Starting phenix.real_space_refine on Thu Nov 20 04:41:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5szs_8331/11_2025/5szs_8331.cif Found real_map, /net/cci-nas-00/data/ceres_data/5szs_8331/11_2025/5szs_8331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5szs_8331/11_2025/5szs_8331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5szs_8331/11_2025/5szs_8331.map" model { file = "/net/cci-nas-00/data/ceres_data/5szs_8331/11_2025/5szs_8331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5szs_8331/11_2025/5szs_8331.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 19089 2.51 5 N 4743 2.21 5 O 6345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30306 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "B" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "C" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "L" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "g" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "1" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 8.09, per 1000 atoms: 0.27 Number of scatterers: 30306 At special positions: 0 Unit cell: (150.96, 141.44, 178.16, 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 6345 8.00 N 4743 7.00 C 19089 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=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 181 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 210 " distance=2.21 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=2.04 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 577 " distance=2.02 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 678 " distance=2.25 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 737 " distance=2.02 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 811 " distance=2.07 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=2.04 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1109 " distance=2.02 Simple disulfide: pdb=" SG CYS A1148 " - pdb=" SG CYS A1195 " distance=1.74 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 181 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 210 " distance=2.21 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=2.04 Simple disulfide: pdb=" SG CYS B 438 " - pdb=" SG CYS B 447 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 577 " distance=2.02 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 678 " distance=2.25 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 737 " distance=2.02 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 811 " distance=2.07 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=2.02 Simple disulfide: pdb=" SG CYS B1148 " - pdb=" SG CYS B1195 " distance=1.74 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 181 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 210 " distance=2.21 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=2.04 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 447 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 678 " distance=2.25 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 737 " distance=2.02 Simple disulfide: pdb=" SG CYS C 789 " - pdb=" SG CYS C 811 " distance=2.07 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=2.04 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1109 " distance=2.02 Simple disulfide: pdb=" SG CYS C1148 " - pdb=" SG CYS C1195 " distance=1.74 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 Atom "HETATM28675 O4 NAG g 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM27812 O4 NAG L 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29538 O4 NAG 1 1 .*. O " rejected from bonding due to valence issues. 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 2 " - " BMA 1 3 " " 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 2 " - " BMA L 3 " " 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 2 " - " BMA g 3 " " 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 1 1 " - " ASN C 486 " " 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 A1439 " - " ASN A 512 " " NAG A1440 " - " ASN A 626 " " NAG A1441 " - " ASN A 645 " " NAG A1474 " - " ASN A1218 " " NAG B1401 " - " ASN B 155 " " NAG B1402 " - " ASN B 187 " " NAG B1403 " - " ASN B 193 " " NAG B1439 " - " ASN B 512 " " NAG B1440 " - " ASN B 626 " " NAG B1441 " - " ASN B 645 " " NAG B1474 " - " ASN B1218 " " NAG C1401 " - " ASN C 155 " " NAG C1402 " - " ASN C 187 " " NAG C1403 " - " ASN C 193 " " NAG C1439 " - " ASN C 512 " " NAG C1440 " - " ASN C 626 " " NAG C1441 " - " ASN C 645 " " NAG C1474 " - " 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 L 1 " - " ASN A 486 " " 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 g 1 " - " ASN B 486 " " 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: 3.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 51 sheets defined 25.1% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.571A pdb=" N ARG A 225 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 807 through 833 removed outlier: 4.801A pdb=" N THR A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 843 Processing helix chain 'A' and resid 844 through 852 removed outlier: 4.138A pdb=" N GLY A 849 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 850 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 892 through 898 removed outlier: 4.118A pdb=" N THR A 897 " --> pdb=" O LYS A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 922 through 936 Processing helix chain 'A' and resid 949 through 960 Processing helix chain 'A' and resid 969 through 992 removed outlier: 4.482A pdb=" N LYS A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1031 Processing helix chain 'A' and resid 1032 through 1034 No H-bonds generated for 'chain 'A' and resid 1032 through 1034' Processing helix chain 'A' and resid 1042 through 1048 Processing helix chain 'A' and resid 1051 through 1099 removed outlier: 5.115A pdb=" N GLN A1057 " --> pdb=" O ILE A1053 " (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 1205 through 1210 Processing helix chain 'A' and resid 1216 through 1224 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.572A pdb=" N ARG B 225 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 530 through 534 Processing helix chain 'B' and resid 536 through 539 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 799 through 804 Processing helix chain 'B' and resid 807 through 833 removed outlier: 4.801A pdb=" N THR B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 832 " --> pdb=" O ASP B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 844 through 852 removed outlier: 4.138A pdb=" N GLY B 849 " --> pdb=" O THR B 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B 850 " --> pdb=" O SER B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 882 Processing helix chain 'B' and resid 892 through 898 removed outlier: 4.118A pdb=" N THR B 897 " --> pdb=" O LYS B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 922 through 936 Processing helix chain 'B' and resid 949 through 960 Processing helix chain 'B' and resid 969 through 992 removed outlier: 4.482A pdb=" N LYS B 973 " --> pdb=" O GLN B 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1031 Processing helix chain 'B' and resid 1032 through 1034 No H-bonds generated for 'chain 'B' and resid 1032 through 1034' Processing helix chain 'B' and resid 1042 through 1048 Processing helix chain 'B' and resid 1051 through 1099 removed outlier: 5.115A pdb=" N GLN B1057 " --> pdb=" O ILE B1053 " (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 1205 through 1210 Processing helix chain 'B' and resid 1216 through 1224 Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.571A pdb=" N ARG C 225 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 530 through 534 Processing helix chain 'C' and resid 536 through 539 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 799 through 804 Processing helix chain 'C' and resid 807 through 833 removed outlier: 4.802A pdb=" N THR C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 815 " --> pdb=" O CYS C 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 832 " --> pdb=" O ASP C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 844 through 852 removed outlier: 4.137A pdb=" N GLY C 849 " --> pdb=" O THR C 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP C 850 " --> pdb=" O SER C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 882 Processing helix chain 'C' and resid 892 through 898 removed outlier: 4.117A pdb=" N THR C 897 " --> pdb=" O LYS C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 911 Processing helix chain 'C' and resid 922 through 936 Processing helix chain 'C' and resid 949 through 960 Processing helix chain 'C' and resid 969 through 992 removed outlier: 4.481A pdb=" N LYS C 973 " --> pdb=" O GLN C 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1031 Processing helix chain 'C' and resid 1032 through 1034 No H-bonds generated for 'chain 'C' and resid 1032 through 1034' Processing helix chain 'C' and resid 1042 through 1048 Processing helix chain 'C' and resid 1051 through 1099 removed outlier: 5.114A pdb=" N GLN C1057 " --> pdb=" O ILE C1053 " (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 1205 through 1210 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: 7.246A pdb=" N THR A 191 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 206 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A 204 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 195 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA A 99 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 133 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 101 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU A 131 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 103 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 129 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 105 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 125 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 161 removed outlier: 3.720A pdb=" N GLY A 62 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL A 248 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 427 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG A 250 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 425 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A 252 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 423 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 421 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 417 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 260 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 415 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP A 413 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A 299 " --> pdb=" O TRP A 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 415 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG A 297 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE A 417 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 295 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE A 384 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL A 248 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 427 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG A 250 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 425 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A 252 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 423 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 421 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 417 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 260 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 415 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP A 413 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP A 422 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR A 437 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 424 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 435 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A 426 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A 356 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 323 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 328 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY A 313 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A 356 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 323 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE A 326 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA9, first strand: chain 'A' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN A 683 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA A 694 " --> pdb=" O GLN A 683 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA A 685 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU A 662 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR A 654 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 504 through 509 removed outlier: 6.457A pdb=" N SER A 601 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A 603 " --> pdb=" O LYS A 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS A 562 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 514 through 515 removed outlier: 4.184A pdb=" N SER A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP A 585 " --> pdb=" O SER A 589 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 581 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A 595 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 579 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR A 597 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS A 577 " --> pdb=" O TYR A 597 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 727 through 731 removed outlier: 6.775A pdb=" N ILE A 736 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR A 730 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE A 734 " --> pdb=" O THR A 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN A 762 " --> pdb=" O LYS A1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A1142 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 764 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A1140 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1138 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 768 " --> pdb=" O THR A1136 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A1114 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN A 762 " --> pdb=" O LYS A1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A1142 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 764 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A1140 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1138 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 768 " --> pdb=" O THR A1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS A1142 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A1164 " --> pdb=" O TRP A1144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB8, first strand: chain 'A' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE A1202 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR B 191 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 206 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 204 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR B 195 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA B 99 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 133 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 101 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B 131 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 103 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN B 129 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 105 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B 125 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 156 through 161 removed outlier: 3.719A pdb=" N GLY B 62 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 247 through 262 removed outlier: 5.506A pdb=" N VAL B 248 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 427 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG B 250 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 425 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 252 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 423 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 421 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 417 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 260 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 415 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP B 413 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN B 299 " --> pdb=" O TRP B 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 415 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 297 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE B 417 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 295 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 384 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 247 through 262 removed outlier: 5.506A pdb=" N VAL B 248 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 427 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG B 250 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 425 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 252 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 423 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 421 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 417 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 260 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 415 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP B 413 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP B 422 " --> pdb=" O TYR B 437 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR B 437 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 424 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 435 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN B 426 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 360 through 368 removed outlier: 6.816A pdb=" N CYS B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 356 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 323 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS B 328 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY B 313 " --> pdb=" O CYS B 328 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 368 removed outlier: 6.816A pdb=" N CYS B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 356 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 323 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE B 326 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AC8, first strand: chain 'B' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN B 683 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA B 694 " --> pdb=" O GLN B 683 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 685 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU B 662 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR B 654 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 504 through 509 removed outlier: 6.456A pdb=" N SER B 601 " --> pdb=" O LYS B 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY B 603 " --> pdb=" O LYS B 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS B 562 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 514 through 515 removed outlier: 4.183A pdb=" N SER B 589 " --> pdb=" O TRP B 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP B 585 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 581 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA B 595 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 579 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 597 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N CYS B 577 " --> pdb=" O TYR B 597 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 727 through 731 removed outlier: 6.775A pdb=" N ILE B 736 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR B 730 " --> pdb=" O PHE B 734 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 734 " --> pdb=" O THR B 730 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 779 removed outlier: 6.895A pdb=" N ASN B 762 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS B1142 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER B 764 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1140 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B1138 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN B 768 " --> pdb=" O THR B1136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B1133 " --> pdb=" O HIS B1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS B1114 " --> pdb=" O LEU B1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 779 removed outlier: 6.895A pdb=" N ASN B 762 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS B1142 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER B 764 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1140 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B1138 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN B 768 " --> pdb=" O THR B1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS B1142 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B1164 " --> pdb=" O TRP B1144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 785 through 787 Processing sheet with id=AD7, first strand: chain 'B' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE B1202 " --> pdb=" O CYS B1148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR C 191 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL C 206 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR C 204 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR C 195 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA C 99 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR C 133 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 101 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C 131 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 103 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN C 129 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 105 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 125 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 156 through 161 removed outlier: 3.719A pdb=" N GLY C 62 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL C 248 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 427 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG C 250 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 425 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR C 252 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 423 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 421 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE C 417 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 260 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 415 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP C 413 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN C 299 " --> pdb=" O TRP C 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 415 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG C 297 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE C 417 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 295 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE C 384 " --> pdb=" O TYR C 391 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL C 248 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 427 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG C 250 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 425 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR C 252 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 423 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 421 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE C 417 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 260 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 415 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP C 413 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASP C 422 " --> pdb=" O TYR C 437 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR C 437 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 424 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 435 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN C 426 " --> pdb=" O GLN C 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 356 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP C 323 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS C 328 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY C 313 " --> pdb=" O CYS C 328 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 356 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP C 323 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE C 326 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 343 through 344 Processing sheet with id=AE7, first strand: chain 'C' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN C 683 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA C 694 " --> pdb=" O GLN C 683 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 685 " --> pdb=" O ILE C 692 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU C 662 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR C 654 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 504 through 509 removed outlier: 6.456A pdb=" N SER C 601 " --> pdb=" O LYS C 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY C 603 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS C 562 " --> pdb=" O GLY C 603 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 514 through 515 removed outlier: 4.184A pdb=" N SER C 589 " --> pdb=" O TRP C 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP C 585 " --> pdb=" O SER C 589 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 581 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 595 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE C 579 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR C 597 " --> pdb=" O CYS C 577 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS C 577 " --> pdb=" O TYR C 597 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 727 through 731 removed outlier: 6.774A pdb=" N ILE C 736 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N THR C 730 " --> pdb=" O PHE C 734 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE C 734 " --> pdb=" O THR C 730 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN C 762 " --> pdb=" O LYS C1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C1142 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 764 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN C1140 " --> pdb=" O SER C 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C1138 " --> pdb=" O PRO C 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 768 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C1133 " --> pdb=" O HIS C1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS C1114 " --> pdb=" O LEU C1133 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN C 762 " --> pdb=" O LYS C1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C1142 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 764 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN C1140 " --> pdb=" O SER C 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C1138 " --> pdb=" O PRO C 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 768 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS C1142 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C1164 " --> pdb=" O TRP C1144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 785 through 787 Processing sheet with id=AF6, first strand: chain 'C' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE C1202 " --> pdb=" O CYS C1148 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3312 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: 8.59 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7568 1.33 - 1.47: 10479 1.47 - 1.61: 12694 1.61 - 1.75: 36 1.75 - 1.89: 141 Bond restraints: 30918 Sorted by residual: bond pdb=" C VAL B1190 " pdb=" N GLN B1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 9.05e+01 bond pdb=" C VAL C1190 " pdb=" N GLN C1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 8.99e+01 bond pdb=" C VAL A1190 " pdb=" N GLN A1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 8.99e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.580 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C1 NAG u 2 " pdb=" O5 NAG u 2 " ideal model delta sigma weight residual 1.406 1.580 -0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 30913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.83: 41393 8.83 - 17.66: 451 17.66 - 26.49: 238 26.49 - 35.33: 65 35.33 - 44.16: 12 Bond angle restraints: 42159 Sorted by residual: angle pdb=" C2 MAN 0 4 " pdb=" C3 MAN 0 4 " pdb=" O3 MAN 0 4 " ideal model delta sigma weight residual 107.58 151.74 -44.16 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C2 MAN f 4 " pdb=" C3 MAN f 4 " pdb=" O3 MAN f 4 " ideal model delta sigma weight residual 107.58 151.73 -44.15 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C2 MAN K 4 " pdb=" C3 MAN K 4 " pdb=" O3 MAN K 4 " ideal model delta sigma weight residual 107.58 151.70 -44.12 3.00e+00 1.11e-01 2.16e+02 angle pdb=" C4 MAN f 4 " pdb=" C3 MAN f 4 " pdb=" O3 MAN f 4 " ideal model delta sigma weight residual 111.95 70.52 41.43 3.00e+00 1.11e-01 1.91e+02 angle pdb=" C4 MAN 0 4 " pdb=" C3 MAN 0 4 " pdb=" O3 MAN 0 4 " ideal model delta sigma weight residual 111.95 70.53 41.42 3.00e+00 1.11e-01 1.91e+02 ... (remaining 42154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 19712 23.75 - 47.50: 823 47.50 - 71.25: 246 71.25 - 95.01: 201 95.01 - 118.76: 78 Dihedral angle restraints: 21060 sinusoidal: 10737 harmonic: 10323 Sorted by residual: dihedral pdb=" C ALA B 810 " pdb=" N ALA B 810 " pdb=" CA ALA B 810 " pdb=" CB ALA B 810 " ideal model delta harmonic sigma weight residual -122.60 -146.41 23.81 0 2.50e+00 1.60e-01 9.07e+01 dihedral pdb=" C ALA C 810 " pdb=" N ALA C 810 " pdb=" CA ALA C 810 " pdb=" CB ALA C 810 " ideal model delta harmonic sigma weight residual -122.60 -146.40 23.80 0 2.50e+00 1.60e-01 9.06e+01 dihedral pdb=" C ALA A 810 " pdb=" N ALA A 810 " pdb=" CA ALA A 810 " pdb=" CB ALA A 810 " ideal model delta harmonic sigma weight residual -122.60 -146.37 23.77 0 2.50e+00 1.60e-01 9.04e+01 ... (remaining 21057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 4966 0.264 - 0.528: 385 0.528 - 0.792: 109 0.792 - 1.056: 51 1.056 - 1.320: 27 Chirality restraints: 5538 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 3.91e+02 chirality pdb=" C1 NAG u 2 " pdb=" O4 NAG u 1 " pdb=" C2 NAG u 2 " pdb=" O5 NAG u 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 3.91e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-02 2.50e+03 3.88e+02 ... (remaining 5535 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 486 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN B 486 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 486 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 486 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 486 " 0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN A 486 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 486 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 486 " -0.157 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 486 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN C 486 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN C 486 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 486 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG 1 1 " -0.120 2.00e-02 2.50e+03 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 42 2.16 - 2.85: 10971 2.85 - 3.53: 39555 3.53 - 4.22: 74296 4.22 - 4.90: 118793 Nonbonded interactions: 243657 Sorted by model distance: nonbonded pdb=" O4 NAG g 1 " pdb=" C1 NAG g 2 " model vdw 1.476 3.470 nonbonded pdb=" O4 NAG L 1 " pdb=" C1 NAG L 2 " model vdw 1.476 3.470 nonbonded pdb=" O4 NAG 1 1 " pdb=" C1 NAG 1 2 " model vdw 1.476 3.470 nonbonded pdb=" O ASN C1111 " pdb=" OD1 ASN C1111 " model vdw 1.738 3.040 nonbonded pdb=" O ASN A1111 " pdb=" OD1 ASN A1111 " model vdw 1.738 3.040 ... (remaining 243652 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' selection = chain '4' selection = chain 'DA' selection = chain 'L' selection = chain 'O' selection = chain 'X' selection = chain 'g' selection = chain 'j' selection = chain 's' } ncs_group { reference = chain '2' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'CA' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' selection = chain 'u' selection = chain 'w' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '3' selection = chain 'BA' selection = chain 'N' selection = chain 'V' selection = chain 'i' selection = chain 'q' } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.400 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.024 0.292 31185 Z= 1.257 Angle : 3.066 44.157 42912 Z= 1.346 Chirality : 0.199 1.320 5538 Planarity : 0.012 0.113 5064 Dihedral : 18.246 118.758 14304 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.70 % Favored : 93.70 % Rotamer: Outliers : 0.68 % Allowed : 1.45 % Favored : 97.87 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3507 helix: 0.72 (0.19), residues: 708 sheet: 0.72 (0.18), residues: 852 loop : -0.95 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 225 TYR 0.037 0.006 TYR C 654 PHE 0.023 0.005 PHE B 950 TRP 0.028 0.006 TRP A 600 HIS 0.007 0.002 HIS B 542 Details of bonding type rmsd covalent geometry : bond 0.02411 (30918) covalent geometry : angle 3.03603 (42159) SS BOND : bond 0.10224 ( 48) SS BOND : angle 4.59662 ( 96) hydrogen bonds : bond 0.15661 ( 1170) hydrogen bonds : angle 7.87241 ( 3312) link_ALPHA1-2 : bond 0.03696 ( 9) link_ALPHA1-2 : angle 2.23527 ( 27) link_ALPHA1-3 : bond 0.03654 ( 21) link_ALPHA1-3 : angle 5.41311 ( 63) link_ALPHA1-6 : bond 0.02856 ( 15) link_ALPHA1-6 : angle 2.62886 ( 45) link_BETA1-4 : bond 0.03008 ( 90) link_BETA1-4 : angle 5.30253 ( 270) link_NAG-ASN : bond 0.03511 ( 84) link_NAG-ASN : angle 3.39731 ( 252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 468 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 VAL cc_start: 0.8463 (t) cc_final: 0.8066 (p) REVERT: A 515 VAL cc_start: 0.8523 (t) cc_final: 0.8288 (p) REVERT: A 851 TYR cc_start: 0.7618 (m-80) cc_final: 0.7017 (m-80) REVERT: A 916 VAL cc_start: 0.8430 (t) cc_final: 0.7994 (t) REVERT: B 153 LEU cc_start: 0.8295 (mt) cc_final: 0.7976 (mt) REVERT: B 362 VAL cc_start: 0.8143 (t) cc_final: 0.7649 (p) REVERT: B 538 ASP cc_start: 0.6525 (m-30) cc_final: 0.6209 (m-30) REVERT: B 916 VAL cc_start: 0.8667 (t) cc_final: 0.8381 (t) REVERT: C 362 VAL cc_start: 0.8268 (t) cc_final: 0.7848 (p) REVERT: C 763 LEU cc_start: 0.9091 (mt) cc_final: 0.8865 (mp) outliers start: 21 outliers final: 13 residues processed: 489 average time/residue: 0.2207 time to fit residues: 167.8172 Evaluate side-chains 185 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 1111 ASN Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 1111 ASN Chi-restraints excluded: chain C residue 1138 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 ASN C 433 GLN C1021 GLN C1054 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.090453 restraints weight = 60324.661| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.34 r_work: 0.3136 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 31185 Z= 0.206 Angle : 1.011 19.960 42912 Z= 0.452 Chirality : 0.053 0.399 5538 Planarity : 0.006 0.070 5064 Dihedral : 15.281 96.433 8369 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.91 % Favored : 95.58 % Rotamer: Outliers : 1.88 % Allowed : 5.66 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3507 helix: 1.36 (0.20), residues: 708 sheet: 0.76 (0.18), residues: 900 loop : -0.88 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 748 TYR 0.019 0.002 TYR A1047 PHE 0.027 0.002 PHE A 402 TRP 0.014 0.002 TRP B 261 HIS 0.005 0.001 HIS B1005 Details of bonding type rmsd covalent geometry : bond 0.00432 (30918) covalent geometry : angle 0.88010 (42159) SS BOND : bond 0.00695 ( 48) SS BOND : angle 1.91902 ( 96) hydrogen bonds : bond 0.07261 ( 1170) hydrogen bonds : angle 6.06139 ( 3312) link_ALPHA1-2 : bond 0.01154 ( 9) link_ALPHA1-2 : angle 1.74476 ( 27) link_ALPHA1-3 : bond 0.01263 ( 21) link_ALPHA1-3 : angle 3.36638 ( 63) link_ALPHA1-6 : bond 0.01204 ( 15) link_ALPHA1-6 : angle 1.99272 ( 45) link_BETA1-4 : bond 0.01363 ( 90) link_BETA1-4 : angle 4.72147 ( 270) link_NAG-ASN : bond 0.00600 ( 84) link_NAG-ASN : angle 3.89820 ( 252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 1016 ASP cc_start: 0.8198 (t0) cc_final: 0.7981 (t0) REVERT: A 1047 TYR cc_start: 0.9185 (m-80) cc_final: 0.8956 (m-80) REVERT: A 1113 THR cc_start: 0.8807 (m) cc_final: 0.8526 (p) REVERT: B 954 LEU cc_start: 0.9251 (mp) cc_final: 0.9041 (mm) REVERT: B 1060 ASP cc_start: 0.7826 (t70) cc_final: 0.7562 (m-30) REVERT: B 1113 THR cc_start: 0.9122 (m) cc_final: 0.8871 (p) REVERT: C 250 ARG cc_start: 0.8877 (mtp180) cc_final: 0.8531 (mtm180) REVERT: C 275 PHE cc_start: 0.7936 (m-80) cc_final: 0.7713 (m-80) REVERT: C 763 LEU cc_start: 0.9021 (mt) cc_final: 0.8780 (mp) REVERT: C 828 ASP cc_start: 0.8133 (t0) cc_final: 0.7913 (t0) REVERT: C 1113 THR cc_start: 0.9144 (m) cc_final: 0.8772 (p) outliers start: 58 outliers final: 36 residues processed: 303 average time/residue: 0.1998 time to fit residues: 98.5807 Evaluate side-chains 197 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1161 ASN Chi-restraints excluded: chain C residue 1193 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 155 optimal weight: 0.5980 chunk 222 optimal weight: 0.4980 chunk 237 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN A 657 ASN A 679 ASN A 827 ASN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 657 ASN ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086229 restraints weight = 60070.548| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.33 r_work: 0.3055 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31185 Z= 0.199 Angle : 0.883 17.477 42912 Z= 0.398 Chirality : 0.053 0.462 5538 Planarity : 0.005 0.058 5064 Dihedral : 10.950 75.052 8361 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.88 % Favored : 94.61 % Rotamer: Outliers : 2.59 % Allowed : 7.92 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3507 helix: 1.80 (0.20), residues: 693 sheet: 0.85 (0.17), residues: 903 loop : -1.24 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 617 TYR 0.022 0.002 TYR B 58 PHE 0.028 0.002 PHE C 124 TRP 0.011 0.001 TRP B 769 HIS 0.007 0.002 HIS C1005 Details of bonding type rmsd covalent geometry : bond 0.00437 (30918) covalent geometry : angle 0.77633 (42159) SS BOND : bond 0.00739 ( 48) SS BOND : angle 1.94088 ( 96) hydrogen bonds : bond 0.06109 ( 1170) hydrogen bonds : angle 5.41765 ( 3312) link_ALPHA1-2 : bond 0.00866 ( 9) link_ALPHA1-2 : angle 1.61633 ( 27) link_ALPHA1-3 : bond 0.01275 ( 21) link_ALPHA1-3 : angle 2.64961 ( 63) link_ALPHA1-6 : bond 0.01192 ( 15) link_ALPHA1-6 : angle 2.04398 ( 45) link_BETA1-4 : bond 0.01193 ( 90) link_BETA1-4 : angle 4.00651 ( 270) link_NAG-ASN : bond 0.00507 ( 84) link_NAG-ASN : angle 3.22214 ( 252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 199 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8712 (mm) REVERT: A 851 TYR cc_start: 0.8082 (m-80) cc_final: 0.7752 (m-80) REVERT: A 867 ILE cc_start: 0.8431 (mt) cc_final: 0.8224 (mp) REVERT: A 1108 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.6999 (t80) REVERT: B 867 ILE cc_start: 0.8534 (mm) cc_final: 0.8333 (mp) REVERT: B 954 LEU cc_start: 0.9449 (mp) cc_final: 0.9203 (mm) REVERT: B 1060 ASP cc_start: 0.7776 (t70) cc_final: 0.7556 (m-30) REVERT: B 1113 THR cc_start: 0.9098 (m) cc_final: 0.8897 (p) REVERT: B 1198 THR cc_start: 0.8029 (p) cc_final: 0.7782 (t) REVERT: C 296 MET cc_start: 0.8745 (mtm) cc_final: 0.8426 (mtm) REVERT: C 763 LEU cc_start: 0.9213 (mt) cc_final: 0.8990 (mp) REVERT: C 1060 ASP cc_start: 0.7931 (t70) cc_final: 0.7465 (m-30) REVERT: C 1113 THR cc_start: 0.9246 (m) cc_final: 0.9039 (p) REVERT: C 1124 ASP cc_start: 0.8642 (m-30) cc_final: 0.8347 (m-30) outliers start: 80 outliers final: 57 residues processed: 263 average time/residue: 0.1805 time to fit residues: 80.4506 Evaluate side-chains 221 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1166 SER Chi-restraints excluded: chain C residue 1193 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 131 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 345 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 267 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 280 optimal weight: 2.9990 chunk 287 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS A1034 HIS A1140 ASN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 ASN ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS C1140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086413 restraints weight = 59778.949| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.33 r_work: 0.3043 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31185 Z= 0.159 Angle : 0.789 17.708 42912 Z= 0.354 Chirality : 0.050 0.430 5538 Planarity : 0.004 0.050 5064 Dihedral : 9.492 65.489 8361 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.11 % Favored : 95.49 % Rotamer: Outliers : 2.39 % Allowed : 8.96 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3507 helix: 1.98 (0.20), residues: 693 sheet: 0.70 (0.17), residues: 951 loop : -1.34 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 380 TYR 0.012 0.001 TYR A 851 PHE 0.030 0.002 PHE A 568 TRP 0.011 0.001 TRP B 769 HIS 0.005 0.001 HIS B1005 Details of bonding type rmsd covalent geometry : bond 0.00336 (30918) covalent geometry : angle 0.68474 (42159) SS BOND : bond 0.00518 ( 48) SS BOND : angle 1.62606 ( 96) hydrogen bonds : bond 0.05617 ( 1170) hydrogen bonds : angle 5.23007 ( 3312) link_ALPHA1-2 : bond 0.00737 ( 9) link_ALPHA1-2 : angle 1.59271 ( 27) link_ALPHA1-3 : bond 0.01135 ( 21) link_ALPHA1-3 : angle 2.63597 ( 63) link_ALPHA1-6 : bond 0.01284 ( 15) link_ALPHA1-6 : angle 1.73604 ( 45) link_BETA1-4 : bond 0.01156 ( 90) link_BETA1-4 : angle 3.77113 ( 270) link_NAG-ASN : bond 0.00354 ( 84) link_NAG-ASN : angle 2.97613 ( 252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8653 (mm) REVERT: B 81 TYR cc_start: 0.7813 (p90) cc_final: 0.7609 (p90) REVERT: B 130 LEU cc_start: 0.8649 (mt) cc_final: 0.8115 (mt) REVERT: B 486 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.7857 (p0) REVERT: B 954 LEU cc_start: 0.9473 (mp) cc_final: 0.9242 (mm) REVERT: B 1060 ASP cc_start: 0.7769 (t70) cc_final: 0.7538 (m-30) REVERT: B 1198 THR cc_start: 0.8183 (p) cc_final: 0.7764 (t) REVERT: C 763 LEU cc_start: 0.9232 (mt) cc_final: 0.9021 (mp) REVERT: C 950 PHE cc_start: 0.8458 (t80) cc_final: 0.8124 (t80) REVERT: C 1060 ASP cc_start: 0.7883 (t70) cc_final: 0.7496 (m-30) REVERT: C 1124 ASP cc_start: 0.8605 (m-30) cc_final: 0.8325 (m-30) outliers start: 74 outliers final: 53 residues processed: 241 average time/residue: 0.1684 time to fit residues: 69.6117 Evaluate side-chains 214 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 277 optimal weight: 0.7980 chunk 253 optimal weight: 0.7980 chunk 275 optimal weight: 0.7980 chunk 341 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.114103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.086447 restraints weight = 59919.869| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.29 r_work: 0.3044 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31185 Z= 0.151 Angle : 0.759 17.587 42912 Z= 0.341 Chirality : 0.049 0.428 5538 Planarity : 0.004 0.047 5064 Dihedral : 8.869 60.062 8361 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.68 % Favored : 94.92 % Rotamer: Outliers : 2.46 % Allowed : 8.99 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3507 helix: 1.79 (0.20), residues: 729 sheet: 0.69 (0.17), residues: 921 loop : -1.30 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 380 TYR 0.014 0.001 TYR B 851 PHE 0.021 0.001 PHE C 124 TRP 0.008 0.001 TRP B 769 HIS 0.009 0.001 HIS C1005 Details of bonding type rmsd covalent geometry : bond 0.00319 (30918) covalent geometry : angle 0.65749 (42159) SS BOND : bond 0.00577 ( 48) SS BOND : angle 1.75481 ( 96) hydrogen bonds : bond 0.05447 ( 1170) hydrogen bonds : angle 5.09792 ( 3312) link_ALPHA1-2 : bond 0.00737 ( 9) link_ALPHA1-2 : angle 1.56484 ( 27) link_ALPHA1-3 : bond 0.01161 ( 21) link_ALPHA1-3 : angle 2.43042 ( 63) link_ALPHA1-6 : bond 0.01311 ( 15) link_ALPHA1-6 : angle 1.89211 ( 45) link_BETA1-4 : bond 0.01128 ( 90) link_BETA1-4 : angle 3.64777 ( 270) link_NAG-ASN : bond 0.00344 ( 84) link_NAG-ASN : angle 2.82171 ( 252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7625 (mtm) cc_final: 0.7289 (ttm) REVERT: A 30 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8674 (mm) REVERT: A 1108 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.6867 (t80) REVERT: B 130 LEU cc_start: 0.8591 (mt) cc_final: 0.8073 (mt) REVERT: B 486 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7675 (p0) REVERT: B 954 LEU cc_start: 0.9461 (mp) cc_final: 0.9241 (mm) REVERT: B 1198 THR cc_start: 0.8148 (p) cc_final: 0.7750 (t) REVERT: C 763 LEU cc_start: 0.9277 (mt) cc_final: 0.9050 (mp) REVERT: C 1005 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7210 (p-80) REVERT: C 1060 ASP cc_start: 0.7705 (t70) cc_final: 0.7407 (m-30) REVERT: C 1124 ASP cc_start: 0.8540 (m-30) cc_final: 0.8282 (m-30) outliers start: 76 outliers final: 61 residues processed: 223 average time/residue: 0.1735 time to fit residues: 66.1283 Evaluate side-chains 218 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 153 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 789 CYS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 91 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 306 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.113782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.085923 restraints weight = 59621.576| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.35 r_work: 0.3036 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31185 Z= 0.153 Angle : 0.745 17.762 42912 Z= 0.336 Chirality : 0.049 0.430 5538 Planarity : 0.004 0.045 5064 Dihedral : 8.467 57.124 8361 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.39 % Favored : 95.21 % Rotamer: Outliers : 2.46 % Allowed : 9.41 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3507 helix: 1.84 (0.20), residues: 729 sheet: 0.65 (0.17), residues: 927 loop : -1.28 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1088 TYR 0.013 0.001 TYR B 851 PHE 0.023 0.001 PHE B 568 TRP 0.008 0.001 TRP B 769 HIS 0.005 0.001 HIS B1005 Details of bonding type rmsd covalent geometry : bond 0.00326 (30918) covalent geometry : angle 0.64798 (42159) SS BOND : bond 0.00589 ( 48) SS BOND : angle 1.73797 ( 96) hydrogen bonds : bond 0.05362 ( 1170) hydrogen bonds : angle 5.02768 ( 3312) link_ALPHA1-2 : bond 0.00721 ( 9) link_ALPHA1-2 : angle 1.53422 ( 27) link_ALPHA1-3 : bond 0.01140 ( 21) link_ALPHA1-3 : angle 2.32910 ( 63) link_ALPHA1-6 : bond 0.01385 ( 15) link_ALPHA1-6 : angle 1.91378 ( 45) link_BETA1-4 : bond 0.01130 ( 90) link_BETA1-4 : angle 3.54956 ( 270) link_NAG-ASN : bond 0.00322 ( 84) link_NAG-ASN : angle 2.72006 ( 252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 162 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7662 (mtm) cc_final: 0.7317 (ttm) REVERT: A 30 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8570 (mm) REVERT: A 648 LEU cc_start: 0.8083 (mm) cc_final: 0.7838 (mt) REVERT: B 130 LEU cc_start: 0.8640 (mt) cc_final: 0.8050 (mt) REVERT: B 486 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7529 (p0) REVERT: B 1198 THR cc_start: 0.8220 (p) cc_final: 0.7819 (t) REVERT: C 763 LEU cc_start: 0.9271 (mt) cc_final: 0.9056 (mp) REVERT: C 1005 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.7062 (p-80) REVERT: C 1060 ASP cc_start: 0.7760 (t70) cc_final: 0.7437 (m-30) REVERT: C 1124 ASP cc_start: 0.8592 (m-30) cc_final: 0.8313 (m-30) outliers start: 76 outliers final: 64 residues processed: 218 average time/residue: 0.1821 time to fit residues: 67.4389 Evaluate side-chains 216 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 149 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 212 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 276 optimal weight: 0.4980 chunk 50 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 318 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 137 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 HIS ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.113987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086172 restraints weight = 59791.413| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.35 r_work: 0.3038 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 31185 Z= 0.140 Angle : 0.730 17.475 42912 Z= 0.329 Chirality : 0.049 0.421 5538 Planarity : 0.004 0.043 5064 Dihedral : 8.174 54.506 8361 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.36 % Favored : 95.18 % Rotamer: Outliers : 2.33 % Allowed : 9.76 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 3507 helix: 2.05 (0.20), residues: 708 sheet: 0.58 (0.17), residues: 942 loop : -1.18 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 925 TYR 0.013 0.001 TYR B 851 PHE 0.021 0.001 PHE C 124 TRP 0.008 0.001 TRP B 769 HIS 0.010 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00294 (30918) covalent geometry : angle 0.63592 (42159) SS BOND : bond 0.00562 ( 48) SS BOND : angle 1.75791 ( 96) hydrogen bonds : bond 0.05208 ( 1170) hydrogen bonds : angle 4.96753 ( 3312) link_ALPHA1-2 : bond 0.00709 ( 9) link_ALPHA1-2 : angle 1.52870 ( 27) link_ALPHA1-3 : bond 0.01132 ( 21) link_ALPHA1-3 : angle 2.20841 ( 63) link_ALPHA1-6 : bond 0.01403 ( 15) link_ALPHA1-6 : angle 1.94202 ( 45) link_BETA1-4 : bond 0.01126 ( 90) link_BETA1-4 : angle 3.47256 ( 270) link_NAG-ASN : bond 0.00304 ( 84) link_NAG-ASN : angle 2.63201 ( 252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 161 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7662 (mtm) cc_final: 0.7342 (ttm) REVERT: A 648 LEU cc_start: 0.8173 (mm) cc_final: 0.7922 (mt) REVERT: A 1108 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.6914 (t80) REVERT: B 130 LEU cc_start: 0.8592 (mt) cc_final: 0.8044 (mt) REVERT: B 486 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7459 (p0) REVERT: B 1138 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: C 65 TYR cc_start: 0.8469 (p90) cc_final: 0.8042 (p90) REVERT: C 274 TYR cc_start: 0.8222 (m-80) cc_final: 0.7919 (m-80) REVERT: C 611 TYR cc_start: 0.8541 (p90) cc_final: 0.8211 (p90) REVERT: C 763 LEU cc_start: 0.9273 (mt) cc_final: 0.9056 (mp) REVERT: C 1124 ASP cc_start: 0.8574 (m-30) cc_final: 0.8304 (m-30) outliers start: 72 outliers final: 60 residues processed: 213 average time/residue: 0.1849 time to fit residues: 65.7335 Evaluate side-chains 211 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 130 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.112738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.085034 restraints weight = 59910.841| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.28 r_work: 0.3020 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 31185 Z= 0.173 Angle : 0.742 17.466 42912 Z= 0.337 Chirality : 0.049 0.425 5538 Planarity : 0.004 0.043 5064 Dihedral : 8.017 53.720 8361 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.70 % Favored : 94.87 % Rotamer: Outliers : 2.39 % Allowed : 10.02 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3507 helix: 1.89 (0.20), residues: 726 sheet: 0.65 (0.17), residues: 927 loop : -1.26 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 925 TYR 0.011 0.001 TYR C 731 PHE 0.024 0.002 PHE A 563 TRP 0.011 0.001 TRP B 769 HIS 0.006 0.001 HIS C1005 Details of bonding type rmsd covalent geometry : bond 0.00382 (30918) covalent geometry : angle 0.64936 (42159) SS BOND : bond 0.00569 ( 48) SS BOND : angle 1.87570 ( 96) hydrogen bonds : bond 0.05469 ( 1170) hydrogen bonds : angle 5.00182 ( 3312) link_ALPHA1-2 : bond 0.00730 ( 9) link_ALPHA1-2 : angle 1.46215 ( 27) link_ALPHA1-3 : bond 0.01107 ( 21) link_ALPHA1-3 : angle 2.23045 ( 63) link_ALPHA1-6 : bond 0.01416 ( 15) link_ALPHA1-6 : angle 1.97998 ( 45) link_BETA1-4 : bond 0.01119 ( 90) link_BETA1-4 : angle 3.42726 ( 270) link_NAG-ASN : bond 0.00322 ( 84) link_NAG-ASN : angle 2.64469 ( 252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 145 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7747 (mtm) cc_final: 0.7443 (ttm) REVERT: A 647 SER cc_start: 0.7967 (m) cc_final: 0.7664 (p) REVERT: A 648 LEU cc_start: 0.8221 (mm) cc_final: 0.8019 (mt) REVERT: A 926 MET cc_start: 0.9002 (mmm) cc_final: 0.8673 (mmm) REVERT: A 1108 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7068 (t80) REVERT: B 130 LEU cc_start: 0.8549 (mt) cc_final: 0.7987 (mt) REVERT: B 486 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7545 (p0) REVERT: B 1138 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: C 65 TYR cc_start: 0.8477 (p90) cc_final: 0.8096 (p90) REVERT: C 611 TYR cc_start: 0.8478 (p90) cc_final: 0.8212 (p90) REVERT: C 1060 ASP cc_start: 0.7732 (t70) cc_final: 0.7452 (m-30) REVERT: C 1124 ASP cc_start: 0.8559 (m-30) cc_final: 0.8300 (m-30) outliers start: 74 outliers final: 66 residues processed: 203 average time/residue: 0.1770 time to fit residues: 61.4074 Evaluate side-chains 207 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 117 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 276 optimal weight: 0.8980 chunk 342 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS C1034 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.112729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085245 restraints weight = 59709.530| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.27 r_work: 0.3022 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 31185 Z= 0.158 Angle : 0.739 26.040 42912 Z= 0.335 Chirality : 0.049 0.422 5538 Planarity : 0.004 0.042 5064 Dihedral : 7.859 53.182 8361 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.45 % Favored : 95.15 % Rotamer: Outliers : 2.49 % Allowed : 10.02 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3507 helix: 1.90 (0.20), residues: 726 sheet: 0.63 (0.17), residues: 927 loop : -1.25 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 925 TYR 0.011 0.001 TYR B 851 PHE 0.020 0.001 PHE C 124 TRP 0.011 0.001 TRP B 769 HIS 0.005 0.001 HIS B1005 Details of bonding type rmsd covalent geometry : bond 0.00345 (30918) covalent geometry : angle 0.64773 (42159) SS BOND : bond 0.00651 ( 48) SS BOND : angle 2.03911 ( 96) hydrogen bonds : bond 0.05403 ( 1170) hydrogen bonds : angle 4.97650 ( 3312) link_ALPHA1-2 : bond 0.00732 ( 9) link_ALPHA1-2 : angle 1.45357 ( 27) link_ALPHA1-3 : bond 0.01093 ( 21) link_ALPHA1-3 : angle 2.14106 ( 63) link_ALPHA1-6 : bond 0.01447 ( 15) link_ALPHA1-6 : angle 1.98914 ( 45) link_BETA1-4 : bond 0.01120 ( 90) link_BETA1-4 : angle 3.38306 ( 270) link_NAG-ASN : bond 0.00304 ( 84) link_NAG-ASN : angle 2.61796 ( 252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 142 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7810 (mtm) cc_final: 0.7527 (ttm) REVERT: A 647 SER cc_start: 0.8136 (m) cc_final: 0.7854 (p) REVERT: A 1108 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7060 (t80) REVERT: B 130 LEU cc_start: 0.8545 (mt) cc_final: 0.7972 (mt) REVERT: B 486 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7512 (p0) REVERT: B 499 VAL cc_start: 0.8504 (t) cc_final: 0.8253 (t) REVERT: B 1138 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: C 65 TYR cc_start: 0.8451 (p90) cc_final: 0.8075 (p90) REVERT: C 1060 ASP cc_start: 0.7776 (t70) cc_final: 0.7450 (m-30) REVERT: C 1124 ASP cc_start: 0.8577 (m-30) cc_final: 0.8308 (m-30) outliers start: 77 outliers final: 67 residues processed: 204 average time/residue: 0.1772 time to fit residues: 62.0065 Evaluate side-chains 205 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 135 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 293 optimal weight: 0.9990 chunk 258 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 348 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 175 optimal weight: 0.0770 chunk 198 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.113120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085461 restraints weight = 59573.075| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.33 r_work: 0.3027 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 31185 Z= 0.141 Angle : 0.724 24.540 42912 Z= 0.327 Chirality : 0.049 0.425 5538 Planarity : 0.003 0.042 5064 Dihedral : 7.713 53.202 8361 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.45 % Favored : 95.15 % Rotamer: Outliers : 2.20 % Allowed : 10.51 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3507 helix: 1.91 (0.20), residues: 726 sheet: 0.70 (0.17), residues: 942 loop : -1.26 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 925 TYR 0.011 0.001 TYR B 851 PHE 0.020 0.001 PHE C 124 TRP 0.009 0.001 TRP B 769 HIS 0.005 0.001 HIS B1005 Details of bonding type rmsd covalent geometry : bond 0.00300 (30918) covalent geometry : angle 0.63264 (42159) SS BOND : bond 0.00586 ( 48) SS BOND : angle 2.07480 ( 96) hydrogen bonds : bond 0.05226 ( 1170) hydrogen bonds : angle 4.93250 ( 3312) link_ALPHA1-2 : bond 0.00712 ( 9) link_ALPHA1-2 : angle 1.46791 ( 27) link_ALPHA1-3 : bond 0.01089 ( 21) link_ALPHA1-3 : angle 2.05874 ( 63) link_ALPHA1-6 : bond 0.01483 ( 15) link_ALPHA1-6 : angle 1.99612 ( 45) link_BETA1-4 : bond 0.01119 ( 90) link_BETA1-4 : angle 3.34591 ( 270) link_NAG-ASN : bond 0.00295 ( 84) link_NAG-ASN : angle 2.57065 ( 252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 141 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7789 (mtm) cc_final: 0.7499 (ttm) REVERT: A 647 SER cc_start: 0.8031 (m) cc_final: 0.7792 (p) REVERT: A 1108 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.6993 (t80) REVERT: B 130 LEU cc_start: 0.8600 (mt) cc_final: 0.7988 (mt) REVERT: B 486 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7420 (p0) REVERT: B 499 VAL cc_start: 0.8499 (t) cc_final: 0.8245 (t) REVERT: B 1138 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: C 65 TYR cc_start: 0.8416 (p90) cc_final: 0.7985 (p90) REVERT: C 1060 ASP cc_start: 0.7827 (t70) cc_final: 0.7382 (m-30) REVERT: C 1124 ASP cc_start: 0.8591 (m-30) cc_final: 0.8311 (m-30) outliers start: 68 outliers final: 63 residues processed: 197 average time/residue: 0.1808 time to fit residues: 60.4476 Evaluate side-chains 197 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 131 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 HIS Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1108 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1208 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1208 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 HIS Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1108 PHE Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain C residue 1193 TYR Chi-restraints excluded: chain C residue 1208 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 329 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 323 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 GLN C1005 HIS C1168 ASN C1191 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.112776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085049 restraints weight = 59890.402| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.34 r_work: 0.3015 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 31185 Z= 0.153 Angle : 0.723 23.598 42912 Z= 0.327 Chirality : 0.049 0.442 5538 Planarity : 0.003 0.042 5064 Dihedral : 7.634 53.083 8361 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.65 % Favored : 95.04 % Rotamer: Outliers : 2.30 % Allowed : 10.67 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3507 helix: 1.90 (0.20), residues: 729 sheet: 0.63 (0.17), residues: 966 loop : -1.24 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 925 TYR 0.017 0.001 TYR A1214 PHE 0.020 0.001 PHE C 124 TRP 0.010 0.001 TRP B 769 HIS 0.010 0.001 HIS C1005 Details of bonding type rmsd covalent geometry : bond 0.00335 (30918) covalent geometry : angle 0.63220 (42159) SS BOND : bond 0.00599 ( 48) SS BOND : angle 2.08662 ( 96) hydrogen bonds : bond 0.05292 ( 1170) hydrogen bonds : angle 4.94282 ( 3312) link_ALPHA1-2 : bond 0.00717 ( 9) link_ALPHA1-2 : angle 1.43334 ( 27) link_ALPHA1-3 : bond 0.01072 ( 21) link_ALPHA1-3 : angle 2.05025 ( 63) link_ALPHA1-6 : bond 0.01469 ( 15) link_ALPHA1-6 : angle 1.99953 ( 45) link_BETA1-4 : bond 0.01118 ( 90) link_BETA1-4 : angle 3.32741 ( 270) link_NAG-ASN : bond 0.00292 ( 84) link_NAG-ASN : angle 2.58108 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6095.76 seconds wall clock time: 106 minutes 0.60 seconds (6360.60 seconds total)