Starting phenix.real_space_refine on Sun Jul 5 22:57:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kip_22889/07_2026/7kip_22889.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kip_22889/07_2026/7kip_22889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kip_22889/07_2026/7kip_22889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kip_22889/07_2026/7kip_22889.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kip_22889/07_2026/7kip_22889.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kip_22889/07_2026/7kip_22889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kip_22889/07_2026/7kip_22889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kip_22889/07_2026/7kip_22889.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.142 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 129 5.16 5 C 19272 2.51 5 N 4794 2.21 5 O 6417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30612 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 9243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9243 Classifications: {'peptide': 1192} Link IDs: {'PTRANS': 41, 'TRANS': 1150} Chain breaks: 1 Chain: "B" Number of atoms: 9243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9243 Classifications: {'peptide': 1192} Link IDs: {'PTRANS': 41, 'TRANS': 1150} Chain breaks: 1 Chain: "C" Number of atoms: 9243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9243 Classifications: {'peptide': 1192} Link IDs: {'PTRANS': 41, 'TRANS': 1150} Chain breaks: 1 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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 chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 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 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 chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "c" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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 chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 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 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 chiralities: 2 Chain: "p" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 2 Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "x" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "0" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "1" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "2" 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 chiralities: 2 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "5" 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 chiralities: 2 Chain: "6" 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 chiralities: 2 Chain: "7" 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 chiralities: 2 Chain: "8" 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 chiralities: 2 Chain: "9" 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 chiralities: 2 Chain: "AA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "BA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "CA" 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 chiralities: 2 Chain: "DA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 8 Chain: "B" 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 chiralities: 8 Chain: "C" 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 chiralities: 8 Time building chain proxies: 7.10, per 1000 atoms: 0.23 Number of scatterers: 30612 At special positions: 0 Unit cell: (144.2, 155.4, 182, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 6417 8.00 N 4794 7.00 C 19272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 210 " distance=2.05 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.01 Simple disulfide: pdb=" SG CYS A 497 " - pdb=" SG CYS A 500 " distance=2.04 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 678 " distance=2.04 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 737 " distance=2.03 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 811 " distance=2.02 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS A 800 " distance=2.02 Simple disulfide: pdb=" SG CYS A 896 " - pdb=" SG CYS A 907 " distance=2.03 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS A1148 " - pdb=" SG CYS A1195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 210 " distance=2.04 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 438 " - pdb=" SG CYS B 447 " distance=2.02 Simple disulfide: pdb=" SG CYS B 497 " - pdb=" SG CYS B 500 " distance=2.04 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 678 " distance=2.04 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 737 " distance=2.03 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 811 " distance=2.02 Simple disulfide: pdb=" SG CYS B 794 " - pdb=" SG CYS B 800 " distance=2.02 Simple disulfide: pdb=" SG CYS B 896 " - pdb=" SG CYS B 907 " distance=2.04 Simple disulfide: pdb=" SG CYS B1098 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B1148 " - pdb=" SG CYS B1195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 210 " distance=2.05 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 447 " distance=2.02 Simple disulfide: pdb=" SG CYS C 497 " - pdb=" SG CYS C 500 " distance=2.04 Simple disulfide: pdb=" SG CYS C 516 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 678 " distance=2.04 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 737 " distance=2.03 Simple disulfide: pdb=" SG CYS C 789 " - pdb=" SG CYS C 811 " distance=2.02 Simple disulfide: pdb=" SG CYS C 794 " - pdb=" SG CYS C 800 " distance=2.02 Simple disulfide: pdb=" SG CYS C 896 " - pdb=" SG CYS C 907 " distance=2.03 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C1148 " - pdb=" SG CYS C1195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 0 5 " - " MAN 0 6 " " MAN D 4 " - " MAN D 5 " " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN Y 4 " - " MAN Y 5 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN t 4 " - " MAN t 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 7 " - " MAN 0 8 " " BMA 3 3 " - " MAN 3 4 " " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " " BMA N 3 " - " MAN N 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " " MAN f 7 " - " MAN f 8 " " BMA i 3 " - " MAN i 4 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 7 " " BMA 3 3 " - " MAN 3 5 " " BMA D 3 " - " MAN D 6 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 7 " " BMA N 3 " - " MAN N 5 " " BMA V 3 " - " MAN V 5 " " BMA Y 3 " - " MAN Y 6 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 7 " " BMA i 3 " - " MAN i 5 " " BMA q 3 " - " MAN q 5 " " BMA t 3 " - " MAN t 6 " " BMA x 3 " - " MAN x 4 " " BMABA 3 " - " MANBA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " BMA 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " BMA g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 0 1 " - " ASN C 426 " " NAG 2 1 " - " ASN C 506 " " NAG 3 1 " - " ASN C 666 " " NAG 4 1 " - " ASN C 699 " " NAG 5 1 " - " ASN C 723 " " NAG 6 1 " - " ASN C 749 " " NAG 7 1 " - " ASN C 762 " " NAG 8 1 " - " ASN C 768 " " NAG 9 1 " - " ASN C 844 " " NAG A1401 " - " ASN A 155 " " NAG A1402 " - " ASN A 187 " " NAG A1403 " - " ASN A 193 " " NAG A1404 " - " ASN A 486 " " NAG A1405 " - " ASN A 512 " " NAG A1406 " - " ASN A 626 " " NAG A1407 " - " ASN A 645 " " NAG A1408 " - " ASN A1218 " " NAG B1401 " - " ASN B 155 " " NAG B1402 " - " ASN B 187 " " NAG B1403 " - " ASN B 193 " " NAG B1404 " - " ASN B 486 " " NAG B1405 " - " ASN B 512 " " NAG B1406 " - " ASN B 626 " " NAG B1407 " - " ASN B 645 " " NAG B1408 " - " ASN B1218 " " NAG C1401 " - " ASN C 155 " " NAG C1402 " - " ASN C 187 " " NAG C1403 " - " ASN C 193 " " NAG C1404 " - " ASN C 486 " " NAG C1405 " - " ASN C 512 " " NAG C1406 " - " ASN C 626 " " NAG C1407 " - " ASN C 645 " " NAG C1408 " - " ASN C1218 " " NAG D 1 " - " ASN A 240 " " NAG E 1 " - " ASN A 276 " " NAG F 1 " - " ASN A 301 " " NAG G 1 " - " ASN A 330 " " NAG H 1 " - " ASN A 354 " " NAG I 1 " - " ASN A 358 " " NAG J 1 " - " ASN A 403 " " NAG K 1 " - " ASN A 426 " " NAG M 1 " - " ASN A 506 " " NAG N 1 " - " ASN A 666 " " NAG O 1 " - " ASN A 699 " " NAG P 1 " - " ASN A 723 " " NAG Q 1 " - " ASN A 749 " " NAG R 1 " - " ASN A 762 " " NAG S 1 " - " ASN A 768 " " NAG T 1 " - " ASN A 844 " " NAG U 1 " - " ASN A 852 " " NAG V 1 " - " ASN A1111 " " NAG W 1 " - " ASN A1196 " " NAG X 1 " - " ASN A1201 " " NAG Y 1 " - " ASN B 240 " " NAG Z 1 " - " ASN B 276 " " NAG a 1 " - " ASN B 301 " " NAG b 1 " - " ASN B 330 " " NAG c 1 " - " ASN B 354 " " NAG d 1 " - " ASN B 358 " " NAG e 1 " - " ASN B 403 " " NAG f 1 " - " ASN B 426 " " NAG h 1 " - " ASN B 506 " " NAG i 1 " - " ASN B 666 " " NAG j 1 " - " ASN B 699 " " NAG k 1 " - " ASN B 723 " " NAG l 1 " - " ASN B 749 " " NAG m 1 " - " ASN B 762 " " NAG n 1 " - " ASN B 768 " " NAG o 1 " - " ASN B 844 " " NAG p 1 " - " ASN B 852 " " NAG q 1 " - " ASN B1111 " " NAG r 1 " - " ASN B1196 " " NAG s 1 " - " ASN B1201 " " NAG t 1 " - " ASN C 240 " " NAG u 1 " - " ASN C 276 " " NAG v 1 " - " ASN C 301 " " NAG w 1 " - " ASN C 330 " " NAG x 1 " - " ASN C 354 " " NAG y 1 " - " ASN C 358 " " NAG z 1 " - " ASN C 403 " " NAGAA 1 " - " ASN C 852 " " NAGBA 1 " - " ASN C1111 " " NAGCA 1 " - " ASN C1196 " " NAGDA 1 " - " ASN C1201 " Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.3 seconds 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 20.9% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.571A pdb=" N ASP A 215 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 216 " --> pdb=" O TYR A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 216' Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.518A pdb=" N GLY A 224 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 225 " --> pdb=" O GLN A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 225' Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.569A pdb=" N GLN A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 788 through 794 removed outlier: 3.868A pdb=" N TYR A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 804 removed outlier: 3.581A pdb=" N LEU A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 808 through 833 removed outlier: 4.317A pdb=" N THR A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 821 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS A 823 " --> pdb=" O ARG A 819 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 removed outlier: 4.104A pdb=" N PHE A 848 " --> pdb=" O VAL A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 882 removed outlier: 4.226A pdb=" N LYS A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 911 removed outlier: 3.571A pdb=" N GLN A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 910 " --> pdb=" O ALA A 906 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 935 removed outlier: 3.687A pdb=" N THR A 930 " --> pdb=" O MET A 926 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 933 " --> pdb=" O TYR A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 954 removed outlier: 3.546A pdb=" N LEU A 954 " --> pdb=" O PHE A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 970 through 990 removed outlier: 4.275A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 removed outlier: 4.211A pdb=" N GLN A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1029 removed outlier: 4.263A pdb=" N ILE A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A1024 " --> pdb=" O GLN A1020 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A1025 " --> pdb=" O GLN A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1033 removed outlier: 3.961A pdb=" N ARG A1033 " --> pdb=" O SER A1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1030 through 1033' Processing helix chain 'A' and resid 1042 through 1048 removed outlier: 3.568A pdb=" N ILE A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A1047 " --> pdb=" O ILE A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1099 removed outlier: 4.091A pdb=" N ASP A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLN A1057 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A1058 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A1061 " --> pdb=" O GLN A1057 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A1062 " --> pdb=" O GLN A1058 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A1065 " --> pdb=" O ARG A1061 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A1072 " --> pdb=" O ALA A1068 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A1089 " --> pdb=" O ARG A1085 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A1090 " --> pdb=" O GLY A1086 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1099 " --> pdb=" O ILE A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1204 through 1210 removed outlier: 4.482A pdb=" N HIS A1208 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1224 Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 212 through 216 removed outlier: 3.571A pdb=" N ASP B 215 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 216 " --> pdb=" O TYR B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 216' Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.518A pdb=" N GLY B 224 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 225 " --> pdb=" O GLN B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.570A pdb=" N GLN B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 539 Processing helix chain 'B' and resid 788 through 794 removed outlier: 3.869A pdb=" N TYR B 792 " --> pdb=" O ASP B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 804 removed outlier: 3.581A pdb=" N LEU B 803 " --> pdb=" O ARG B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 808 through 833 removed outlier: 4.318A pdb=" N THR B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 817 " --> pdb=" O THR B 813 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 818 " --> pdb=" O ILE B 814 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 821 " --> pdb=" O ALA B 817 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 826 " --> pdb=" O ALA B 822 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET B 832 " --> pdb=" O ASP B 828 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 833 " --> pdb=" O VAL B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 4.103A pdb=" N PHE B 848 " --> pdb=" O VAL B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 882 removed outlier: 4.226A pdb=" N LYS B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 removed outlier: 3.571A pdb=" N GLN B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 910 " --> pdb=" O ALA B 906 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 911 " --> pdb=" O CYS B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 935 removed outlier: 3.686A pdb=" N THR B 930 " --> pdb=" O MET B 926 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 933 " --> pdb=" O TYR B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 954 removed outlier: 3.546A pdb=" N LEU B 954 " --> pdb=" O PHE B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 959 Processing helix chain 'B' and resid 970 through 990 removed outlier: 4.275A pdb=" N ILE B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 980 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS B 981 " --> pdb=" O ALA B 977 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 986 " --> pdb=" O ALA B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 999 removed outlier: 4.210A pdb=" N GLN B 999 " --> pdb=" O ASP B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1029 removed outlier: 4.264A pdb=" N ILE B1009 " --> pdb=" O HIS B1005 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B1018 " --> pdb=" O ILE B1014 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B1024 " --> pdb=" O GLN B1020 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU B1025 " --> pdb=" O GLN B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1033 removed outlier: 3.961A pdb=" N ARG B1033 " --> pdb=" O SER B1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1030 through 1033' Processing helix chain 'B' and resid 1042 through 1048 removed outlier: 3.568A pdb=" N ILE B1046 " --> pdb=" O SER B1042 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B1047 " --> pdb=" O ILE B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1099 removed outlier: 4.091A pdb=" N ASP B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN B1057 " --> pdb=" O ILE B1053 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B1058 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B1061 " --> pdb=" O GLN B1057 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B1062 " --> pdb=" O GLN B1058 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B1065 " --> pdb=" O ARG B1061 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B1072 " --> pdb=" O ALA B1068 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B1076 " --> pdb=" O ALA B1072 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN B1079 " --> pdb=" O SER B1075 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG B1089 " --> pdb=" O ARG B1085 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU B1090 " --> pdb=" O GLY B1086 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B1091 " --> pdb=" O SER B1087 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B1099 " --> pdb=" O ILE B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1187 No H-bonds generated for 'chain 'B' and resid 1185 through 1187' Processing helix chain 'B' and resid 1204 through 1210 removed outlier: 4.482A pdb=" N HIS B1208 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1224 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.571A pdb=" N ASP C 215 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 216 " --> pdb=" O TYR C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 216' Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.518A pdb=" N GLY C 224 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 225 " --> pdb=" O GLN C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 225' Processing helix chain 'C' and resid 442 through 450 removed outlier: 3.570A pdb=" N GLN C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 539 Processing helix chain 'C' and resid 788 through 794 removed outlier: 3.869A pdb=" N TYR C 792 " --> pdb=" O ASP C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 804 removed outlier: 3.582A pdb=" N LEU C 803 " --> pdb=" O ARG C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 807 No H-bonds generated for 'chain 'C' and resid 805 through 807' Processing helix chain 'C' and resid 808 through 833 removed outlier: 4.318A pdb=" N THR C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 815 " --> pdb=" O CYS C 811 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 817 " --> pdb=" O THR C 813 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 821 " --> pdb=" O ALA C 817 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS C 823 " --> pdb=" O ARG C 819 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 826 " --> pdb=" O ALA C 822 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET C 832 " --> pdb=" O ASP C 828 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 833 " --> pdb=" O VAL C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 848 removed outlier: 4.102A pdb=" N PHE C 848 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 882 removed outlier: 4.226A pdb=" N LYS C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 911 removed outlier: 3.571A pdb=" N GLN C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C 910 " --> pdb=" O ALA C 906 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 935 removed outlier: 3.687A pdb=" N THR C 930 " --> pdb=" O MET C 926 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 933 " --> pdb=" O TYR C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 954 removed outlier: 3.545A pdb=" N LEU C 954 " --> pdb=" O PHE C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 959 Processing helix chain 'C' and resid 970 through 990 removed outlier: 4.274A pdb=" N ILE C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 980 " --> pdb=" O ALA C 976 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 986 " --> pdb=" O ALA C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 999 removed outlier: 4.210A pdb=" N GLN C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1029 removed outlier: 4.263A pdb=" N ILE C1009 " --> pdb=" O HIS C1005 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C1018 " --> pdb=" O ILE C1014 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA C1024 " --> pdb=" O GLN C1020 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU C1025 " --> pdb=" O GLN C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1033 removed outlier: 3.962A pdb=" N ARG C1033 " --> pdb=" O SER C1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1030 through 1033' Processing helix chain 'C' and resid 1042 through 1048 removed outlier: 3.568A pdb=" N ILE C1046 " --> pdb=" O SER C1042 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C1047 " --> pdb=" O ILE C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1099 removed outlier: 4.092A pdb=" N ASP C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN C1057 " --> pdb=" O ILE C1053 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN C1058 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C1061 " --> pdb=" O GLN C1057 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C1062 " --> pdb=" O GLN C1058 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY C1065 " --> pdb=" O ARG C1061 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C1072 " --> pdb=" O ALA C1068 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C1076 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN C1079 " --> pdb=" O SER C1075 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG C1089 " --> pdb=" O ARG C1085 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU C1090 " --> pdb=" O GLY C1086 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA C1091 " --> pdb=" O SER C1087 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C1099 " --> pdb=" O ILE C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1185 through 1187 No H-bonds generated for 'chain 'C' and resid 1185 through 1187' Processing helix chain 'C' and resid 1204 through 1210 removed outlier: 4.482A pdb=" N HIS C1208 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1224 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 42 removed outlier: 3.527A pdb=" N VAL A 194 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 195 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS A 197 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 4.129A pdb=" N PHE A 183 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 182 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 64 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 142 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 65 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 140 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 141 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR A 143 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.790A pdb=" N HIS A 78 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 73 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 89 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 90 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU A 103 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN A 129 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE A 105 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.790A pdb=" N HIS A 78 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 73 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 89 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 90 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 260 removed outlier: 3.597A pdb=" N VAL A 425 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 251 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 423 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 255 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 419 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 257 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE A 417 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 418 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 295 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 378 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 379 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE A 384 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 260 removed outlier: 3.597A pdb=" N VAL A 425 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 251 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 423 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 255 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 419 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 257 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE A 417 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 424 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A 435 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN A 426 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.512A pdb=" N GLY A 313 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N CYS A 328 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR A 327 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N CYS A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 353 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 340 through 341 removed outlier: 4.596A pdb=" N SER A 312 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AB1, first strand: chain 'A' and resid 457 through 459 removed outlier: 6.983A pdb=" N ALA A 685 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 471 through 474 removed outlier: 3.802A pdb=" N THR A 472 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 504 through 508 removed outlier: 3.565A pdb=" N GLN A 504 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 508 " --> pdb=" O THR A 488 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AB5, first strand: chain 'A' and resid 521 through 522 removed outlier: 3.610A pdb=" N ILE A 606 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 541 through 545 removed outlier: 7.048A pdb=" N CYS A 577 " --> pdb=" O TYR A 597 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR A 597 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 579 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 595 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 581 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 640 through 643 Processing sheet with id=AB8, first strand: chain 'A' and resid 653 through 655 Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 748 through 749 removed outlier: 6.273A pdb=" N ARG A 748 " --> pdb=" O PHE B 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 762 through 766 Processing sheet with id=AC3, first strand: chain 'A' and resid 769 through 777 removed outlier: 3.595A pdb=" N SER A 772 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A1125 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A1116 " --> pdb=" O THR A1131 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS A1114 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 785 through 786 Processing sheet with id=AC5, first strand: chain 'A' and resid 834 through 835 Processing sheet with id=AC6, first strand: chain 'A' and resid 1189 through 1191 removed outlier: 3.578A pdb=" N VAL A1156 " --> pdb=" O VAL A1190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A1202 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1162 through 1166 Processing sheet with id=AC8, first strand: chain 'B' and resid 37 through 42 removed outlier: 3.528A pdb=" N VAL B 194 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 195 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS B 197 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL B 201 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 48 through 49 removed outlier: 4.129A pdb=" N PHE B 183 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 182 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 64 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 142 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 65 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 140 " --> pdb=" O TYR B 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 141 " --> pdb=" O HIS B 152 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 143 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.789A pdb=" N HIS B 78 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 73 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 89 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 90 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 103 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN B 129 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE B 105 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.789A pdb=" N HIS B 78 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 73 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 89 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 90 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 246 through 260 removed outlier: 3.598A pdb=" N VAL B 425 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 251 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL B 423 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 255 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR B 419 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU B 257 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE B 417 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 418 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 295 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 378 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 379 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE B 384 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 246 through 260 removed outlier: 3.598A pdb=" N VAL B 425 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 251 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL B 423 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 255 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR B 419 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU B 257 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE B 417 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 424 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 435 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN B 426 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.511A pdb=" N GLY B 313 " --> pdb=" O CYS B 328 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N CYS B 328 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B 327 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N CYS B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 353 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 340 through 341 removed outlier: 4.596A pdb=" N SER B 312 " --> pdb=" O THR B 405 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AD8, first strand: chain 'B' and resid 457 through 459 removed outlier: 6.984A pdb=" N ALA B 685 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 471 through 474 removed outlier: 3.801A pdb=" N THR B 472 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 504 through 508 removed outlier: 3.564A pdb=" N GLN B 504 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 508 " --> pdb=" O THR B 488 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 514 through 515 Processing sheet with id=AE3, first strand: chain 'B' and resid 521 through 522 removed outlier: 3.610A pdb=" N ILE B 606 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 541 through 545 removed outlier: 7.049A pdb=" N CYS B 577 " --> pdb=" O TYR B 597 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR B 597 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE B 579 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA B 595 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 581 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 640 through 643 Processing sheet with id=AE6, first strand: chain 'B' and resid 653 through 655 Processing sheet with id=AE7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'B' and resid 748 through 749 removed outlier: 6.272A pdb=" N ARG B 748 " --> pdb=" O PHE C 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'B' and resid 762 through 766 Processing sheet with id=AF1, first strand: chain 'B' and resid 769 through 777 removed outlier: 3.594A pdb=" N SER B 772 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B1125 " --> pdb=" O ALA B1122 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B1116 " --> pdb=" O THR B1131 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B1133 " --> pdb=" O HIS B1114 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS B1114 " --> pdb=" O LEU B1133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 785 through 786 Processing sheet with id=AF3, first strand: chain 'B' and resid 1189 through 1191 removed outlier: 3.579A pdb=" N VAL B1156 " --> pdb=" O VAL B1190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B1202 " --> pdb=" O CYS B1148 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1162 through 1166 Processing sheet with id=AF5, first strand: chain 'C' and resid 37 through 42 removed outlier: 3.527A pdb=" N VAL C 194 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 195 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS C 197 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL C 201 " --> pdb=" O HIS C 197 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 48 through 49 removed outlier: 4.129A pdb=" N PHE C 183 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 182 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 64 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 142 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR C 65 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 140 " --> pdb=" O TYR C 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 141 " --> pdb=" O HIS C 152 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR C 143 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.790A pdb=" N HIS C 78 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 73 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 89 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 90 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU C 103 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN C 129 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE C 105 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.790A pdb=" N HIS C 78 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 73 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 89 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 90 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 246 through 260 removed outlier: 3.598A pdb=" N VAL C 425 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 251 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 423 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 255 " --> pdb=" O THR C 419 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR C 419 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU C 257 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE C 417 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 418 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 295 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 378 " --> pdb=" O MET C 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 379 " --> pdb=" O GLN C 383 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLN C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE C 384 " --> pdb=" O TYR C 391 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 246 through 260 removed outlier: 3.598A pdb=" N VAL C 425 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 251 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 423 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 255 " --> pdb=" O THR C 419 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR C 419 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU C 257 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE C 417 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 424 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU C 435 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN C 426 " --> pdb=" O GLN C 433 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 340 through 341 removed outlier: 7.511A pdb=" N GLY C 313 " --> pdb=" O CYS C 328 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N CYS C 328 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR C 327 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N CYS C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 353 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 340 through 341 removed outlier: 4.596A pdb=" N SER C 312 " --> pdb=" O THR C 405 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 343 through 344 Processing sheet with id=AG5, first strand: chain 'C' and resid 457 through 459 removed outlier: 6.983A pdb=" N ALA C 685 " --> pdb=" O ILE C 692 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 471 through 474 removed outlier: 3.801A pdb=" N THR C 472 " --> pdb=" O LYS C 629 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 504 through 508 removed outlier: 3.566A pdb=" N GLN C 504 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 508 " --> pdb=" O THR C 488 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 514 through 515 Processing sheet with id=AG9, first strand: chain 'C' and resid 521 through 522 removed outlier: 3.611A pdb=" N ILE C 606 " --> pdb=" O PHE C 563 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 541 through 545 removed outlier: 7.048A pdb=" N CYS C 577 " --> pdb=" O TYR C 597 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR C 597 " --> pdb=" O CYS C 577 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE C 579 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA C 595 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU C 581 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 640 through 643 Processing sheet with id=AH3, first strand: chain 'C' and resid 653 through 655 Processing sheet with id=AH4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AH5, first strand: chain 'C' and resid 762 through 766 Processing sheet with id=AH6, first strand: chain 'C' and resid 769 through 777 removed outlier: 3.594A pdb=" N SER C 772 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C1125 " --> pdb=" O ALA C1122 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C1116 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C1133 " --> pdb=" O HIS C1114 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS C1114 " --> pdb=" O LEU C1133 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 785 through 786 Processing sheet with id=AH8, first strand: chain 'C' and resid 1189 through 1191 removed outlier: 3.578A pdb=" N VAL C1156 " --> pdb=" O VAL C1190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C1202 " --> pdb=" O CYS C1148 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 1162 through 1166 808 hydrogen bonds defined for protein. 2145 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: 7.81 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9218 1.34 - 1.46: 8500 1.46 - 1.59: 13349 1.59 - 1.71: 4 1.71 - 1.84: 159 Bond restraints: 31230 Sorted by residual: bond pdb=" C1 NAG 6 2 " pdb=" O5 NAG 6 2 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C1 NAG l 2 " pdb=" O5 NAG l 2 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 MAN K 7 " pdb=" O5 MAN K 7 " ideal model delta sigma weight residual 1.399 1.475 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 MAN 0 7 " pdb=" O5 MAN 0 7 " ideal model delta sigma weight residual 1.399 1.475 -0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 31225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 40638 2.30 - 4.59: 1657 4.59 - 6.89: 239 6.89 - 9.18: 48 9.18 - 11.48: 18 Bond angle restraints: 42600 Sorted by residual: angle pdb=" C TYR A1193 " pdb=" N ASN A1194 " pdb=" CA ASN A1194 " ideal model delta sigma weight residual 121.54 132.23 -10.69 1.91e+00 2.74e-01 3.13e+01 angle pdb=" C TYR B1193 " pdb=" N ASN B1194 " pdb=" CA ASN B1194 " ideal model delta sigma weight residual 121.54 132.22 -10.68 1.91e+00 2.74e-01 3.13e+01 angle pdb=" C TYR C1193 " pdb=" N ASN C1194 " pdb=" CA ASN C1194 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 angle pdb=" N TYR A1193 " pdb=" CA TYR A1193 " pdb=" C TYR A1193 " ideal model delta sigma weight residual 110.80 122.28 -11.48 2.13e+00 2.20e-01 2.90e+01 angle pdb=" N TYR C1193 " pdb=" CA TYR C1193 " pdb=" C TYR C1193 " ideal model delta sigma weight residual 110.80 122.28 -11.48 2.13e+00 2.20e-01 2.90e+01 ... (remaining 42595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.40: 15500 12.40 - 24.80: 991 24.80 - 37.20: 135 37.20 - 49.60: 93 49.60 - 62.00: 12 Dihedral angle restraints: 16731 sinusoidal: 6279 harmonic: 10452 Sorted by residual: dihedral pdb=" CA ASN C1194 " pdb=" C ASN C1194 " pdb=" N CYS C1195 " pdb=" CA CYS C1195 " ideal model delta harmonic sigma weight residual 180.00 124.61 55.39 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA ASN B1194 " pdb=" C ASN B1194 " pdb=" N CYS B1195 " pdb=" CA CYS B1195 " ideal model delta harmonic sigma weight residual 180.00 124.65 55.35 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA ASN A1194 " pdb=" C ASN A1194 " pdb=" N CYS A1195 " pdb=" CA CYS A1195 " ideal model delta harmonic sigma weight residual 180.00 124.67 55.33 0 5.00e+00 4.00e-02 1.22e+02 ... (remaining 16728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4798 0.093 - 0.186: 710 0.186 - 0.279: 54 0.279 - 0.372: 36 0.372 - 0.465: 3 Chirality restraints: 5601 Sorted by residual: chirality pdb=" C1 NAG A1406 " pdb=" ND2 ASN A 626 " pdb=" C2 NAG A1406 " pdb=" O5 NAG A1406 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1 NAG C1406 " pdb=" ND2 ASN C 626 " pdb=" C2 NAG C1406 " pdb=" O5 NAG C1406 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" C1 NAG B1406 " pdb=" ND2 ASN B 626 " pdb=" C2 NAG B1406 " pdb=" O5 NAG B1406 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.32e+00 ... (remaining 5598 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 261 " 0.027 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP A 261 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 261 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 261 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 261 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 261 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 261 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 261 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 261 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 261 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 261 " 0.027 2.00e-02 2.50e+03 2.38e-02 1.42e+01 pdb=" CG TRP C 261 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 261 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP C 261 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 261 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 261 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 261 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 261 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 261 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 261 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 261 " -0.027 2.00e-02 2.50e+03 2.37e-02 1.41e+01 pdb=" CG TRP B 261 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP B 261 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 261 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 261 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 261 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 261 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 261 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 261 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 261 " -0.006 2.00e-02 2.50e+03 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8491 2.81 - 3.33: 24741 3.33 - 3.86: 44928 3.86 - 4.38: 48023 4.38 - 4.90: 85735 Nonbonded interactions: 211918 Sorted by model distance: nonbonded pdb=" O4 BMABA 3 " pdb=" O6 BMABA 3 " model vdw 2.290 3.040 nonbonded pdb=" O4 BMA V 3 " pdb=" O6 BMA V 3 " model vdw 2.290 3.040 nonbonded pdb=" O4 BMA q 3 " pdb=" O6 BMA q 3 " model vdw 2.291 3.040 nonbonded pdb=" O ASN A 994 " pdb=" OG1 THR A 998 " model vdw 2.299 3.040 nonbonded pdb=" O ASN B 994 " pdb=" OG1 THR B 998 " model vdw 2.299 3.040 ... (remaining 211913 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: 0.08 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'K' selection = chain 'f' } ncs_group { reference = (chain '1' and resid 1) selection = (chain '2' and resid 1) selection = (chain '5' and resid 1) selection = (chain '6' and resid 1) selection = (chain '7' and resid 1) selection = (chain '8' and resid 1) selection = (chain '9' and resid 1) selection = (chain 'CA' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'k' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'r' and resid 1) selection = (chain 'u' and resid 1) selection = (chain 'w' and resid 1) selection = (chain 'y' and resid 1) selection = (chain 'z' and resid 1) } ncs_group { reference = chain '3' selection = chain 'BA' selection = chain 'N' selection = chain 'V' selection = chain 'i' selection = chain 'q' } ncs_group { reference = chain '4' selection = chain 'DA' selection = chain 'O' selection = chain 'X' selection = chain 'j' selection = chain 's' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'AA' selection = chain 'F' selection = chain 'H' selection = chain 'U' selection = chain 'a' selection = chain 'c' selection = chain 'p' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain 'D' selection = chain 'Y' selection = chain 't' } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.240 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.010 0.090 31497 Z= 0.435 Angle : 1.206 23.378 43353 Z= 0.559 Chirality : 0.068 0.465 5601 Planarity : 0.006 0.054 5124 Dihedral : 8.778 62.004 9897 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.86 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.05 (0.12), residues: 3564 helix: -2.94 (0.14), residues: 576 sheet: -1.77 (0.17), residues: 846 loop : -3.15 (0.11), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 819 TYR 0.030 0.003 TYR C 498 PHE 0.023 0.003 PHE C 230 TRP 0.064 0.004 TRP A 261 HIS 0.017 0.002 HIS C 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00971 / 0.43 (31230) covalent geometry : angle 1.07201 / 0.53 (42600) SS BOND : bond 0.00757 / 0.47 ( 48) SS BOND : angle 2.56993 / 1.67 ( 96) hydrogen bonds : bond 0.27066 / 18.32 ( 745) hydrogen bonds : angle 8.62989 / 6.01 ( 2145) link_ALPHA1-2 : bond 0.00292 / 0.19 ( 9) link_ALPHA1-2 : angle 2.12703 / 1.57 ( 27) link_ALPHA1-3 : bond 0.00715 / 0.46 ( 21) link_ALPHA1-3 : angle 2.54599 / 1.41 ( 63) link_ALPHA1-6 : bond 0.01031 / 0.53 ( 15) link_ALPHA1-6 : angle 2.43892 / 1.51 ( 45) link_BETA1-4 : bond 0.01730 / 1.04 ( 90) link_BETA1-4 : angle 5.66714 / 4.00 ( 270) link_NAG-ASN : bond 0.00969 / 0.66 ( 84) link_NAG-ASN : angle 3.98776 / 2.84 ( 252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 MET cc_start: 0.8352 (mtm) cc_final: 0.8101 (mtm) REVERT: B 729 MET cc_start: 0.9344 (mtm) cc_final: 0.8903 (mtp) REVERT: B 1219 LYS cc_start: 0.9119 (tttm) cc_final: 0.8846 (tppt) REVERT: C 729 MET cc_start: 0.9244 (mtm) cc_final: 0.9034 (mtp) REVERT: C 731 TYR cc_start: 0.6951 (t80) cc_final: 0.6660 (t80) REVERT: C 874 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7118 (mt-10) REVERT: C 926 MET cc_start: 0.9153 (mmm) cc_final: 0.8663 (mmt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2297 time to fit residues: 80.9750 Evaluate side-chains 95 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0270 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 HIS A1019 ASN B 482 HIS B1019 ASN B1222 GLN C 455 GLN C 482 HIS C1019 ASN C1222 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.100704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.075504 restraints weight = 64971.630| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.72 r_work: 0.3058 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31497 Z= 0.131 Angle : 0.771 17.177 43353 Z= 0.349 Chirality : 0.049 0.440 5601 Planarity : 0.004 0.047 5124 Dihedral : 5.539 48.679 3882 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 0.61 % Allowed : 3.52 % Favored : 95.88 % 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: -3.09 (0.13), residues: 3564 helix: -1.63 (0.19), residues: 615 sheet: -1.20 (0.17), residues: 879 loop : -2.67 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1085 TYR 0.012 0.001 TYR B 611 PHE 0.032 0.001 PHE B1224 TRP 0.020 0.001 TRP B 261 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (31230) covalent geometry : angle 0.67043 / 0.33 (42600) SS BOND : bond 0.00429 / 0.23 ( 48) SS BOND : angle 1.44542 / 0.90 ( 96) hydrogen bonds : bond 0.05781 / 3.79 ( 745) hydrogen bonds : angle 5.80304 / 4.07 ( 2145) link_ALPHA1-2 : bond 0.00402 / 0.25 ( 9) link_ALPHA1-2 : angle 1.85058 / 1.30 ( 27) link_ALPHA1-3 : bond 0.00697 / 0.44 ( 21) link_ALPHA1-3 : angle 2.49758 / 1.42 ( 63) link_ALPHA1-6 : bond 0.01076 / 0.60 ( 15) link_ALPHA1-6 : angle 1.73791 / 1.06 ( 45) link_BETA1-4 : bond 0.01293 / 0.79 ( 90) link_BETA1-4 : angle 3.88648 / 2.77 ( 270) link_NAG-ASN : bond 0.00593 / 0.42 ( 84) link_NAG-ASN : angle 2.63795 / 1.87 ( 252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 695 MET cc_start: 0.8422 (mtm) cc_final: 0.8179 (mtm) REVERT: C 926 MET cc_start: 0.9112 (mmm) cc_final: 0.8545 (mmt) REVERT: C 1221 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8562 (pp) outliers start: 19 outliers final: 11 residues processed: 143 average time/residue: 0.2158 time to fit residues: 49.4778 Evaluate side-chains 98 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 46 optimal weight: 0.1980 chunk 107 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071274 restraints weight = 66097.845| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.78 r_work: 0.2977 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31497 Z= 0.225 Angle : 0.806 17.248 43353 Z= 0.368 Chirality : 0.050 0.408 5601 Planarity : 0.004 0.048 5124 Dihedral : 5.454 48.837 3882 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.77 % Favored : 92.14 % Rotamer: Outliers : 1.15 % Allowed : 4.28 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.76 (0.13), residues: 3564 helix: -0.75 (0.20), residues: 594 sheet: -1.07 (0.17), residues: 906 loop : -2.64 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1088 TYR 0.016 0.002 TYR B 630 PHE 0.015 0.002 PHE A1128 TRP 0.014 0.002 TRP C 261 HIS 0.011 0.002 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (31230) covalent geometry : angle 0.71163 / 0.35 (42600) SS BOND : bond 0.00687 / 0.37 ( 48) SS BOND : angle 1.64806 / 1.05 ( 96) hydrogen bonds : bond 0.06142 / 4.03 ( 745) hydrogen bonds : angle 5.45153 / 3.82 ( 2145) link_ALPHA1-2 : bond 0.00508 / 0.32 ( 9) link_ALPHA1-2 : angle 1.75915 / 1.26 ( 27) link_ALPHA1-3 : bond 0.00752 / 0.48 ( 21) link_ALPHA1-3 : angle 2.31595 / 1.31 ( 63) link_ALPHA1-6 : bond 0.00948 / 0.53 ( 15) link_ALPHA1-6 : angle 1.69914 / 1.04 ( 45) link_BETA1-4 : bond 0.01280 / 0.78 ( 90) link_BETA1-4 : angle 3.94004 / 2.79 ( 270) link_NAG-ASN : bond 0.00486 / 0.35 ( 84) link_NAG-ASN : angle 2.51856 / 1.76 ( 252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.6684 (m-10) cc_final: 0.6009 (m-10) REVERT: C 695 MET cc_start: 0.8571 (mtm) cc_final: 0.8267 (mtp) REVERT: C 898 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8172 (tttp) REVERT: C 937 MET cc_start: 0.8870 (mtp) cc_final: 0.8587 (mtm) outliers start: 36 outliers final: 25 residues processed: 113 average time/residue: 0.1962 time to fit residues: 37.3947 Evaluate side-chains 102 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 898 LYS Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1221 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 142 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1222 GLN B1092 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.098420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073444 restraints weight = 73437.750| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.86 r_work: 0.2978 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 31497 Z= 0.315 Angle : 0.892 17.169 43353 Z= 0.413 Chirality : 0.053 0.407 5601 Planarity : 0.005 0.049 5124 Dihedral : 5.812 49.844 3882 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.90 % Favored : 90.04 % Rotamer: Outliers : 1.69 % Allowed : 5.02 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.76 (0.13), residues: 3564 helix: -0.26 (0.21), residues: 594 sheet: -1.21 (0.17), residues: 909 loop : -2.74 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1033 TYR 0.025 0.002 TYR B 630 PHE 0.024 0.003 PHE A 463 TRP 0.013 0.002 TRP C 585 HIS 0.014 0.002 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.31 (31230) covalent geometry : angle 0.80464 / 0.39 (42600) SS BOND : bond 0.00682 / 0.38 ( 48) SS BOND : angle 1.98676 / 1.28 ( 96) hydrogen bonds : bond 0.06631 / 4.34 ( 745) hydrogen bonds : angle 5.54880 / 3.87 ( 2145) link_ALPHA1-2 : bond 0.00554 / 0.35 ( 9) link_ALPHA1-2 : angle 1.82321 / 1.32 ( 27) link_ALPHA1-3 : bond 0.00754 / 0.48 ( 21) link_ALPHA1-3 : angle 2.28567 / 1.30 ( 63) link_ALPHA1-6 : bond 0.00893 / 0.48 ( 15) link_ALPHA1-6 : angle 1.73760 / 1.07 ( 45) link_BETA1-4 : bond 0.01268 / 0.76 ( 90) link_BETA1-4 : angle 3.97889 / 2.80 ( 270) link_NAG-ASN : bond 0.00543 / 0.39 ( 84) link_NAG-ASN : angle 2.60022 / 1.81 ( 252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 84 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: B 67 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7348 (t0) REVERT: C 447 CYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8774 (m) REVERT: C 695 MET cc_start: 0.8614 (mtm) cc_final: 0.8371 (mtp) REVERT: C 937 MET cc_start: 0.9105 (mtp) cc_final: 0.8871 (mtm) REVERT: C 1026 ASN cc_start: 0.9263 (t0) cc_final: 0.9010 (t0) outliers start: 53 outliers final: 35 residues processed: 131 average time/residue: 0.1693 time to fit residues: 39.0977 Evaluate side-chains 112 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 812 LYS Chi-restraints excluded: chain A residue 955 GLN Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 1101 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1221 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 343 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 338 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 334 optimal weight: 30.0000 chunk 45 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.100936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076133 restraints weight = 72403.686| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.87 r_work: 0.3104 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31497 Z= 0.141 Angle : 0.740 16.778 43353 Z= 0.332 Chirality : 0.048 0.404 5601 Planarity : 0.003 0.045 5124 Dihedral : 5.238 47.469 3882 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 1.21 % Allowed : 6.10 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.35 (0.14), residues: 3564 helix: 0.15 (0.22), residues: 591 sheet: -0.82 (0.18), residues: 900 loop : -2.56 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1033 TYR 0.013 0.001 TYR B1193 PHE 0.015 0.001 PHE B 568 TRP 0.010 0.001 TRP C 261 HIS 0.014 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (31230) covalent geometry : angle 0.64531 / 0.31 (42600) SS BOND : bond 0.00526 / 0.31 ( 48) SS BOND : angle 1.67665 / 1.04 ( 96) hydrogen bonds : bond 0.05368 / 3.50 ( 745) hydrogen bonds : angle 5.11763 / 3.59 ( 2145) link_ALPHA1-2 : bond 0.00355 / 0.23 ( 9) link_ALPHA1-2 : angle 1.88529 / 1.36 ( 27) link_ALPHA1-3 : bond 0.00699 / 0.44 ( 21) link_ALPHA1-3 : angle 2.15976 / 1.22 ( 63) link_ALPHA1-6 : bond 0.00919 / 0.50 ( 15) link_ALPHA1-6 : angle 1.76322 / 1.07 ( 45) link_BETA1-4 : bond 0.01242 / 0.75 ( 90) link_BETA1-4 : angle 3.72519 / 2.64 ( 270) link_NAG-ASN : bond 0.00462 / 0.32 ( 84) link_NAG-ASN : angle 2.39080 / 1.68 ( 252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 1.132 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: B 1108 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.5697 (t80) REVERT: C 898 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8251 (tttp) REVERT: C 926 MET cc_start: 0.9088 (mmm) cc_final: 0.8494 (mmt) REVERT: C 1026 ASN cc_start: 0.9141 (t0) cc_final: 0.8794 (t0) REVERT: C 1221 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8548 (pp) outliers start: 38 outliers final: 25 residues processed: 114 average time/residue: 0.1726 time to fit residues: 34.6559 Evaluate side-chains 98 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 737 CYS Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 1108 PHE Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 CYS Chi-restraints excluded: chain C residue 898 LYS Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 225 optimal weight: 0.3980 chunk 243 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 329 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 323 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1092 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.100887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.075653 restraints weight = 72398.929| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.94 r_work: 0.3024 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31497 Z= 0.156 Angle : 0.725 16.832 43353 Z= 0.325 Chirality : 0.048 0.398 5601 Planarity : 0.003 0.041 5124 Dihedral : 5.055 45.229 3882 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.46 % Favored : 92.51 % Rotamer: Outliers : 1.25 % Allowed : 6.55 % Favored : 92.20 % 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: -2.15 (0.14), residues: 3564 helix: 0.43 (0.22), residues: 591 sheet: -0.73 (0.18), residues: 915 loop : -2.45 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 866 TYR 0.011 0.001 TYR C 597 PHE 0.012 0.001 PHE B 568 TRP 0.008 0.001 TRP C 413 HIS 0.009 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (31230) covalent geometry : angle 0.63316 / 0.30 (42600) SS BOND : bond 0.00514 / 0.30 ( 48) SS BOND : angle 1.57672 / 0.99 ( 96) hydrogen bonds : bond 0.05139 / 3.36 ( 745) hydrogen bonds : angle 4.95581 / 3.49 ( 2145) link_ALPHA1-2 : bond 0.00348 / 0.23 ( 9) link_ALPHA1-2 : angle 1.86296 / 1.35 ( 27) link_ALPHA1-3 : bond 0.00662 / 0.42 ( 21) link_ALPHA1-3 : angle 2.09826 / 1.19 ( 63) link_ALPHA1-6 : bond 0.00910 / 0.49 ( 15) link_ALPHA1-6 : angle 1.71523 / 1.05 ( 45) link_BETA1-4 : bond 0.01216 / 0.73 ( 90) link_BETA1-4 : angle 3.68305 / 2.62 ( 270) link_NAG-ASN : bond 0.00418 / 0.30 ( 84) link_NAG-ASN : angle 2.26012 / 1.58 ( 252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: B 1108 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.5526 (t80) REVERT: C 898 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8419 (tttp) REVERT: C 1026 ASN cc_start: 0.9141 (t0) cc_final: 0.8840 (t0) REVERT: C 1221 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8580 (pp) REVERT: C 1224 PHE cc_start: 0.6534 (t80) cc_final: 0.6292 (t80) outliers start: 39 outliers final: 32 residues processed: 109 average time/residue: 0.1782 time to fit residues: 34.5242 Evaluate side-chains 106 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 737 CYS Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 812 LYS Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 1108 PHE Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 737 CYS Chi-restraints excluded: chain C residue 898 LYS Chi-restraints excluded: chain C residue 1101 SER Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 229 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 319 optimal weight: 7.9990 chunk 12 optimal weight: 0.1980 chunk 142 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1092 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.097766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.072537 restraints weight = 65414.638| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.72 r_work: 0.3011 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31497 Z= 0.130 Angle : 0.691 16.761 43353 Z= 0.309 Chirality : 0.047 0.394 5601 Planarity : 0.003 0.043 5124 Dihedral : 4.839 43.480 3882 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.25 % Allowed : 6.84 % Favored : 91.91 % 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: -1.95 (0.14), residues: 3564 helix: 0.67 (0.22), residues: 591 sheet: -0.60 (0.18), residues: 915 loop : -2.34 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1033 TYR 0.010 0.001 TYR C 597 PHE 0.017 0.001 PHE A 132 TRP 0.007 0.001 TRP C 261 HIS 0.007 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (31230) covalent geometry : angle 0.60168 / 0.29 (42600) SS BOND : bond 0.00417 / 0.24 ( 48) SS BOND : angle 1.31947 / 0.82 ( 96) hydrogen bonds : bond 0.04702 / 3.07 ( 745) hydrogen bonds : angle 4.77915 / 3.37 ( 2145) link_ALPHA1-2 : bond 0.00309 / 0.20 ( 9) link_ALPHA1-2 : angle 1.91658 / 1.39 ( 27) link_ALPHA1-3 : bond 0.00641 / 0.40 ( 21) link_ALPHA1-3 : angle 2.01751 / 1.15 ( 63) link_ALPHA1-6 : bond 0.00920 / 0.50 ( 15) link_ALPHA1-6 : angle 1.74329 / 1.07 ( 45) link_BETA1-4 : bond 0.01207 / 0.73 ( 90) link_BETA1-4 : angle 3.57762 / 2.55 ( 270) link_NAG-ASN : bond 0.00407 / 0.29 ( 84) link_NAG-ASN : angle 2.14508 / 1.51 ( 252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: B 1108 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.5526 (t80) REVERT: C 1221 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8544 (pp) outliers start: 39 outliers final: 31 residues processed: 110 average time/residue: 0.1841 time to fit residues: 35.3612 Evaluate side-chains 101 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 737 CYS Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 1108 PHE Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 1101 SER Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 18 optimal weight: 1.9990 chunk 121 optimal weight: 0.0870 chunk 141 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 286 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.072492 restraints weight = 65444.465| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.72 r_work: 0.3004 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31497 Z= 0.136 Angle : 0.689 16.769 43353 Z= 0.308 Chirality : 0.047 0.394 5601 Planarity : 0.003 0.042 5124 Dihedral : 4.757 40.939 3882 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.28 % Allowed : 6.97 % Favored : 91.75 % 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: -1.86 (0.14), residues: 3564 helix: 0.77 (0.22), residues: 594 sheet: -0.54 (0.18), residues: 921 loop : -2.30 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 200 TYR 0.010 0.001 TYR C 731 PHE 0.013 0.001 PHE B 568 TRP 0.006 0.001 TRP C 413 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (31230) covalent geometry : angle 0.60148 / 0.29 (42600) SS BOND : bond 0.00397 / 0.22 ( 48) SS BOND : angle 1.27559 / 0.79 ( 96) hydrogen bonds : bond 0.04673 / 3.05 ( 745) hydrogen bonds : angle 4.71214 / 3.33 ( 2145) link_ALPHA1-2 : bond 0.00312 / 0.21 ( 9) link_ALPHA1-2 : angle 1.89257 / 1.37 ( 27) link_ALPHA1-3 : bond 0.00627 / 0.39 ( 21) link_ALPHA1-3 : angle 1.97944 / 1.12 ( 63) link_ALPHA1-6 : bond 0.00931 / 0.50 ( 15) link_ALPHA1-6 : angle 1.73488 / 1.06 ( 45) link_BETA1-4 : bond 0.01198 / 0.72 ( 90) link_BETA1-4 : angle 3.55602 / 2.54 ( 270) link_NAG-ASN : bond 0.00379 / 0.27 ( 84) link_NAG-ASN : angle 2.09466 / 1.47 ( 252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 69 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: B 1108 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.5537 (t80) outliers start: 40 outliers final: 31 residues processed: 105 average time/residue: 0.1683 time to fit residues: 31.9696 Evaluate side-chains 99 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 1108 PHE Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 1101 SER Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 225 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 326 optimal weight: 0.0670 chunk 57 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.072875 restraints weight = 65552.747| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.72 r_work: 0.3009 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31497 Z= 0.127 Angle : 0.678 16.750 43353 Z= 0.303 Chirality : 0.047 0.392 5601 Planarity : 0.003 0.043 5124 Dihedral : 4.692 40.468 3882 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.12 % Allowed : 7.09 % Favored : 91.79 % 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: -1.76 (0.14), residues: 3564 helix: 0.94 (0.22), residues: 588 sheet: -0.48 (0.18), residues: 921 loop : -2.26 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 200 TYR 0.009 0.001 TYR B1193 PHE 0.019 0.001 PHE C 132 TRP 0.005 0.001 TRP C 413 HIS 0.005 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (31230) covalent geometry : angle 0.59165 / 0.28 (42600) SS BOND : bond 0.00382 / 0.22 ( 48) SS BOND : angle 1.28430 / 0.82 ( 96) hydrogen bonds : bond 0.04519 / 2.95 ( 745) hydrogen bonds : angle 4.64396 / 3.30 ( 2145) link_ALPHA1-2 : bond 0.00302 / 0.20 ( 9) link_ALPHA1-2 : angle 1.90787 / 1.38 ( 27) link_ALPHA1-3 : bond 0.00619 / 0.39 ( 21) link_ALPHA1-3 : angle 1.93992 / 1.10 ( 63) link_ALPHA1-6 : bond 0.00911 / 0.49 ( 15) link_ALPHA1-6 : angle 1.74032 / 1.07 ( 45) link_BETA1-4 : bond 0.01190 / 0.72 ( 90) link_BETA1-4 : angle 3.50766 / 2.51 ( 270) link_NAG-ASN : bond 0.00379 / 0.27 ( 84) link_NAG-ASN : angle 2.03647 / 1.42 ( 252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 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: A 498 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: B 28 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8821 (tp) REVERT: B 1108 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.5510 (t80) outliers start: 35 outliers final: 31 residues processed: 100 average time/residue: 0.1671 time to fit residues: 30.0860 Evaluate side-chains 99 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 1101 SER Chi-restraints excluded: chain B residue 1108 PHE Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 1101 SER Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 122 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 327 optimal weight: 9.9990 chunk 263 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1092 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.100365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.075022 restraints weight = 72039.848| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.93 r_work: 0.3013 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31497 Z= 0.190 Angle : 0.728 16.831 43353 Z= 0.330 Chirality : 0.048 0.393 5601 Planarity : 0.003 0.041 5124 Dihedral : 4.897 41.320 3882 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 1.15 % Allowed : 7.22 % Favored : 91.63 % 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: -1.86 (0.14), residues: 3564 helix: 0.91 (0.23), residues: 594 sheet: -0.56 (0.18), residues: 918 loop : -2.34 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 200 TYR 0.014 0.001 TYR B 630 PHE 0.012 0.002 PHE A 365 TRP 0.008 0.001 TRP C 585 HIS 0.006 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (31230) covalent geometry : angle 0.64506 / 0.31 (42600) SS BOND : bond 0.00482 / 0.28 ( 48) SS BOND : angle 1.52726 / 0.98 ( 96) hydrogen bonds : bond 0.05164 / 3.37 ( 745) hydrogen bonds : angle 4.80666 / 3.40 ( 2145) link_ALPHA1-2 : bond 0.00360 / 0.23 ( 9) link_ALPHA1-2 : angle 1.86418 / 1.34 ( 27) link_ALPHA1-3 : bond 0.00631 / 0.39 ( 21) link_ALPHA1-3 : angle 1.97578 / 1.12 ( 63) link_ALPHA1-6 : bond 0.00907 / 0.49 ( 15) link_ALPHA1-6 : angle 1.72740 / 1.06 ( 45) link_BETA1-4 : bond 0.01198 / 0.72 ( 90) link_BETA1-4 : angle 3.58225 / 2.55 ( 270) link_NAG-ASN : bond 0.00377 / 0.26 ( 84) link_NAG-ASN : angle 2.07628 / 1.45 ( 252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7128 Ramachandran restraints generated. 3564 Oldfield, 0 Emsley, 3564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: B 28 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8900 (tp) REVERT: B 1108 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.5506 (t80) REVERT: C 28 LEU cc_start: 0.9274 (tp) cc_final: 0.8985 (tt) REVERT: C 1221 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8561 (pp) outliers start: 36 outliers final: 32 residues processed: 103 average time/residue: 0.1681 time to fit residues: 31.4106 Evaluate side-chains 105 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 1101 SER Chi-restraints excluded: chain B residue 1108 PHE Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 1101 SER Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1195 CYS Chi-restraints excluded: chain C residue 1221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 324 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 318 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1092 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.076036 restraints weight = 72661.453| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.99 r_work: 0.3031 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31497 Z= 0.137 Angle : 0.686 16.715 43353 Z= 0.308 Chirality : 0.047 0.391 5601 Planarity : 0.003 0.043 5124 Dihedral : 4.742 40.374 3882 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.18 % Allowed : 7.19 % Favored : 91.63 % 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: -1.74 (0.14), residues: 3564 helix: 1.02 (0.23), residues: 591 sheet: -0.50 (0.18), residues: 918 loop : -2.25 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 200 TYR 0.010 0.001 TYR C 597 PHE 0.015 0.001 PHE C 132 TRP 0.007 0.001 TRP B 585 HIS 0.004 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (31230) covalent geometry : angle 0.60191 / 0.29 (42600) SS BOND : bond 0.00394 / 0.22 ( 48) SS BOND : angle 1.31237 / 0.84 ( 96) hydrogen bonds : bond 0.04716 / 3.08 ( 745) hydrogen bonds : angle 4.67373 / 3.31 ( 2145) link_ALPHA1-2 : bond 0.00304 / 0.20 ( 9) link_ALPHA1-2 : angle 1.90590 / 1.38 ( 27) link_ALPHA1-3 : bond 0.00626 / 0.39 ( 21) link_ALPHA1-3 : angle 1.92073 / 1.09 ( 63) link_ALPHA1-6 : bond 0.00920 / 0.50 ( 15) link_ALPHA1-6 : angle 1.75581 / 1.08 ( 45) link_BETA1-4 : bond 0.01193 / 0.72 ( 90) link_BETA1-4 : angle 3.50378 / 2.50 ( 270) link_NAG-ASN : bond 0.00368 / 0.26 ( 84) link_NAG-ASN : angle 2.02093 / 1.41 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5266.50 seconds wall clock time: 91 minutes 58.55 seconds (5518.55 seconds total)