERT: C 985 ASP cc_start: 0.7777 (p0) cc_final: 0.7193 (m-30) REVERT: H 13 LYS cc_start: 0.5038 (mtmm) cc_final: 0.4314 (tptt) REVERT: H 83 LEU cc_start: 0.0122 (OUTLIER) cc_final: -0.0202 (tp) REVERT: H 120 SER cc_start: 0.2290 (p) cc_final: 0.1631 (t) REVERT: H 124 LYS cc_start: 0.2848 (OUTLIER) cc_final: 0.2637 (tppt) REVERT: H 148 LEU cc_start: 0.1905 (tt) cc_final: 0.1495 (mp) REVERT: H 171 HIS cc_start: 0.3291 (OUTLIER) cc_final: 0.3044 (t-170) REVERT: L 203 GLU cc_start: 0.4495 (OUTLIER) cc_final: 0.3768 (mp0) REVERT: M 36 GLN cc_start: 0.5060 (tm-30) cc_final: 0.4173 (mm-40) REVERT: M 88 GLN cc_start: 0.2042 (tt0) cc_final: 0.0946 (tp-100) REVERT: M 162 THR cc_start: 0.1169 (OUTLIER) cc_final: 0.0537 (p) REVERT: J 70 MET cc_start: 0.4367 (mtt) cc_final: 0.3810 (mtm) REVERT: N 41 GLN cc_start: 0.4376 (mp10) cc_final: 0.2917 (mm110) outliers start: 215 outliers final: 107 residues processed: 405 average time/residue: 0.4768 time to fit residues: 248.9471 Evaluate side-chains 310 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 184 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 171 LYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 171 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 207 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 432 optimal weight: 0.0020 chunk 225 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 370 optimal weight: 40.0000 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 675 GLN A 949 GLN B 207 HIS B 271 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 690 GLN B 804 GLN B1113 GLN C 99 ASN C 675 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 39 GLN N 6 GLN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.217503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.181438 restraints weight = 60608.425| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 3.69 r_work: 0.3327 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 37017 Z= 0.136 Angle : 0.720 14.464 50611 Z= 0.346 Chirality : 0.049 0.642 5924 Planarity : 0.005 0.058 6381 Dihedral : 7.586 89.723 6657 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.63 % Favored : 93.28 % Rotamer: Outliers : 3.81 % Allowed : 21.10 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.12), residues: 4465 helix: 0.92 (0.20), residues: 711 sheet: 0.42 (0.14), residues: 1374 loop : -1.86 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.022 0.001 TYR B 170 PHE 0.030 0.001 PHE I 103 TRP 0.016 0.001 TRP N 34 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00313 (36877) covalent geometry : angle 0.68463 (50245) SS BOND : bond 0.00531 ( 54) SS BOND : angle 2.27295 ( 108) hydrogen bonds : bond 0.04247 ( 1318) hydrogen bonds : angle 5.39436 ( 3783) link_BETA1-4 : bond 0.00770 ( 32) link_BETA1-4 : angle 2.54579 ( 96) link_NAG-ASN : bond 0.00638 ( 54) link_NAG-ASN : angle 3.01525 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 202 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.4922 (mtt180) REVERT: A 66 HIS cc_start: 0.6809 (m-70) cc_final: 0.6067 (t-90) REVERT: A 152 TRP cc_start: 0.6132 (t60) cc_final: 0.5531 (t60) REVERT: A 245 HIS cc_start: 0.5664 (OUTLIER) cc_final: 0.5081 (t70) REVERT: A 326 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.6386 (pp) REVERT: A 745 ASP cc_start: 0.7949 (p0) cc_final: 0.7737 (p0) REVERT: B 166 CYS cc_start: 0.3202 (OUTLIER) cc_final: 0.2568 (p) REVERT: B 177 MET cc_start: 0.5274 (pmm) cc_final: 0.3150 (tpt) REVERT: B 246 ARG cc_start: 0.6019 (tpt90) cc_final: 0.5393 (tpm-80) REVERT: B 394 ASN cc_start: 0.7635 (m-40) cc_final: 0.6719 (p0) REVERT: B 508 TYR cc_start: 0.6226 (m-80) cc_final: 0.5540 (m-80) REVERT: B 517 LEU cc_start: -0.1299 (OUTLIER) cc_final: -0.1532 (pp) REVERT: B 546 LEU cc_start: 0.7585 (tp) cc_final: 0.6770 (mm) REVERT: C 417 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7471 (mptm) REVERT: C 493 GLN cc_start: 0.5618 (OUTLIER) cc_final: 0.5229 (tm-30) REVERT: C 531 THR cc_start: 0.8083 (t) cc_final: 0.7686 (p) REVERT: C 558 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6837 (mtpm) REVERT: C 564 GLN cc_start: 0.6461 (tm-30) cc_final: 0.5940 (tm-30) REVERT: C 985 ASP cc_start: 0.7516 (p0) cc_final: 0.6826 (m-30) REVERT: H 13 LYS cc_start: 0.4875 (mtmm) cc_final: 0.4174 (tptp) REVERT: H 120 SER cc_start: 0.2268 (p) cc_final: 0.1399 (t) REVERT: H 171 HIS cc_start: 0.3297 (OUTLIER) cc_final: 0.3036 (t-170) REVERT: H 180 SER cc_start: 0.0812 (OUTLIER) cc_final: 0.0526 (m) REVERT: L 203 GLU cc_start: 0.4568 (OUTLIER) cc_final: 0.3881 (mp0) REVERT: I 154 PRO cc_start: 0.2844 (Cg_endo) cc_final: 0.2644 (Cg_exo) REVERT: M 36 GLN cc_start: 0.4998 (tm-30) cc_final: 0.4187 (mm-40) REVERT: M 162 THR cc_start: 0.1140 (OUTLIER) cc_final: 0.0457 (p) REVERT: J 70 MET cc_start: 0.4389 (mtt) cc_final: 0.3236 (mtm) REVERT: N 34 TRP cc_start: 0.1314 (m100) cc_final: 0.0918 (t-100) REVERT: N 41 GLN cc_start: 0.4962 (mp10) cc_final: 0.3331 (mm110) outliers start: 149 outliers final: 89 residues processed: 340 average time/residue: 0.5201 time to fit residues: 223.7271 Evaluate side-chains 287 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 186 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 199 GLN Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 171 LYS Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 171 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 186 optimal weight: 1.9990 chunk 348 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 310 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS B 207 HIS B 271 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN N 6 GLN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.216504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.168869 restraints weight = 60117.020| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.79 r_work: 0.3388 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 37017 Z= 0.175 Angle : 0.745 14.887 50611 Z= 0.358 Chirality : 0.050 0.642 5924 Planarity : 0.005 0.056 6381 Dihedral : 7.503 89.928 6655 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 4.04 % Allowed : 21.18 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.12), residues: 4465 helix: 0.95 (0.20), residues: 713 sheet: 0.41 (0.14), residues: 1386 loop : -1.86 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.024 0.002 TYR A 170 PHE 0.031 0.002 PHE I 103 TRP 0.012 0.001 TRP A 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00425 (36877) covalent geometry : angle 0.71200 (50245) SS BOND : bond 0.00550 ( 54) SS BOND : angle 2.21523 ( 108) hydrogen bonds : bond 0.04722 ( 1318) hydrogen bonds : angle 5.42102 ( 3783) link_BETA1-4 : bond 0.00703 ( 32) link_BETA1-4 : angle 2.50218 ( 96) link_NAG-ASN : bond 0.00585 ( 54) link_NAG-ASN : angle 3.06149 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 196 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6742 (m-70) cc_final: 0.6147 (t-90) REVERT: A 152 TRP cc_start: 0.6076 (t60) cc_final: 0.5537 (t60) REVERT: A 326 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.6289 (pp) REVERT: A 329 PHE cc_start: 0.6722 (m-80) cc_final: 0.6328 (m-80) REVERT: A 1017 GLU cc_start: 0.8684 (tt0) cc_final: 0.8321 (pt0) REVERT: B 66 HIS cc_start: 0.4584 (OUTLIER) cc_final: 0.3347 (m-70) REVERT: B 133 PHE cc_start: 0.6175 (m-80) cc_final: 0.5777 (m-80) REVERT: B 166 CYS cc_start: 0.3005 (OUTLIER) cc_final: 0.2326 (p) REVERT: B 177 MET cc_start: 0.5126 (pmm) cc_final: 0.3143 (tpt) REVERT: B 508 TYR cc_start: 0.6009 (m-80) cc_final: 0.5321 (m-80) REVERT: B 546 LEU cc_start: 0.7662 (tp) cc_final: 0.6858 (mm) REVERT: C 73 THR cc_start: 0.1549 (OUTLIER) cc_final: 0.1344 (t) REVERT: C 324 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6596 (pm20) REVERT: C 417 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7232 (mptm) REVERT: C 423 TYR cc_start: 0.7002 (t80) cc_final: 0.6795 (t80) REVERT: C 493 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.5259 (tm-30) REVERT: C 531 THR cc_start: 0.8166 (t) cc_final: 0.7857 (p) REVERT: C 558 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6784 (mtpm) REVERT: H 13 LYS cc_start: 0.4794 (mtmm) cc_final: 0.4065 (tptt) REVERT: H 83 LEU cc_start: 0.0314 (OUTLIER) cc_final: -0.0126 (tp) REVERT: H 120 SER cc_start: 0.2464 (p) cc_final: 0.1946 (t) REVERT: H 171 HIS cc_start: 0.3194 (OUTLIER) cc_final: 0.2962 (t-170) REVERT: H 180 SER cc_start: 0.1044 (p) cc_final: 0.0735 (m) REVERT: L 203 GLU cc_start: 0.4572 (OUTLIER) cc_final: 0.3832 (mp0) REVERT: M 36 GLN cc_start: 0.4897 (tm-30) cc_final: 0.4254 (mm-40) REVERT: M 162 THR cc_start: 0.1785 (OUTLIER) cc_final: 0.0799 (p) REVERT: J 70 MET cc_start: 0.4419 (mtt) cc_final: 0.3360 (mtm) REVERT: N 41 GLN cc_start: 0.5404 (mp10) cc_final: 0.3660 (mm110) outliers start: 158 outliers final: 105 residues processed: 344 average time/residue: 0.4831 time to fit residues: 214.3012 Evaluate side-chains 297 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 180 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 199 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 171 LYS Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 171 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 353 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 312 optimal weight: 0.7980 chunk 371 optimal weight: 20.0000 chunk 367 optimal weight: 0.7980 chunk 328 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 949 GLN B 14 GLN B 207 HIS B 481 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN L 37 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN N 6 GLN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.217674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.181742 restraints weight = 60331.223| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 3.62 r_work: 0.3345 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37017 Z= 0.131 Angle : 0.716 16.600 50611 Z= 0.341 Chirality : 0.049 0.605 5924 Planarity : 0.005 0.055 6381 Dihedral : 7.193 88.314 6655 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 3.25 % Allowed : 22.20 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.12), residues: 4465 helix: 1.21 (0.20), residues: 711 sheet: 0.51 (0.14), residues: 1366 loop : -1.78 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 158 TYR 0.023 0.001 TYR B 170 PHE 0.030 0.001 PHE I 103 TRP 0.019 0.001 TRP N 34 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00302 (36877) covalent geometry : angle 0.67984 (50245) SS BOND : bond 0.00535 ( 54) SS BOND : angle 1.83544 ( 108) hydrogen bonds : bond 0.04094 ( 1318) hydrogen bonds : angle 5.27435 ( 3783) link_BETA1-4 : bond 0.00754 ( 32) link_BETA1-4 : angle 2.44094 ( 96) link_NAG-ASN : bond 0.00507 ( 54) link_NAG-ASN : angle 3.30181 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 195 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.6065 (t60) cc_final: 0.5506 (t60) REVERT: A 326 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6141 (pp) REVERT: A 329 PHE cc_start: 0.6658 (m-80) cc_final: 0.6266 (m-80) REVERT: A 1017 GLU cc_start: 0.8958 (tt0) cc_final: 0.8613 (pt0) REVERT: B 66 HIS cc_start: 0.4578 (OUTLIER) cc_final: 0.3384 (m-70) REVERT: B 133 PHE cc_start: 0.6248 (m-80) cc_final: 0.5825 (m-80) REVERT: B 166 CYS cc_start: 0.3715 (OUTLIER) cc_final: 0.2971 (p) REVERT: B 177 MET cc_start: 0.5261 (pmm) cc_final: 0.3156 (tpt) REVERT: B 423 TYR cc_start: 0.7565 (t80) cc_final: 0.7352 (t80) REVERT: B 508 TYR cc_start: 0.6221 (m-80) cc_final: 0.5523 (m-80) REVERT: B 546 LEU cc_start: 0.7407 (tp) cc_final: 0.6582 (mm) REVERT: C 237 ARG cc_start: 0.5986 (mmt90) cc_final: 0.5533 (mtp180) REVERT: C 324 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6605 (pm20) REVERT: C 400 PHE cc_start: 0.7572 (p90) cc_final: 0.7053 (p90) REVERT: C 417 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7192 (mptm) REVERT: C 493 GLN cc_start: 0.5580 (OUTLIER) cc_final: 0.5204 (tm-30) REVERT: C 531 THR cc_start: 0.8075 (t) cc_final: 0.7772 (p) REVERT: C 558 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6757 (mtpm) REVERT: H 13 LYS cc_start: 0.4792 (mtmm) cc_final: 0.4058 (tptt) REVERT: H 120 SER cc_start: 0.2498 (p) cc_final: 0.1816 (t) REVERT: H 171 HIS cc_start: 0.3205 (OUTLIER) cc_final: 0.2994 (m170) REVERT: H 180 SER cc_start: 0.0583 (p) cc_final: 0.0359 (m) REVERT: L 203 GLU cc_start: 0.4513 (OUTLIER) cc_final: 0.3837 (mp0) REVERT: M 36 GLN cc_start: 0.4889 (tm-30) cc_final: 0.4247 (mm-40) REVERT: M 162 THR cc_start: 0.1602 (OUTLIER) cc_final: 0.0610 (p) REVERT: J 70 MET cc_start: 0.4211 (mtt) cc_final: 0.3465 (mtm) REVERT: N 41 GLN cc_start: 0.5413 (mp10) cc_final: 0.3678 (mm110) outliers start: 127 outliers final: 93 residues processed: 312 average time/residue: 0.5031 time to fit residues: 200.7865 Evaluate side-chains 284 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 181 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 199 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 171 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 169 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 318 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 446 optimal weight: 30.0000 chunk 296 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS B 207 HIS ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 675 GLN C 99 ASN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.219677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.170943 restraints weight = 59888.905| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.85 r_work: 0.3393 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37017 Z= 0.168 Angle : 0.739 15.240 50611 Z= 0.353 Chirality : 0.050 0.628 5924 Planarity : 0.005 0.053 6381 Dihedral : 7.046 57.997 6647 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.01 % Favored : 92.88 % Rotamer: Outliers : 3.12 % Allowed : 22.51 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.12), residues: 4465 helix: 1.14 (0.20), residues: 711 sheet: 0.48 (0.14), residues: 1370 loop : -1.79 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.024 0.001 TYR A 170 PHE 0.031 0.002 PHE I 103 TRP 0.027 0.001 TRP N 34 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00405 (36877) covalent geometry : angle 0.70367 (50245) SS BOND : bond 0.00535 ( 54) SS BOND : angle 1.91642 ( 108) hydrogen bonds : bond 0.04566 ( 1318) hydrogen bonds : angle 5.33213 ( 3783) link_BETA1-4 : bond 0.00732 ( 32) link_BETA1-4 : angle 2.46631 ( 96) link_NAG-ASN : bond 0.00493 ( 54) link_NAG-ASN : angle 3.29070 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 191 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.5975 (t60) cc_final: 0.5527 (t60) REVERT: A 326 ILE cc_start: 0.6486 (OUTLIER) cc_final: 0.6217 (pp) REVERT: A 329 PHE cc_start: 0.6690 (m-80) cc_final: 0.6295 (m-80) REVERT: A 1017 GLU cc_start: 0.8821 (tt0) cc_final: 0.8480 (pt0) REVERT: B 66 HIS cc_start: 0.4527 (OUTLIER) cc_final: 0.3317 (m-70) REVERT: B 133 PHE cc_start: 0.6180 (m-80) cc_final: 0.5757 (m-80) REVERT: B 166 CYS cc_start: 0.3386 (OUTLIER) cc_final: 0.2619 (p) REVERT: B 177 MET cc_start: 0.5072 (pmm) cc_final: 0.3089 (tpt) REVERT: B 508 TYR cc_start: 0.6140 (m-80) cc_final: 0.5418 (m-80) REVERT: B 613 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8530 (mt0) REVERT: C 73 THR cc_start: 0.1596 (OUTLIER) cc_final: 0.1360 (t) REVERT: C 237 ARG cc_start: 0.5978 (mmt90) cc_final: 0.5546 (mtp180) REVERT: C 324 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6567 (pm20) REVERT: C 355 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7641 (mmm-85) REVERT: C 403 ARG cc_start: 0.6859 (tpp80) cc_final: 0.6641 (mmm160) REVERT: C 417 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7213 (mptm) REVERT: C 493 GLN cc_start: 0.5579 (OUTLIER) cc_final: 0.5267 (tm-30) REVERT: C 531 THR cc_start: 0.8079 (t) cc_final: 0.7812 (p) REVERT: C 558 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6730 (mtpm) REVERT: H 13 LYS cc_start: 0.4852 (mtmm) cc_final: 0.4149 (tptt) REVERT: H 120 SER cc_start: 0.2559 (p) cc_final: 0.1890 (t) REVERT: H 166 LEU cc_start: 0.2200 (tp) cc_final: 0.1823 (pt) REVERT: H 171 HIS cc_start: 0.3201 (OUTLIER) cc_final: 0.2988 (m170) REVERT: H 180 SER cc_start: 0.0556 (p) cc_final: 0.0334 (m) REVERT: L 37 GLN cc_start: 0.3347 (tt0) cc_final: 0.3008 (pt0) REVERT: L 203 GLU cc_start: 0.4531 (OUTLIER) cc_final: 0.3842 (mp0) REVERT: M 162 THR cc_start: 0.1498 (OUTLIER) cc_final: 0.0464 (p) REVERT: J 48 MET cc_start: 0.4353 (pmt) cc_final: 0.2355 (mpt) REVERT: J 70 MET cc_start: 0.4464 (mtt) cc_final: 0.3308 (mtm) REVERT: N 41 GLN cc_start: 0.5483 (mp10) cc_final: 0.3755 (mm110) outliers start: 122 outliers final: 98 residues processed: 305 average time/residue: 0.4939 time to fit residues: 193.3222 Evaluate side-chains 294 residues out of total 3910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 183 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 199 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 171 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 301 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 97 optimal weight: 0.3980 chunk 399 optimal weight: 30.0000 chunk 320 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 350 optimal weight: 30.0000 chunk 352 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS B 207 HIS ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.216917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.165541 restraints weight = 60382.737| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.66 r_work: 0.3404 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 37017 Z= 0.171 Angle : 0.736 14.495 50611 Z= 0.353 Chirality : 0.050 0.626 5924 Planarity : 0.005 0.055 6381 Dihedral : 7.024 57.625 6647 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.99 % Favored : 92.90 % Rotamer: Outliers : 3.07 % Allowed : 22.56 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.12), residues: 4465 helix: 1.09 (0.20), residues: 712 sheet: 0.46 (0.14), residues: 1378 loop : -1.78 (0.12), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1000 TYR 0.030 0.002 TYR B 674 PHE 0.030 0.002 PHE I 103 TRP 0.034 0.002 TRP N 34 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00411 (36877) covalent geometry : angle 0.70336 (50245) SS BOND : bond 0.00531 ( 54) SS BOND : angle 1.87603 ( 108) hydrogen bonds : bond 0.04607 ( 1318) hydrogen bonds : angle 5.34166 ( 3783) link_BETA1-4 : bond 0.00747 ( 32) link_BETA1-4 : angle 2.46225 ( 96) link_NAG-ASN : bond 0.00482 ( 54) link_NAG-ASN : angle 3.17440 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16974.48 seconds wall clock time: 288 minutes 8.47 seconds (17288.47 seconds total)