Starting phenix.real_space_refine on Fri Mar 6 17:16:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jx7_9891/03_2026/6jx7_9891.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jx7_9891/03_2026/6jx7_9891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jx7_9891/03_2026/6jx7_9891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jx7_9891/03_2026/6jx7_9891.map" model { file = "/net/cci-nas-00/data/ceres_data/6jx7_9891/03_2026/6jx7_9891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jx7_9891/03_2026/6jx7_9891.cif" } resolution = 3.31 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= -0.008 sd= 0.895 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 156 5.16 5 C 20265 2.51 5 N 4938 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32115 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "B" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "C" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: 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: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: "J" 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: "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: 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: "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: 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: "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: 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "S" 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: "T" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "k" 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: "l" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: "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: 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: 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: "r" 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: "s" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: "t" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 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: "z" 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: "0" 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: "1" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "2" 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: "3" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: "4" 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: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.35, per 1000 atoms: 0.23 Number of scatterers: 32115 At special positions: 0 Unit cell: (180.96, 194.01, 180.09, 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 156 16.00 O 6756 8.00 N 4938 7.00 C 20265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 178 " distance=2.05 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 510 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 644 " distance=2.05 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 702 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 820 " - pdb=" SG CYS A 832 " distance=2.03 Simple disulfide: pdb=" SG CYS A 889 " - pdb=" SG CYS A 911 " distance=2.03 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS A1003 " - pdb=" SG CYS A1014 " distance=2.03 Simple disulfide: pdb=" SG CYS A1205 " - pdb=" SG CYS A1216 " distance=2.02 Simple disulfide: pdb=" SG CYS A1255 " - pdb=" SG CYS A1302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 178 " distance=2.05 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 644 " distance=2.05 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 702 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 820 " - pdb=" SG CYS B 832 " distance=2.03 Simple disulfide: pdb=" SG CYS B 889 " - pdb=" SG CYS B 911 " distance=2.03 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B1003 " - pdb=" SG CYS B1014 " distance=2.03 Simple disulfide: pdb=" SG CYS B1205 " - pdb=" SG CYS B1216 " distance=2.02 Simple disulfide: pdb=" SG CYS B1255 " - pdb=" SG CYS B1302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 178 " distance=2.05 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 510 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 644 " distance=2.05 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 702 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 820 " - pdb=" SG CYS C 832 " distance=2.03 Simple disulfide: pdb=" SG CYS C 889 " - pdb=" SG CYS C 911 " distance=2.03 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS C1003 " - pdb=" SG CYS C1014 " distance=2.03 Simple disulfide: pdb=" SG CYS C1205 " - pdb=" SG CYS C1216 " distance=2.02 Simple disulfide: pdb=" SG CYS C1255 " - pdb=" SG CYS C1302 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN I 4 " - " MAN I 5 " " MAN T 4 " - " MAN T 5 " " MAN a 4 " - " MAN a 5 " " MAN l 4 " - " MAN l 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA I 3 " - " MAN I 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA a 3 " - " MAN a 4 " " BMA k 3 " - " MAN k 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA 2 3 " - " MAN 2 5 " " BMA 3 3 " - " MAN 3 6 " " BMA I 3 " - " MAN I 6 " " MAN I 6 " - " MAN I 7 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 6 " " BMA a 3 " - " MAN a 6 " " MAN a 6 " - " MAN a 7 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 4 " " BMA k 3 " - " MAN k 5 " " BMA l 3 " - " MAN l 6 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 7 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " 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 L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 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 g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " 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 j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " 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 q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " 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 y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " BETA1-6 " NAG 1 1 " - " FUC 1 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 4 " " NAG j 1 " - " FUC j 4 " NAG-ASN " NAG 0 1 " - " ASN C 868 " " NAG 1 1 " - " ASN C 949 " " NAG 2 1 " - " ASN C1092 " " NAG 3 1 " - " ASN C1218 " " NAG 4 1 " - " ASN C1308 " " NAG A1508 " - " ASN A 260 " " NAG A1522 " - " ASN A 380 " " NAG A1523 " - " ASN A 464 " " NAG A1535 " - " ASN A 585 " " NAG A1536 " - " ASN A 590 " " NAG A1541 " - " ASN A 819 " " NAG A1568 " - " ASN A1257 " " NAG A1569 " - " ASN A1275 " " NAG A1572 " - " ASN A1325 " " NAG B1508 " - " ASN B 260 " " NAG B1522 " - " ASN B 380 " " NAG B1523 " - " ASN B 464 " " NAG B1535 " - " ASN B 585 " " NAG B1536 " - " ASN B 590 " " NAG B1541 " - " ASN B 819 " " NAG B1568 " - " ASN B1257 " " NAG B1569 " - " ASN B1275 " " NAG B1572 " - " ASN B1325 " " NAG C1509 " - " ASN C 260 " " NAG C1523 " - " ASN C 380 " " NAG C1524 " - " ASN C 464 " " NAG C1536 " - " ASN C 585 " " NAG C1537 " - " ASN C 590 " " NAG C1542 " - " ASN C 819 " " NAG C1569 " - " ASN C1257 " " NAG C1570 " - " ASN C1275 " " NAG C1573 " - " ASN C1325 " " NAG D 1 " - " ASN A 161 " " NAG E 1 " - " ASN A 246 " " NAG F 1 " - " ASN A 254 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 346 " " NAG I 1 " - " ASN A 357 " " NAG J 1 " - " ASN A 482 " " NAG K 1 " - " ASN A 491 " " NAG L 1 " - " ASN A 547 " " NAG M 1 " - " ASN A 774 " " NAG N 1 " - " ASN A 814 " " NAG O 1 " - " ASN A 841 " " NAG P 1 " - " ASN A 862 " " NAG Q 1 " - " ASN A 868 " " NAG R 1 " - " ASN A 949 " " NAG S 1 " - " ASN A1092 " " NAG T 1 " - " ASN A1218 " " NAG U 1 " - " ASN A1308 " " NAG V 1 " - " ASN B 161 " " NAG W 1 " - " ASN B 246 " " NAG X 1 " - " ASN B 254 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN B 346 " " NAG a 1 " - " ASN B 357 " " NAG b 1 " - " ASN B 482 " " NAG c 1 " - " ASN B 491 " " NAG d 1 " - " ASN B 547 " " NAG e 1 " - " ASN B 774 " " NAG f 1 " - " ASN B 814 " " NAG g 1 " - " ASN B 841 " " NAG h 1 " - " ASN B 862 " " NAG i 1 " - " ASN B 868 " " NAG j 1 " - " ASN B 949 " " NAG k 1 " - " ASN B1092 " " NAG l 1 " - " ASN B1218 " " NAG m 1 " - " ASN B1308 " " NAG n 1 " - " ASN C 161 " " NAG o 1 " - " ASN C 246 " " NAG p 1 " - " ASN C 254 " " NAG q 1 " - " ASN C 331 " " NAG r 1 " - " ASN C 346 " " NAG s 1 " - " ASN C 357 " " NAG t 1 " - " ASN C 482 " " NAG u 1 " - " ASN C 491 " " NAG v 1 " - " ASN C 547 " " NAG w 1 " - " ASN C 774 " " NAG x 1 " - " ASN C 814 " " NAG y 1 " - " ASN C 841 " " NAG z 1 " - " ASN C 862 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.2 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 54 sheets defined 22.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 removed outlier: 3.556A pdb=" N ILE A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 574' Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR A 892 " --> pdb=" O ASP A 888 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 893 " --> pdb=" O CYS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN A 902 " --> pdb=" O ARG A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 902' Processing helix chain 'A' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN A 906 " --> pdb=" O LEU A 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 903 through 906' Processing helix chain 'A' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 915 " --> pdb=" O CYS A 911 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 970 removed outlier: 4.194A pdb=" N SER A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 969 " --> pdb=" O GLY A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 1011 through 1019 removed outlier: 3.784A pdb=" N ASN A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY A1043 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.873A pdb=" N ASN A1066 " --> pdb=" O GLN A1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A1080 " --> pdb=" O GLN A1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A1098 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER A1116 " --> pdb=" O ASN A1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1117 " --> pdb=" O SER A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU A1132 " --> pdb=" O GLN A1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1140 No H-bonds generated for 'chain 'A' and resid 1138 through 1140' Processing helix chain 'A' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA A1164 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A1168 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A1169 " --> pdb=" O GLN A1165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A1187 " --> pdb=" O GLN A1183 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A1200 " --> pdb=" O GLN A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1294 No H-bonds generated for 'chain 'A' and resid 1292 through 1294' Processing helix chain 'A' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A1316 " --> pdb=" O THR A1312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1317 " --> pdb=" O THR A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR A1327 " --> pdb=" O ASP A1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A1329 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A1330 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.556A pdb=" N ILE B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU B 571 " --> pdb=" O GLY B 567 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 573 " --> pdb=" O PRO B 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 567 through 574' Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 893 " --> pdb=" O CYS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU B 901 " --> pdb=" O ASN B 897 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 902 " --> pdb=" O ARG B 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 897 through 902' Processing helix chain 'B' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN B 906 " --> pdb=" O LEU B 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 903 through 906' Processing helix chain 'B' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR B 913 " --> pdb=" O SER B 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 915 " --> pdb=" O CYS B 911 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 925 " --> pdb=" O GLY B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 970 removed outlier: 4.193A pdb=" N SER B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 969 " --> pdb=" O GLY B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 1011 through 1019 removed outlier: 3.783A pdb=" N ASN B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY B1043 " --> pdb=" O SER B1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B1045 " --> pdb=" O ILE B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1067 removed outlier: 3.872A pdb=" N ASN B1066 " --> pdb=" O GLN B1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B1067 " --> pdb=" O ALA B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B1080 " --> pdb=" O GLN B1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B1098 " --> pdb=" O THR B1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B1099 " --> pdb=" O LEU B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER B1116 " --> pdb=" O ASN B1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B1117 " --> pdb=" O SER B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU B1132 " --> pdb=" O GLN B1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B1133 " --> pdb=" O GLY B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1140 No H-bonds generated for 'chain 'B' and resid 1138 through 1140' Processing helix chain 'B' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE B1153 " --> pdb=" O SER B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA B1164 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B1168 " --> pdb=" O ALA B1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B1169 " --> pdb=" O GLN B1165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B1183 " --> pdb=" O ALA B1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B1187 " --> pdb=" O GLN B1183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B1200 " --> pdb=" O GLN B1196 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1294 No H-bonds generated for 'chain 'B' and resid 1292 through 1294' Processing helix chain 'B' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN B1315 " --> pdb=" O HIS B1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B1316 " --> pdb=" O THR B1312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B1317 " --> pdb=" O THR B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR B1327 " --> pdb=" O ASP B1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B1329 " --> pdb=" O ASN B1325 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B1330 " --> pdb=" O LYS B1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B1331 " --> pdb=" O THR B1327 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 513 removed outlier: 3.555A pdb=" N ILE C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 573 " --> pdb=" O PRO C 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 574' Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR C 892 " --> pdb=" O ASP C 888 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 893 " --> pdb=" O CYS C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU C 901 " --> pdb=" O ASN C 897 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 897 through 902' Processing helix chain 'C' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN C 906 " --> pdb=" O LEU C 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 903 through 906' Processing helix chain 'C' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR C 913 " --> pdb=" O SER C 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 914 " --> pdb=" O ALA C 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 915 " --> pdb=" O CYS C 911 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY C 921 " --> pdb=" O SER C 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 970 removed outlier: 4.194A pdb=" N SER C 968 " --> pdb=" O ASP C 964 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 969 " --> pdb=" O GLY C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 985 Processing helix chain 'C' and resid 1011 through 1019 removed outlier: 3.783A pdb=" N ASN C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY C1043 " --> pdb=" O SER C1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C1045 " --> pdb=" O ILE C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1067 removed outlier: 3.873A pdb=" N ASN C1066 " --> pdb=" O GLN C1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C1067 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN C1079 " --> pdb=" O LEU C1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C1080 " --> pdb=" O GLN C1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C1098 " --> pdb=" O THR C1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C1099 " --> pdb=" O LEU C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER C1116 " --> pdb=" O ASN C1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C1117 " --> pdb=" O SER C1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU C1132 " --> pdb=" O GLN C1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER C1133 " --> pdb=" O GLY C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1140 No H-bonds generated for 'chain 'C' and resid 1138 through 1140' Processing helix chain 'C' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE C1153 " --> pdb=" O SER C1149 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA C1164 " --> pdb=" O VAL C1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN C1165 " --> pdb=" O GLU C1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C1168 " --> pdb=" O ALA C1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C1169 " --> pdb=" O GLN C1165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C1183 " --> pdb=" O ALA C1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C1187 " --> pdb=" O GLN C1183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C1200 " --> pdb=" O GLN C1196 " (cutoff:3.500A) Processing helix chain 'C' and resid 1292 through 1294 No H-bonds generated for 'chain 'C' and resid 1292 through 1294' Processing helix chain 'C' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN C1315 " --> pdb=" O HIS C1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C1316 " --> pdb=" O THR C1312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C1317 " --> pdb=" O THR C1313 " (cutoff:3.500A) Processing helix chain 'C' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR C1327 " --> pdb=" O ASP C1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C1329 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP C1330 " --> pdb=" O LYS C1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C1331 " --> pdb=" O THR C1327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA A 227 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 107 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 124 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 151 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 180 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN A 199 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 324 removed outlier: 3.785A pdb=" N VAL A 312 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 482 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 320 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR A 480 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A 322 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 478 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE A 447 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 324 removed outlier: 3.785A pdb=" N VAL A 312 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 482 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 320 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR A 480 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A 322 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 478 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP A 485 " --> pdb=" O TYR A 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR A 500 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 487 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU A 498 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP A 489 " --> pdb=" O THR A 496 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA A 334 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 383 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 removed outlier: 5.796A pdb=" N TYR A 413 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 431 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N CYS A 415 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 427 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE A 770 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 809 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 771 " --> pdb=" O TYR A 807 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 807 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.503A pdb=" N GLY A 712 " --> pdb=" O TYR A 705 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU A 737 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 591 removed outlier: 3.553A pdb=" N HIS A 578 " --> pdb=" O HIS A 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 552 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 554 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU A 601 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 623 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 659 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 621 " --> pdb=" O VAL A 659 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU A 601 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 642 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 678 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 829 through 831 Processing sheet with id=AB4, first strand: chain 'A' and resid 843 through 844 removed outlier: 6.089A pdb=" N THR A 843 " --> pdb=" O VAL C 935 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 862 through 864 Processing sheet with id=AB6, first strand: chain 'A' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY A1232 " --> pdb=" O SER A1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER A1228 " --> pdb=" O GLY A1232 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A1234 " --> pdb=" O VAL A1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1226 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A1236 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A1224 " --> pdb=" O PHE A1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A1238 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AB8, first strand: chain 'A' and resid 934 through 935 Processing sheet with id=AB9, first strand: chain 'A' and resid 1296 through 1299 Processing sheet with id=AC1, first strand: chain 'A' and resid 1269 through 1273 Processing sheet with id=AC2, first strand: chain 'B' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA B 227 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 107 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 124 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 151 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 180 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN B 199 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL B 312 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 482 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 320 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 480 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS B 322 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 478 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 447 " --> pdb=" O TYR B 454 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL B 312 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 482 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 320 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 480 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS B 322 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 478 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP B 485 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR B 500 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET B 487 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU B 498 " --> pdb=" O MET B 487 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP B 489 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA B 334 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 383 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 386 through 387 removed outlier: 5.796A pdb=" N TYR B 413 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B 431 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS B 415 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 427 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE B 770 " --> pdb=" O GLN B 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 809 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 771 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 807 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 534 through 537 removed outlier: 3.504A pdb=" N GLY B 712 " --> pdb=" O TYR B 705 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU B 737 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 588 through 591 removed outlier: 3.552A pdb=" N HIS B 578 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 552 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 554 " --> pdb=" O THR B 608 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU B 601 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 623 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 659 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 621 " --> pdb=" O VAL B 659 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU B 601 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 642 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 678 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 829 through 831 Processing sheet with id=AD5, first strand: chain 'B' and resid 862 through 864 Processing sheet with id=AD6, first strand: chain 'B' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY B1232 " --> pdb=" O SER B1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER B1228 " --> pdb=" O GLY B1232 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B1234 " --> pdb=" O VAL B1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B1226 " --> pdb=" O LEU B1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE B1236 " --> pdb=" O SER B1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B1224 " --> pdb=" O PHE B1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR B1238 " --> pdb=" O LEU B1222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 885 through 887 Processing sheet with id=AD8, first strand: chain 'B' and resid 934 through 935 Processing sheet with id=AD9, first strand: chain 'B' and resid 1296 through 1299 Processing sheet with id=AE1, first strand: chain 'B' and resid 1269 through 1273 Processing sheet with id=AE2, first strand: chain 'C' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA C 227 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 107 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 124 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 151 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 180 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN C 199 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL C 312 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 482 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 320 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR C 480 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS C 322 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 478 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 447 " --> pdb=" O TYR C 454 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL C 312 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 482 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 320 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR C 480 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS C 322 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 478 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP C 485 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR C 500 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET C 487 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 498 " --> pdb=" O MET C 487 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP C 489 " --> pdb=" O THR C 496 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA C 334 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 383 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 386 through 387 removed outlier: 5.797A pdb=" N TYR C 413 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 431 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS C 415 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 427 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE C 770 " --> pdb=" O GLN C 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 809 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 771 " --> pdb=" O TYR C 807 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 807 " --> pdb=" O THR C 771 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 534 through 537 removed outlier: 3.503A pdb=" N GLY C 712 " --> pdb=" O TYR C 705 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU C 737 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 588 through 591 removed outlier: 3.553A pdb=" N HIS C 578 " --> pdb=" O HIS C 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 552 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 554 " --> pdb=" O THR C 608 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU C 601 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 623 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 659 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 621 " --> pdb=" O VAL C 659 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU C 601 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 642 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 678 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 829 through 831 Processing sheet with id=AF5, first strand: chain 'C' and resid 862 through 864 Processing sheet with id=AF6, first strand: chain 'C' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY C1232 " --> pdb=" O SER C1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER C1228 " --> pdb=" O GLY C1232 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C1234 " --> pdb=" O VAL C1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL C1226 " --> pdb=" O LEU C1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE C1236 " --> pdb=" O SER C1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER C1224 " --> pdb=" O PHE C1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C1238 " --> pdb=" O LEU C1222 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 885 through 887 Processing sheet with id=AF8, first strand: chain 'C' and resid 1296 through 1299 Processing sheet with id=AF9, first strand: chain 'C' and resid 1269 through 1273 875 hydrogen bonds defined for protein. 2427 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: 8.48 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9685 1.34 - 1.47: 9241 1.47 - 1.60: 13642 1.60 - 1.73: 0 1.73 - 1.86: 222 Bond restraints: 32790 Sorted by residual: bond pdb=" C3 NAG 3 1 " pdb=" C4 NAG 3 1 " ideal model delta sigma weight residual 1.524 1.455 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C3 NAG l 1 " pdb=" C4 NAG l 1 " ideal model delta sigma weight residual 1.524 1.456 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C3 NAG T 1 " pdb=" C4 NAG T 1 " ideal model delta sigma weight residual 1.524 1.456 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" N LYS B 85 " pdb=" CA LYS B 85 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.13e+00 bond pdb=" N TYR B 253 " pdb=" CA TYR B 253 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 9.08e+00 ... (remaining 32785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 43580 3.35 - 6.71: 946 6.71 - 10.06: 127 10.06 - 13.42: 35 13.42 - 16.77: 15 Bond angle restraints: 44703 Sorted by residual: angle pdb=" C GLN C 775 " pdb=" N THR C 776 " pdb=" CA THR C 776 " ideal model delta sigma weight residual 120.87 110.35 10.52 1.42e+00 4.96e-01 5.49e+01 angle pdb=" C GLN A 775 " pdb=" N THR A 776 " pdb=" CA THR A 776 " ideal model delta sigma weight residual 120.87 110.35 10.52 1.42e+00 4.96e-01 5.48e+01 angle pdb=" C GLN B 775 " pdb=" N THR B 776 " pdb=" CA THR B 776 " ideal model delta sigma weight residual 120.87 110.37 10.50 1.42e+00 4.96e-01 5.47e+01 angle pdb=" C ASN A 774 " pdb=" CA ASN A 774 " pdb=" CB ASN A 774 " ideal model delta sigma weight residual 110.42 95.72 14.70 1.99e+00 2.53e-01 5.45e+01 angle pdb=" C ASN B 774 " pdb=" CA ASN B 774 " pdb=" CB ASN B 774 " ideal model delta sigma weight residual 110.42 95.73 14.69 1.99e+00 2.53e-01 5.45e+01 ... (remaining 44698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 20360 23.84 - 47.67: 1138 47.67 - 71.51: 237 71.51 - 95.34: 198 95.34 - 119.18: 105 Dihedral angle restraints: 22038 sinusoidal: 11079 harmonic: 10959 Sorted by residual: dihedral pdb=" C ASN A 774 " pdb=" N ASN A 774 " pdb=" CA ASN A 774 " pdb=" CB ASN A 774 " ideal model delta harmonic sigma weight residual -122.60 -99.83 -22.77 0 2.50e+00 1.60e-01 8.30e+01 dihedral pdb=" C ASN C 774 " pdb=" N ASN C 774 " pdb=" CA ASN C 774 " pdb=" CB ASN C 774 " ideal model delta harmonic sigma weight residual -122.60 -99.84 -22.76 0 2.50e+00 1.60e-01 8.29e+01 dihedral pdb=" C ASN B 774 " pdb=" N ASN B 774 " pdb=" CA ASN B 774 " pdb=" CB ASN B 774 " ideal model delta harmonic sigma weight residual -122.60 -99.84 -22.76 0 2.50e+00 1.60e-01 8.29e+01 ... (remaining 22035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 5703 0.310 - 0.619: 56 0.619 - 0.929: 13 0.929 - 1.239: 3 1.239 - 1.548: 3 Chirality restraints: 5778 Sorted by residual: chirality pdb=" C1 MAN T 6 " pdb=" O6 BMA T 3 " pdb=" C2 MAN T 6 " pdb=" O5 MAN T 6 " both_signs ideal model delta sigma weight residual False 2.40 0.85 1.55 2.00e-02 2.50e+03 5.99e+03 chirality pdb=" C1 MAN l 6 " pdb=" O6 BMA l 3 " pdb=" C2 MAN l 6 " pdb=" O5 MAN l 6 " both_signs ideal model delta sigma weight residual False 2.40 0.85 1.55 2.00e-02 2.50e+03 5.99e+03 chirality pdb=" C1 MAN 3 6 " pdb=" O6 BMA 3 3 " pdb=" C2 MAN 3 6 " pdb=" O5 MAN 3 6 " both_signs ideal model delta sigma weight residual False 2.40 0.86 1.54 2.00e-02 2.50e+03 5.95e+03 ... (remaining 5775 not shown) Planarity restraints: 5457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG M 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG e 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG e 2 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG e 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG e 2 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG w 2 " 0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG w 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG w 2 " 0.161 2.00e-02 2.50e+03 pdb=" N2 NAG w 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG w 2 " 0.104 2.00e-02 2.50e+03 ... (remaining 5454 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 847 2.65 - 3.21: 29237 3.21 - 3.78: 49006 3.78 - 4.34: 62037 4.34 - 4.90: 100985 Nonbonded interactions: 242112 Sorted by model distance: nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.092 3.040 nonbonded pdb=" O3 NAG w 1 " pdb=" O7 NAG w 1 " model vdw 2.092 3.040 nonbonded pdb=" O3 NAG e 1 " pdb=" O7 NAG e 1 " model vdw 2.092 3.040 nonbonded pdb=" OD1 ASN B 254 " pdb=" OG1 THR B 256 " model vdw 2.172 3.040 nonbonded pdb=" OD1 ASN C 254 " pdb=" OG1 THR C 256 " model vdw 2.173 3.040 ... (remaining 242107 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: 0.06 Found NCS groups: ncs_group { reference = chain '0' selection = chain '4' selection = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = (chain '1' and resid 1 through 3) selection = (chain 'J' and resid 1 through 3) selection = (chain 'L' and resid 1 through 3) selection = (chain 'O' and resid 1 through 3) selection = (chain 'P' and resid 1 through 3) selection = (chain 'R' and resid 1 through 3) selection = (chain 'b' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) selection = (chain 'g' and resid 1 through 3) selection = (chain 'h' and resid 1 through 3) selection = (chain 'j' and resid 1 through 3) selection = (chain 't' and resid 1 through 3) selection = (chain 'v' and resid 1 through 3) selection = (chain 'y' and resid 1 through 3) selection = (chain 'z' and resid 1 through 3) } ncs_group { reference = chain '2' selection = chain 'S' selection = chain 'k' } ncs_group { reference = chain '3' selection = chain 'I' selection = chain 'T' selection = chain 'a' selection = chain 'l' selection = chain 's' } ncs_group { reference = (chain 'A' and (resid 62 through 1337 or resid 1522 through 1523 or resid 1536 t \ hrough 1572)) selection = (chain 'B' and (resid 62 through 1337 or resid 1522 through 1523 or resid 1536 t \ hrough 1572)) selection = (chain 'C' and (resid 62 through 1337 or resid 1509 through 1523 or resid 1536 t \ hrough 1570)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'o' selection = chain 'q' selection = chain 'r' } 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: 7.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.420 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.160 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 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 : 0.011 0.574 33048 Z= 0.722 Angle : 1.427 25.948 45426 Z= 0.642 Chirality : 0.098 1.548 5778 Planarity : 0.020 0.299 5376 Dihedral : 19.253 119.180 14880 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.32 % Favored : 87.36 % Rotamer: Outliers : 0.82 % Allowed : 9.10 % Favored : 90.07 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.20 (0.10), residues: 3717 helix: -3.94 (0.08), residues: 729 sheet: -2.68 (0.16), residues: 906 loop : -3.75 (0.10), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1283 TYR 0.035 0.002 TYR B 826 PHE 0.016 0.002 PHE C 629 TRP 0.010 0.002 TRP A 200 HIS 0.010 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00967 (32790) covalent geometry : angle 1.26308 (44703) SS BOND : bond 0.00733 ( 42) SS BOND : angle 2.13244 ( 84) hydrogen bonds : bond 0.30914 ( 851) hydrogen bonds : angle 10.82716 ( 2427) Misc. bond : bond 0.57358 ( 3) link_ALPHA1-2 : bond 0.01071 ( 6) link_ALPHA1-2 : angle 4.81943 ( 18) link_ALPHA1-3 : bond 0.00719 ( 12) link_ALPHA1-3 : angle 5.08004 ( 36) link_ALPHA1-6 : bond 0.00636 ( 24) link_ALPHA1-6 : angle 4.08315 ( 72) link_BETA1-4 : bond 0.01090 ( 87) link_BETA1-4 : angle 5.16963 ( 261) link_BETA1-6 : bond 0.00188 ( 3) link_BETA1-6 : angle 2.02275 ( 9) link_NAG-ASN : bond 0.02247 ( 81) link_NAG-ASN : angle 6.81487 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 782 time to evaluate : 1.067 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: 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 158 ASN cc_start: 0.2529 (OUTLIER) cc_final: 0.2141 (m-40) REVERT: A 309 GLN cc_start: 0.8763 (mt0) cc_final: 0.8439 (tt0) REVERT: A 341 ASP cc_start: 0.8068 (p0) cc_final: 0.6875 (p0) REVERT: A 444 ASP cc_start: 0.7505 (p0) cc_final: 0.7256 (p0) REVERT: A 461 LYS cc_start: 0.8293 (tttt) cc_final: 0.7940 (tmtt) REVERT: A 477 THR cc_start: 0.7415 (p) cc_final: 0.7141 (p) REVERT: A 592 THR cc_start: 0.8005 (p) cc_final: 0.7754 (t) REVERT: A 597 GLN cc_start: 0.8432 (mt0) cc_final: 0.8203 (mt0) REVERT: A 611 GLN cc_start: 0.8094 (pt0) cc_final: 0.7736 (pt0) REVERT: A 641 GLU cc_start: 0.7851 (tp30) cc_final: 0.7553 (tp30) REVERT: A 680 MET cc_start: 0.7596 (mmt) cc_final: 0.7081 (mtp) REVERT: A 701 GLU cc_start: 0.7856 (pt0) cc_final: 0.7289 (pm20) REVERT: A 702 CYS cc_start: 0.6646 (m) cc_final: 0.6373 (m) REVERT: A 803 MET cc_start: 0.8738 (mmm) cc_final: 0.8416 (mmm) REVERT: A 812 TRP cc_start: 0.7001 (p-90) cc_final: 0.6465 (p-90) REVERT: A 824 ILE cc_start: 0.8488 (mm) cc_final: 0.8212 (tp) REVERT: A 898 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7527 (ttp80) REVERT: A 928 MET cc_start: 0.7900 (tpp) cc_final: 0.7423 (tpp) REVERT: A 973 ARG cc_start: 0.6400 (mtt180) cc_final: 0.6131 (mtp85) REVERT: A 1059 MET cc_start: 0.8265 (ttm) cc_final: 0.7888 (ttm) REVERT: A 1067 TYR cc_start: 0.8552 (m-80) cc_final: 0.8340 (m-10) REVERT: A 1076 GLN cc_start: 0.7390 (mm-40) cc_final: 0.6768 (tp40) REVERT: A 1141 LYS cc_start: 0.8210 (mttt) cc_final: 0.7915 (mtpt) REVERT: A 1152 GLU cc_start: 0.7675 (tp30) cc_final: 0.7269 (tp30) REVERT: A 1155 ASN cc_start: 0.8715 (m-40) cc_final: 0.8213 (m-40) REVERT: A 1159 LYS cc_start: 0.8380 (tttt) cc_final: 0.8097 (ttmt) REVERT: A 1260 TYR cc_start: 0.7422 (m-80) cc_final: 0.7068 (m-10) REVERT: A 1279 MET cc_start: 0.7451 (mmm) cc_final: 0.7236 (mmt) REVERT: A 1315 GLN cc_start: 0.7542 (mp10) cc_final: 0.7175 (tm-30) REVERT: A 1331 MET cc_start: 0.6853 (mpp) cc_final: 0.6578 (tmm) REVERT: B 158 ASN cc_start: 0.2839 (OUTLIER) cc_final: 0.2425 (m-40) REVERT: B 592 THR cc_start: 0.8093 (p) cc_final: 0.7829 (t) REVERT: B 611 GLN cc_start: 0.8083 (pt0) cc_final: 0.7700 (pt0) REVERT: B 633 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7982 (mm-40) REVERT: B 680 MET cc_start: 0.7803 (mmt) cc_final: 0.7285 (mtp) REVERT: B 701 GLU cc_start: 0.7783 (pt0) cc_final: 0.7215 (pm20) REVERT: B 702 CYS cc_start: 0.6816 (m) cc_final: 0.6448 (m) REVERT: B 803 MET cc_start: 0.8706 (mmm) cc_final: 0.8296 (mmm) REVERT: B 824 ILE cc_start: 0.8461 (mm) cc_final: 0.8086 (tp) REVERT: B 883 LYS cc_start: 0.8646 (mttm) cc_final: 0.8342 (mttm) REVERT: B 928 MET cc_start: 0.7869 (tpp) cc_final: 0.7572 (tpp) REVERT: B 973 ARG cc_start: 0.6383 (mtt180) cc_final: 0.6060 (mtp85) REVERT: B 1011 ASP cc_start: 0.6372 (t0) cc_final: 0.6050 (t0) REVERT: B 1059 MET cc_start: 0.8184 (ttm) cc_final: 0.7757 (ttm) REVERT: B 1076 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6631 (tp-100) REVERT: B 1155 ASN cc_start: 0.8718 (m-40) cc_final: 0.8148 (m-40) REVERT: B 1159 LYS cc_start: 0.8310 (tttt) cc_final: 0.8108 (mttt) REVERT: B 1161 GLU cc_start: 0.6639 (pm20) cc_final: 0.6404 (pm20) REVERT: B 1283 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7366 (mtm-85) REVERT: B 1307 LEU cc_start: 0.8270 (tp) cc_final: 0.8051 (tt) REVERT: B 1315 GLN cc_start: 0.7678 (mp10) cc_final: 0.7205 (tm-30) REVERT: B 1319 ILE cc_start: 0.7309 (tt) cc_final: 0.7094 (pt) REVERT: C 158 ASN cc_start: 0.2821 (OUTLIER) cc_final: 0.2430 (m110) REVERT: C 364 TYR cc_start: 0.8266 (m-10) cc_final: 0.7895 (m-80) REVERT: C 444 ASP cc_start: 0.7428 (p0) cc_final: 0.7159 (p0) REVERT: C 455 PHE cc_start: 0.8290 (p90) cc_final: 0.8079 (p90) REVERT: C 571 LEU cc_start: 0.7110 (mp) cc_final: 0.6868 (mp) REVERT: C 592 THR cc_start: 0.8001 (p) cc_final: 0.7757 (t) REVERT: C 611 GLN cc_start: 0.8069 (pt0) cc_final: 0.7689 (pt0) REVERT: C 623 GLN cc_start: 0.7844 (mt0) cc_final: 0.7420 (mt0) REVERT: C 641 GLU cc_start: 0.7724 (tp30) cc_final: 0.7497 (tp30) REVERT: C 668 PHE cc_start: 0.8064 (m-10) cc_final: 0.7851 (m-10) REVERT: C 680 MET cc_start: 0.7682 (mmt) cc_final: 0.7092 (mtp) REVERT: C 701 GLU cc_start: 0.7746 (pt0) cc_final: 0.7253 (pm20) REVERT: C 702 CYS cc_start: 0.6689 (m) cc_final: 0.6211 (m) REVERT: C 803 MET cc_start: 0.8612 (mmm) cc_final: 0.8118 (mmm) REVERT: C 883 LYS cc_start: 0.8569 (mttm) cc_final: 0.8248 (mttm) REVERT: C 898 ARG cc_start: 0.7739 (ttp80) cc_final: 0.6963 (tpp80) REVERT: C 902 ASN cc_start: 0.8529 (m-40) cc_final: 0.8312 (m-40) REVERT: C 928 MET cc_start: 0.7867 (tpp) cc_final: 0.7431 (tpp) REVERT: C 973 ARG cc_start: 0.6274 (mtt180) cc_final: 0.6033 (mtp85) REVERT: C 1059 MET cc_start: 0.8118 (ttm) cc_final: 0.7787 (ttm) REVERT: C 1076 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6626 (tp40) REVERT: C 1084 ASN cc_start: 0.8592 (m-40) cc_final: 0.8375 (m-40) REVERT: C 1141 LYS cc_start: 0.8132 (mttt) cc_final: 0.7908 (mtmt) REVERT: C 1155 ASN cc_start: 0.8664 (m-40) cc_final: 0.7418 (t0) REVERT: C 1159 LYS cc_start: 0.8312 (tttt) cc_final: 0.7922 (tttt) REVERT: C 1283 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7049 (mtm-85) REVERT: C 1293 MET cc_start: 0.8211 (pmm) cc_final: 0.7989 (tpp) REVERT: C 1307 LEU cc_start: 0.8390 (tp) cc_final: 0.8176 (tt) REVERT: C 1315 GLN cc_start: 0.7586 (mp10) cc_final: 0.7178 (tm-30) REVERT: C 1331 MET cc_start: 0.6848 (mpp) cc_final: 0.6422 (tpt) outliers start: 27 outliers final: 9 residues processed: 807 average time/residue: 0.1789 time to fit residues: 236.5164 Evaluate side-chains 558 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 546 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 595 CYS Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 595 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 93 ASN A 95 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 177 GLN A 220 ASN A 418 ASN A 611 GLN A 623 GLN A 660 HIS A 667 GLN A1122 GLN A1126 ASN A1311 HIS B 83 ASN B 93 ASN B 95 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 177 GLN B 220 ASN B 418 ASN B 450 ASN B 551 HIS B 611 GLN B 623 GLN B 660 HIS B 667 GLN B1122 GLN B1126 ASN ** B1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 83 ASN C 93 ASN C 95 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 177 GLN C 220 ASN C 372 GLN C 611 GLN C 623 GLN C 624 ASN C 660 HIS C 667 GLN C 758 GLN C 986 ASN C1122 GLN C1126 ASN ** C1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118036 restraints weight = 51269.021| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 4.00 r_work: 0.3315 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33048 Z= 0.185 Angle : 0.948 14.737 45426 Z= 0.426 Chirality : 0.054 0.472 5778 Planarity : 0.004 0.054 5376 Dihedral : 15.537 99.772 8457 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.43 % Favored : 88.49 % Rotamer: Outliers : 2.69 % Allowed : 14.39 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.12), residues: 3717 helix: -1.41 (0.16), residues: 759 sheet: -2.38 (0.16), residues: 873 loop : -3.45 (0.11), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1283 TYR 0.025 0.001 TYR A 204 PHE 0.027 0.001 PHE C 428 TRP 0.021 0.001 TRP B 812 HIS 0.006 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00378 (32790) covalent geometry : angle 0.84200 (44703) SS BOND : bond 0.00555 ( 42) SS BOND : angle 1.67770 ( 84) hydrogen bonds : bond 0.05675 ( 851) hydrogen bonds : angle 6.40932 ( 2427) Misc. bond : bond 0.00257 ( 3) link_ALPHA1-2 : bond 0.02573 ( 6) link_ALPHA1-2 : angle 4.14511 ( 18) link_ALPHA1-3 : bond 0.01164 ( 12) link_ALPHA1-3 : angle 3.69649 ( 36) link_ALPHA1-6 : bond 0.01788 ( 24) link_ALPHA1-6 : angle 2.58663 ( 72) link_BETA1-4 : bond 0.01299 ( 87) link_BETA1-4 : angle 3.42639 ( 261) link_BETA1-6 : bond 0.00312 ( 3) link_BETA1-6 : angle 1.44188 ( 9) link_NAG-ASN : bond 0.00714 ( 81) link_NAG-ASN : angle 4.33473 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 665 time to evaluate : 0.992 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.6873 (m-80) cc_final: 0.6671 (m-80) REVERT: A 461 LYS cc_start: 0.8903 (tttt) cc_final: 0.8594 (tttm) REVERT: A 471 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7198 (tp30) REVERT: A 516 GLU cc_start: 0.8243 (tp30) cc_final: 0.8039 (tp30) REVERT: A 592 THR cc_start: 0.8187 (p) cc_final: 0.7919 (t) REVERT: A 595 CYS cc_start: 0.6902 (t) cc_final: 0.6680 (t) REVERT: A 641 GLU cc_start: 0.8446 (tp30) cc_final: 0.8020 (tp30) REVERT: A 680 MET cc_start: 0.8144 (mmt) cc_final: 0.7567 (mtp) REVERT: A 702 CYS cc_start: 0.8033 (m) cc_final: 0.7787 (m) REVERT: A 775 GLN cc_start: 0.8592 (pm20) cc_final: 0.8055 (pm20) REVERT: A 803 MET cc_start: 0.8986 (mmm) cc_final: 0.8553 (mmm) REVERT: A 812 TRP cc_start: 0.7317 (p-90) cc_final: 0.7110 (p-90) REVERT: A 824 ILE cc_start: 0.8786 (mm) cc_final: 0.8527 (tp) REVERT: A 829 PHE cc_start: 0.7477 (m-80) cc_final: 0.6877 (p90) REVERT: A 883 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8884 (mmtp) REVERT: A 898 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7560 (tpp80) REVERT: A 973 ARG cc_start: 0.7039 (mtt180) cc_final: 0.6689 (mtp85) REVERT: A 1059 MET cc_start: 0.8731 (ttm) cc_final: 0.8495 (ttm) REVERT: A 1076 GLN cc_start: 0.7421 (mm-40) cc_final: 0.6893 (tp40) REVERT: A 1141 LYS cc_start: 0.8851 (mttt) cc_final: 0.8483 (mtpt) REVERT: A 1152 GLU cc_start: 0.8394 (tp30) cc_final: 0.7862 (tp30) REVERT: A 1155 ASN cc_start: 0.8868 (m-40) cc_final: 0.7776 (t0) REVERT: A 1260 TYR cc_start: 0.7800 (m-80) cc_final: 0.7575 (m-10) REVERT: A 1279 MET cc_start: 0.8217 (mmm) cc_final: 0.8017 (mmt) REVERT: A 1315 GLN cc_start: 0.7564 (mp10) cc_final: 0.7238 (tm-30) REVERT: B 286 ASP cc_start: 0.8670 (t0) cc_final: 0.8415 (t0) REVERT: B 455 PHE cc_start: 0.8458 (p90) cc_final: 0.8138 (p90) REVERT: B 592 THR cc_start: 0.8301 (p) cc_final: 0.8011 (t) REVERT: B 595 CYS cc_start: 0.6882 (t) cc_final: 0.6601 (t) REVERT: B 633 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8227 (mm-40) REVERT: B 641 GLU cc_start: 0.8365 (tp30) cc_final: 0.7573 (tp30) REVERT: B 680 MET cc_start: 0.8261 (mmt) cc_final: 0.7637 (mtp) REVERT: B 701 GLU cc_start: 0.8227 (pt0) cc_final: 0.7807 (pm20) REVERT: B 702 CYS cc_start: 0.8159 (m) cc_final: 0.7840 (m) REVERT: B 775 GLN cc_start: 0.8585 (pm20) cc_final: 0.8034 (pm20) REVERT: B 803 MET cc_start: 0.9016 (mmm) cc_final: 0.8802 (mmp) REVERT: B 824 ILE cc_start: 0.8807 (mm) cc_final: 0.8421 (tp) REVERT: B 829 PHE cc_start: 0.7394 (m-80) cc_final: 0.6925 (p90) REVERT: B 883 LYS cc_start: 0.9068 (mttm) cc_final: 0.8859 (mmtp) REVERT: B 898 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7458 (tpp80) REVERT: B 928 MET cc_start: 0.8488 (tpp) cc_final: 0.7991 (tpp) REVERT: B 973 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6710 (mtp85) REVERT: B 1029 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: B 1059 MET cc_start: 0.8607 (ttm) cc_final: 0.8309 (ttm) REVERT: B 1066 ASN cc_start: 0.8945 (m-40) cc_final: 0.8593 (m110) REVERT: B 1076 GLN cc_start: 0.7409 (mm-40) cc_final: 0.6810 (tp40) REVERT: B 1155 ASN cc_start: 0.8836 (m-40) cc_final: 0.7928 (t0) REVERT: B 1161 GLU cc_start: 0.7412 (pm20) cc_final: 0.7058 (pm20) REVERT: B 1283 ARG cc_start: 0.8930 (mtt90) cc_final: 0.7977 (mtm180) REVERT: B 1307 LEU cc_start: 0.8497 (tp) cc_final: 0.8243 (tt) REVERT: B 1321 TYR cc_start: 0.8259 (t80) cc_final: 0.7934 (t80) REVERT: C 158 ASN cc_start: 0.2363 (OUTLIER) cc_final: 0.2116 (m-40) REVERT: C 198 PHE cc_start: 0.8645 (m-10) cc_final: 0.8340 (m-10) REVERT: C 286 ASP cc_start: 0.8580 (t0) cc_final: 0.8326 (t0) REVERT: C 455 PHE cc_start: 0.8397 (p90) cc_final: 0.8148 (p90) REVERT: C 571 LEU cc_start: 0.7646 (mp) cc_final: 0.7420 (mp) REVERT: C 592 THR cc_start: 0.8181 (p) cc_final: 0.7928 (t) REVERT: C 595 CYS cc_start: 0.7091 (t) cc_final: 0.6831 (t) REVERT: C 623 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: C 702 CYS cc_start: 0.8049 (m) cc_final: 0.7646 (m) REVERT: C 775 GLN cc_start: 0.8539 (pm20) cc_final: 0.8031 (pm20) REVERT: C 803 MET cc_start: 0.9021 (mmm) cc_final: 0.8463 (mmm) REVERT: C 805 GLN cc_start: 0.8670 (mt0) cc_final: 0.8181 (mp10) REVERT: C 829 PHE cc_start: 0.7427 (m-80) cc_final: 0.6821 (p90) REVERT: C 883 LYS cc_start: 0.9154 (mttm) cc_final: 0.8891 (mmtp) REVERT: C 898 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7433 (tpp80) REVERT: C 928 MET cc_start: 0.8554 (tpp) cc_final: 0.8286 (tpt) REVERT: C 973 ARG cc_start: 0.7041 (mtt180) cc_final: 0.6675 (mtp85) REVERT: C 986 ASN cc_start: 0.8230 (m-40) cc_final: 0.7957 (m110) REVERT: C 1066 ASN cc_start: 0.8957 (m-40) cc_final: 0.8548 (m110) REVERT: C 1076 GLN cc_start: 0.7371 (mm-40) cc_final: 0.6739 (tp40) REVERT: C 1141 LYS cc_start: 0.8752 (mttt) cc_final: 0.8451 (mtmt) REVERT: C 1152 GLU cc_start: 0.8360 (tp30) cc_final: 0.7675 (tp30) REVERT: C 1155 ASN cc_start: 0.8879 (m-40) cc_final: 0.7972 (t0) REVERT: C 1159 LYS cc_start: 0.8722 (tttt) cc_final: 0.8429 (tttt) REVERT: C 1279 MET cc_start: 0.8314 (mmt) cc_final: 0.8105 (mmt) REVERT: C 1307 LEU cc_start: 0.8451 (tp) cc_final: 0.8151 (tt) REVERT: C 1331 MET cc_start: 0.6496 (mpp) cc_final: 0.6103 (tpt) outliers start: 88 outliers final: 51 residues processed: 725 average time/residue: 0.1686 time to fit residues: 205.9301 Evaluate side-chains 617 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 563 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1238 THR Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 623 GLN Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 191 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 341 optimal weight: 0.5980 chunk 174 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 147 optimal weight: 0.0770 chunk 134 optimal weight: 10.0000 chunk 305 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 109 HIS ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS A 583 GLN A 623 GLN A 763 ASN A1066 ASN B 109 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN B 758 GLN B 763 ASN B1066 ASN B1227 ASN C 83 ASN C 109 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN C 515 HIS C 583 GLN C 611 GLN C 623 GLN C 763 ASN C1066 ASN ** C1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117156 restraints weight = 51370.325| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 4.00 r_work: 0.3314 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33048 Z= 0.160 Angle : 0.857 14.430 45426 Z= 0.383 Chirality : 0.052 0.377 5778 Planarity : 0.004 0.049 5376 Dihedral : 12.719 89.247 8448 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 4.31 % Allowed : 15.55 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.12), residues: 3717 helix: -0.27 (0.18), residues: 765 sheet: -2.11 (0.16), residues: 927 loop : -3.34 (0.11), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 977 TYR 0.021 0.001 TYR A 204 PHE 0.036 0.001 PHE A 104 TRP 0.022 0.002 TRP A 200 HIS 0.004 0.001 HIS C 660 Details of bonding type rmsd covalent geometry : bond 0.00335 (32790) covalent geometry : angle 0.74761 (44703) SS BOND : bond 0.00407 ( 42) SS BOND : angle 1.69650 ( 84) hydrogen bonds : bond 0.04632 ( 851) hydrogen bonds : angle 5.70218 ( 2427) Misc. bond : bond 0.00319 ( 3) link_ALPHA1-2 : bond 0.02458 ( 6) link_ALPHA1-2 : angle 4.09817 ( 18) link_ALPHA1-3 : bond 0.00865 ( 12) link_ALPHA1-3 : angle 3.51656 ( 36) link_ALPHA1-6 : bond 0.01664 ( 24) link_ALPHA1-6 : angle 2.32711 ( 72) link_BETA1-4 : bond 0.01150 ( 87) link_BETA1-4 : angle 3.23482 ( 261) link_BETA1-6 : bond 0.00295 ( 3) link_BETA1-6 : angle 1.27985 ( 9) link_NAG-ASN : bond 0.00568 ( 81) link_NAG-ASN : angle 4.19359 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 590 time to evaluate : 1.081 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: symmetry clash revert: symmetry clash REVERT: A 115 TRP cc_start: 0.7450 (p-90) cc_final: 0.7176 (p-90) REVERT: A 286 ASP cc_start: 0.8438 (t0) cc_final: 0.8171 (t0) REVERT: A 371 ASP cc_start: 0.7158 (p0) cc_final: 0.6410 (m-30) REVERT: A 372 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: A 382 THR cc_start: 0.7928 (m) cc_final: 0.7597 (t) REVERT: A 461 LYS cc_start: 0.8893 (tttt) cc_final: 0.8586 (tttm) REVERT: A 592 THR cc_start: 0.8117 (p) cc_final: 0.7828 (t) REVERT: A 597 GLN cc_start: 0.8426 (mt0) cc_final: 0.8093 (tt0) REVERT: A 641 GLU cc_start: 0.8396 (tp30) cc_final: 0.7908 (tp30) REVERT: A 664 TRP cc_start: 0.6852 (m-10) cc_final: 0.6333 (m100) REVERT: A 680 MET cc_start: 0.8162 (mmt) cc_final: 0.7532 (mtp) REVERT: A 701 GLU cc_start: 0.8275 (pt0) cc_final: 0.7850 (pm20) REVERT: A 702 CYS cc_start: 0.7974 (m) cc_final: 0.7740 (m) REVERT: A 824 ILE cc_start: 0.8773 (mm) cc_final: 0.8502 (tp) REVERT: A 829 PHE cc_start: 0.7488 (m-80) cc_final: 0.6938 (p90) REVERT: A 883 LYS cc_start: 0.9074 (mmtp) cc_final: 0.8872 (mmtp) REVERT: A 898 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7487 (tpp80) REVERT: A 928 MET cc_start: 0.8674 (tpt) cc_final: 0.8214 (tpt) REVERT: A 973 ARG cc_start: 0.6816 (mtt180) cc_final: 0.6498 (mtp85) REVERT: A 1059 MET cc_start: 0.8714 (ttm) cc_final: 0.8479 (ttm) REVERT: A 1141 LYS cc_start: 0.8869 (mttt) cc_final: 0.8462 (mtpt) REVERT: A 1152 GLU cc_start: 0.8363 (tp30) cc_final: 0.7721 (tp30) REVERT: A 1155 ASN cc_start: 0.8786 (m-40) cc_final: 0.7679 (t0) REVERT: A 1260 TYR cc_start: 0.7740 (m-10) cc_final: 0.7445 (m-10) REVERT: B 247 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7107 (mtt90) REVERT: B 286 ASP cc_start: 0.8706 (t70) cc_final: 0.8285 (t0) REVERT: B 293 PHE cc_start: 0.8878 (t80) cc_final: 0.8523 (t80) REVERT: B 382 THR cc_start: 0.8034 (m) cc_final: 0.7728 (t) REVERT: B 592 THR cc_start: 0.8289 (p) cc_final: 0.7979 (t) REVERT: B 633 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8167 (mm-40) REVERT: B 641 GLU cc_start: 0.8406 (tp30) cc_final: 0.7775 (tp30) REVERT: B 663 LYS cc_start: 0.8792 (tttt) cc_final: 0.8587 (tppt) REVERT: B 664 TRP cc_start: 0.6969 (m-10) cc_final: 0.6476 (m100) REVERT: B 680 MET cc_start: 0.8323 (mmt) cc_final: 0.7647 (mtp) REVERT: B 701 GLU cc_start: 0.8216 (pt0) cc_final: 0.7768 (pm20) REVERT: B 702 CYS cc_start: 0.8139 (m) cc_final: 0.7821 (m) REVERT: B 775 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: B 803 MET cc_start: 0.8993 (mmm) cc_final: 0.8792 (mmp) REVERT: B 822 SER cc_start: 0.8758 (m) cc_final: 0.8535 (t) REVERT: B 824 ILE cc_start: 0.8778 (mm) cc_final: 0.8395 (tp) REVERT: B 829 PHE cc_start: 0.7381 (m-80) cc_final: 0.6889 (p90) REVERT: B 883 LYS cc_start: 0.9062 (mttm) cc_final: 0.8855 (mmtp) REVERT: B 898 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7438 (tpp80) REVERT: B 928 MET cc_start: 0.8478 (tpp) cc_final: 0.8042 (tpp) REVERT: B 973 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6765 (mtp85) REVERT: B 982 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: B 1059 MET cc_start: 0.8558 (ttm) cc_final: 0.8233 (ttm) REVERT: B 1066 ASN cc_start: 0.8901 (m110) cc_final: 0.8533 (m110) REVERT: B 1152 GLU cc_start: 0.8407 (tp30) cc_final: 0.7695 (tp30) REVERT: B 1155 ASN cc_start: 0.8766 (m-40) cc_final: 0.7904 (t0) REVERT: B 1161 GLU cc_start: 0.7378 (pm20) cc_final: 0.7045 (pm20) REVERT: B 1268 ASP cc_start: 0.8536 (m-30) cc_final: 0.7882 (m-30) REVERT: B 1283 ARG cc_start: 0.8933 (mtt90) cc_final: 0.7865 (mtm180) REVERT: B 1293 MET cc_start: 0.8456 (tpt) cc_final: 0.8239 (tpt) REVERT: B 1307 LEU cc_start: 0.8542 (tp) cc_final: 0.8255 (tt) REVERT: C 286 ASP cc_start: 0.8667 (t70) cc_final: 0.8194 (t0) REVERT: C 382 THR cc_start: 0.7980 (m) cc_final: 0.7748 (t) REVERT: C 455 PHE cc_start: 0.8390 (p90) cc_final: 0.8171 (p90) REVERT: C 592 THR cc_start: 0.8095 (p) cc_final: 0.7818 (t) REVERT: C 623 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: C 663 LYS cc_start: 0.8850 (tttt) cc_final: 0.8593 (tppp) REVERT: C 664 TRP cc_start: 0.7104 (m100) cc_final: 0.6884 (m100) REVERT: C 680 MET cc_start: 0.8042 (mmt) cc_final: 0.7491 (mtp) REVERT: C 702 CYS cc_start: 0.7919 (m) cc_final: 0.7535 (m) REVERT: C 803 MET cc_start: 0.8982 (mmm) cc_final: 0.8587 (mmm) REVERT: C 805 GLN cc_start: 0.8636 (mt0) cc_final: 0.8171 (mp10) REVERT: C 829 PHE cc_start: 0.7452 (m-80) cc_final: 0.6836 (p90) REVERT: C 883 LYS cc_start: 0.9134 (mttm) cc_final: 0.8879 (mmtp) REVERT: C 898 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7411 (tpp80) REVERT: C 928 MET cc_start: 0.8593 (tpp) cc_final: 0.8006 (tpp) REVERT: C 938 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8115 (tpm-80) REVERT: C 973 ARG cc_start: 0.6965 (mtt180) cc_final: 0.6620 (mtp85) REVERT: C 1066 ASN cc_start: 0.8886 (m110) cc_final: 0.8425 (m110) REVERT: C 1141 LYS cc_start: 0.8729 (mttt) cc_final: 0.8349 (mtpt) REVERT: C 1152 GLU cc_start: 0.8305 (tp30) cc_final: 0.7592 (tp30) REVERT: C 1155 ASN cc_start: 0.8842 (m-40) cc_final: 0.7932 (t0) REVERT: C 1279 MET cc_start: 0.8284 (mmt) cc_final: 0.8077 (mmt) REVERT: C 1331 MET cc_start: 0.6546 (mpp) cc_final: 0.6238 (tpt) outliers start: 141 outliers final: 91 residues processed: 688 average time/residue: 0.1631 time to fit residues: 191.1717 Evaluate side-chains 645 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 549 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 623 GLN Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1029 ASP Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 49 optimal weight: 3.9990 chunk 326 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 77 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 367 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS A1078 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN B1269 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1078 ASN C1311 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.166396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.124361 restraints weight = 51347.357| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 4.20 r_work: 0.3434 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33048 Z= 0.177 Angle : 0.836 14.018 45426 Z= 0.378 Chirality : 0.051 0.366 5778 Planarity : 0.004 0.047 5376 Dihedral : 10.917 82.111 8439 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 4.52 % Allowed : 16.62 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.13), residues: 3717 helix: 0.32 (0.19), residues: 744 sheet: -1.99 (0.17), residues: 906 loop : -3.17 (0.12), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 977 TYR 0.022 0.001 TYR A 204 PHE 0.044 0.001 PHE B 104 TRP 0.017 0.001 TRP C 222 HIS 0.009 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00382 (32790) covalent geometry : angle 0.73216 (44703) SS BOND : bond 0.00380 ( 42) SS BOND : angle 1.78732 ( 84) hydrogen bonds : bond 0.04140 ( 851) hydrogen bonds : angle 5.40267 ( 2427) Misc. bond : bond 0.00144 ( 3) link_ALPHA1-2 : bond 0.02444 ( 6) link_ALPHA1-2 : angle 3.85674 ( 18) link_ALPHA1-3 : bond 0.00905 ( 12) link_ALPHA1-3 : angle 3.27147 ( 36) link_ALPHA1-6 : bond 0.01587 ( 24) link_ALPHA1-6 : angle 2.25434 ( 72) link_BETA1-4 : bond 0.01109 ( 87) link_BETA1-4 : angle 3.13210 ( 261) link_BETA1-6 : bond 0.00301 ( 3) link_BETA1-6 : angle 1.23940 ( 9) link_NAG-ASN : bond 0.00658 ( 81) link_NAG-ASN : angle 4.01718 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 587 time to evaluate : 1.006 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: symmetry clash REVERT: A 115 TRP cc_start: 0.7558 (p-90) cc_final: 0.7242 (p-90) REVERT: A 286 ASP cc_start: 0.8428 (t70) cc_final: 0.8165 (t0) REVERT: A 371 ASP cc_start: 0.7158 (p0) cc_final: 0.6496 (m-30) REVERT: A 372 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: A 382 THR cc_start: 0.7996 (m) cc_final: 0.7702 (t) REVERT: A 461 LYS cc_start: 0.8960 (tttt) cc_final: 0.8669 (tttm) REVERT: A 477 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7598 (p) REVERT: A 597 GLN cc_start: 0.8440 (mt0) cc_final: 0.8147 (tt0) REVERT: A 641 GLU cc_start: 0.8453 (tp30) cc_final: 0.8203 (tp30) REVERT: A 663 LYS cc_start: 0.8830 (tptp) cc_final: 0.8457 (tptt) REVERT: A 664 TRP cc_start: 0.6942 (m-10) cc_final: 0.6421 (m100) REVERT: A 680 MET cc_start: 0.8344 (mmt) cc_final: 0.7869 (mtp) REVERT: A 701 GLU cc_start: 0.8340 (pt0) cc_final: 0.7958 (pm20) REVERT: A 702 CYS cc_start: 0.7898 (m) cc_final: 0.7656 (m) REVERT: A 824 ILE cc_start: 0.8843 (mm) cc_final: 0.8598 (tp) REVERT: A 829 PHE cc_start: 0.7503 (m-80) cc_final: 0.7011 (p90) REVERT: A 898 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7645 (tpp80) REVERT: A 928 MET cc_start: 0.8783 (tpt) cc_final: 0.8332 (tpt) REVERT: A 973 ARG cc_start: 0.7019 (mtt180) cc_final: 0.6670 (mtp85) REVERT: A 1059 MET cc_start: 0.8744 (ttm) cc_final: 0.8519 (ttm) REVERT: A 1067 TYR cc_start: 0.8726 (m-80) cc_final: 0.8449 (m-10) REVERT: A 1076 GLN cc_start: 0.8015 (mp10) cc_final: 0.7195 (tp40) REVERT: A 1141 LYS cc_start: 0.8906 (mttt) cc_final: 0.8499 (mtpt) REVERT: A 1152 GLU cc_start: 0.8376 (tp30) cc_final: 0.7810 (tp30) REVERT: A 1155 ASN cc_start: 0.8783 (m-40) cc_final: 0.7796 (t0) REVERT: A 1260 TYR cc_start: 0.7856 (m-10) cc_final: 0.7576 (m-10) REVERT: A 1268 ASP cc_start: 0.8796 (m-30) cc_final: 0.8531 (m-30) REVERT: A 1279 MET cc_start: 0.8250 (mmt) cc_final: 0.8038 (mmt) REVERT: B 198 PHE cc_start: 0.8828 (m-10) cc_final: 0.8618 (m-10) REVERT: B 247 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7212 (mtt90) REVERT: B 286 ASP cc_start: 0.8651 (t70) cc_final: 0.8295 (t0) REVERT: B 293 PHE cc_start: 0.8817 (t80) cc_final: 0.8521 (t80) REVERT: B 382 THR cc_start: 0.8049 (m) cc_final: 0.7772 (t) REVERT: B 592 THR cc_start: 0.8360 (p) cc_final: 0.8080 (t) REVERT: B 603 LEU cc_start: 0.9105 (tp) cc_final: 0.8775 (tp) REVERT: B 633 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8244 (mm-40) REVERT: B 641 GLU cc_start: 0.8489 (tp30) cc_final: 0.8267 (tp30) REVERT: B 664 TRP cc_start: 0.7080 (m-10) cc_final: 0.6595 (m100) REVERT: B 701 GLU cc_start: 0.8256 (pt0) cc_final: 0.7857 (pm20) REVERT: B 702 CYS cc_start: 0.7962 (m) cc_final: 0.7605 (m) REVERT: B 775 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: B 822 SER cc_start: 0.8798 (m) cc_final: 0.8545 (t) REVERT: B 824 ILE cc_start: 0.8816 (mm) cc_final: 0.8456 (tp) REVERT: B 829 PHE cc_start: 0.7428 (m-80) cc_final: 0.6993 (p90) REVERT: B 898 ARG cc_start: 0.8370 (ttp80) cc_final: 0.7604 (tpp80) REVERT: B 973 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6887 (mtp85) REVERT: B 1059 MET cc_start: 0.8632 (ttm) cc_final: 0.8340 (ttm) REVERT: B 1066 ASN cc_start: 0.8876 (m110) cc_final: 0.8552 (m110) REVERT: B 1076 GLN cc_start: 0.8007 (mp10) cc_final: 0.7262 (tp-100) REVERT: B 1152 GLU cc_start: 0.8367 (tp30) cc_final: 0.7706 (tp30) REVERT: B 1155 ASN cc_start: 0.8814 (m-40) cc_final: 0.8096 (t0) REVERT: B 1161 GLU cc_start: 0.7457 (pm20) cc_final: 0.7133 (pm20) REVERT: B 1268 ASP cc_start: 0.8552 (m-30) cc_final: 0.8168 (m-30) REVERT: B 1283 ARG cc_start: 0.8997 (mtt90) cc_final: 0.8143 (mtm180) REVERT: C 286 ASP cc_start: 0.8570 (t70) cc_final: 0.8235 (t70) REVERT: C 592 THR cc_start: 0.8203 (p) cc_final: 0.7951 (t) REVERT: C 663 LYS cc_start: 0.8892 (tttt) cc_final: 0.8641 (tppp) REVERT: C 664 TRP cc_start: 0.7218 (m100) cc_final: 0.6984 (m100) REVERT: C 680 MET cc_start: 0.8236 (mmt) cc_final: 0.7703 (mtp) REVERT: C 701 GLU cc_start: 0.8362 (pt0) cc_final: 0.7996 (pm20) REVERT: C 805 GLN cc_start: 0.8683 (mt0) cc_final: 0.8289 (mp10) REVERT: C 829 PHE cc_start: 0.7433 (m-80) cc_final: 0.6967 (p90) REVERT: C 883 LYS cc_start: 0.9148 (mttm) cc_final: 0.8904 (mmtp) REVERT: C 898 ARG cc_start: 0.8433 (ttp80) cc_final: 0.7641 (tpp80) REVERT: C 925 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8255 (tt0) REVERT: C 928 MET cc_start: 0.8709 (tpp) cc_final: 0.8256 (tpp) REVERT: C 938 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8132 (tpm-80) REVERT: C 973 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6860 (mtp85) REVERT: C 1067 TYR cc_start: 0.8889 (m-80) cc_final: 0.8686 (m-10) REVERT: C 1076 GLN cc_start: 0.7934 (mp10) cc_final: 0.7150 (tp40) REVERT: C 1141 LYS cc_start: 0.8780 (mttt) cc_final: 0.8366 (mtpt) REVERT: C 1152 GLU cc_start: 0.8318 (tp30) cc_final: 0.7693 (tp30) REVERT: C 1155 ASN cc_start: 0.8863 (m-40) cc_final: 0.8079 (t0) REVERT: C 1331 MET cc_start: 0.6573 (mpp) cc_final: 0.6216 (tpt) outliers start: 148 outliers final: 97 residues processed: 687 average time/residue: 0.1640 time to fit residues: 190.2626 Evaluate side-chains 648 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 547 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 476 TRP Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1029 ASP Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 170 optimal weight: 2.9990 chunk 149 optimal weight: 0.0010 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 332 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 346 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 515 HIS A 844 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS C 623 GLN C 844 HIS C1269 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.170138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125861 restraints weight = 52271.451| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.98 r_work: 0.3445 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 33048 Z= 0.154 Angle : 0.800 13.926 45426 Z= 0.362 Chirality : 0.050 0.351 5778 Planarity : 0.003 0.046 5376 Dihedral : 9.871 76.558 8439 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 4.28 % Allowed : 18.79 % Favored : 76.93 % 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: -2.89 (0.13), residues: 3717 helix: 0.62 (0.20), residues: 747 sheet: -1.93 (0.17), residues: 891 loop : -3.02 (0.12), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 977 TYR 0.027 0.001 TYR B1067 PHE 0.033 0.001 PHE B 104 TRP 0.027 0.001 TRP B 222 HIS 0.012 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00330 (32790) covalent geometry : angle 0.70269 (44703) SS BOND : bond 0.00560 ( 42) SS BOND : angle 1.60258 ( 84) hydrogen bonds : bond 0.03793 ( 851) hydrogen bonds : angle 5.19536 ( 2427) Misc. bond : bond 0.00120 ( 3) link_ALPHA1-2 : bond 0.02453 ( 6) link_ALPHA1-2 : angle 3.72353 ( 18) link_ALPHA1-3 : bond 0.00934 ( 12) link_ALPHA1-3 : angle 3.10443 ( 36) link_ALPHA1-6 : bond 0.01630 ( 24) link_ALPHA1-6 : angle 2.25056 ( 72) link_BETA1-4 : bond 0.01063 ( 87) link_BETA1-4 : angle 2.90656 ( 261) link_BETA1-6 : bond 0.00337 ( 3) link_BETA1-6 : angle 1.23116 ( 9) link_NAG-ASN : bond 0.00638 ( 81) link_NAG-ASN : angle 3.84478 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 562 time to evaluate : 1.049 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: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8552 (mttt) cc_final: 0.8258 (mttt) REVERT: A 286 ASP cc_start: 0.8503 (t70) cc_final: 0.8292 (t0) REVERT: A 371 ASP cc_start: 0.7192 (p0) cc_final: 0.6424 (m-30) REVERT: A 372 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8638 (tt0) REVERT: A 382 THR cc_start: 0.8046 (m) cc_final: 0.7747 (t) REVERT: A 461 LYS cc_start: 0.8929 (tttt) cc_final: 0.8636 (tttm) REVERT: A 477 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7600 (p) REVERT: A 597 GLN cc_start: 0.8515 (mt0) cc_final: 0.8191 (tt0) REVERT: A 641 GLU cc_start: 0.8439 (tp30) cc_final: 0.8139 (tp30) REVERT: A 663 LYS cc_start: 0.8839 (tptp) cc_final: 0.8392 (tptt) REVERT: A 680 MET cc_start: 0.8283 (mmt) cc_final: 0.7783 (mtp) REVERT: A 701 GLU cc_start: 0.8315 (pt0) cc_final: 0.7916 (pm20) REVERT: A 702 CYS cc_start: 0.7829 (m) cc_final: 0.7598 (m) REVERT: A 824 ILE cc_start: 0.8815 (mm) cc_final: 0.8555 (tp) REVERT: A 829 PHE cc_start: 0.7412 (m-80) cc_final: 0.6981 (p90) REVERT: A 898 ARG cc_start: 0.8378 (ttp80) cc_final: 0.7616 (tpp80) REVERT: A 928 MET cc_start: 0.8771 (tpt) cc_final: 0.8440 (tpt) REVERT: A 973 ARG cc_start: 0.6919 (mtt180) cc_final: 0.6608 (mtp85) REVERT: A 1059 MET cc_start: 0.8726 (ttm) cc_final: 0.8495 (ttm) REVERT: A 1076 GLN cc_start: 0.8006 (mp10) cc_final: 0.7110 (tp40) REVERT: A 1141 LYS cc_start: 0.8896 (mttt) cc_final: 0.8464 (mtpt) REVERT: A 1152 GLU cc_start: 0.8392 (tp30) cc_final: 0.7727 (tp30) REVERT: A 1155 ASN cc_start: 0.8777 (m-40) cc_final: 0.7974 (t0) REVERT: A 1260 TYR cc_start: 0.7819 (m-10) cc_final: 0.7512 (m-10) REVERT: A 1268 ASP cc_start: 0.8820 (m-30) cc_final: 0.8508 (m-30) REVERT: A 1279 MET cc_start: 0.8276 (mmt) cc_final: 0.8052 (mmt) REVERT: A 1331 MET cc_start: 0.6740 (ttt) cc_final: 0.6278 (tmm) REVERT: B 286 ASP cc_start: 0.8694 (t70) cc_final: 0.8338 (t0) REVERT: B 293 PHE cc_start: 0.8776 (t80) cc_final: 0.8536 (t80) REVERT: B 382 THR cc_start: 0.8048 (m) cc_final: 0.7759 (t) REVERT: B 592 THR cc_start: 0.8304 (p) cc_final: 0.8032 (t) REVERT: B 603 LEU cc_start: 0.9118 (tp) cc_final: 0.8735 (tp) REVERT: B 623 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: B 633 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8152 (mm-40) REVERT: B 664 TRP cc_start: 0.6895 (m-10) cc_final: 0.6583 (m100) REVERT: B 680 MET cc_start: 0.8604 (mmm) cc_final: 0.8026 (mtp) REVERT: B 701 GLU cc_start: 0.8243 (pt0) cc_final: 0.8040 (pt0) REVERT: B 702 CYS cc_start: 0.7911 (m) cc_final: 0.7541 (m) REVERT: B 775 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: B 822 SER cc_start: 0.8825 (m) cc_final: 0.8588 (t) REVERT: B 824 ILE cc_start: 0.8798 (mm) cc_final: 0.8514 (tp) REVERT: B 829 PHE cc_start: 0.7348 (m-80) cc_final: 0.6998 (p90) REVERT: B 925 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8247 (tt0) REVERT: B 973 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6803 (mtp85) REVERT: B 1059 MET cc_start: 0.8602 (ttm) cc_final: 0.8317 (ttm) REVERT: B 1066 ASN cc_start: 0.8864 (m110) cc_final: 0.8533 (m110) REVERT: B 1120 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8331 (mttt) REVERT: B 1152 GLU cc_start: 0.8368 (tp30) cc_final: 0.7646 (tp30) REVERT: B 1155 ASN cc_start: 0.8812 (m-40) cc_final: 0.8163 (t0) REVERT: B 1161 GLU cc_start: 0.7406 (pm20) cc_final: 0.7118 (pm20) REVERT: B 1263 LEU cc_start: 0.9031 (tp) cc_final: 0.8824 (tt) REVERT: B 1293 MET cc_start: 0.8520 (tpt) cc_final: 0.8284 (tpt) REVERT: C 286 ASP cc_start: 0.8583 (t70) cc_final: 0.8106 (t70) REVERT: C 570 GLU cc_start: 0.7560 (mp0) cc_final: 0.7306 (mp0) REVERT: C 592 THR cc_start: 0.8138 (p) cc_final: 0.7874 (t) REVERT: C 623 GLN cc_start: 0.8672 (mt0) cc_final: 0.8307 (mt0) REVERT: C 663 LYS cc_start: 0.8844 (tttt) cc_final: 0.8612 (tppp) REVERT: C 664 TRP cc_start: 0.7162 (m100) cc_final: 0.6925 (m100) REVERT: C 680 MET cc_start: 0.8153 (mmt) cc_final: 0.7647 (mtp) REVERT: C 701 GLU cc_start: 0.7996 (pt0) cc_final: 0.7668 (pm20) REVERT: C 805 GLN cc_start: 0.8658 (mt0) cc_final: 0.8255 (mp10) REVERT: C 829 PHE cc_start: 0.7422 (m-80) cc_final: 0.6983 (p90) REVERT: C 883 LYS cc_start: 0.9141 (mttm) cc_final: 0.8894 (mmtp) REVERT: C 898 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7528 (tpp80) REVERT: C 925 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8171 (tt0) REVERT: C 928 MET cc_start: 0.8710 (tpp) cc_final: 0.8220 (tpp) REVERT: C 938 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8192 (tpm-80) REVERT: C 973 ARG cc_start: 0.6970 (mtt180) cc_final: 0.6712 (mtp85) REVERT: C 1066 ASN cc_start: 0.8767 (m110) cc_final: 0.8474 (m110) REVERT: C 1075 LEU cc_start: 0.8695 (mm) cc_final: 0.8351 (mm) REVERT: C 1076 GLN cc_start: 0.8006 (mp10) cc_final: 0.7161 (tp40) REVERT: C 1141 LYS cc_start: 0.8782 (mttt) cc_final: 0.8354 (mtpt) REVERT: C 1152 GLU cc_start: 0.8343 (tp30) cc_final: 0.7665 (tp30) REVERT: C 1155 ASN cc_start: 0.8873 (m-40) cc_final: 0.8143 (t0) outliers start: 140 outliers final: 95 residues processed: 654 average time/residue: 0.1725 time to fit residues: 190.8604 Evaluate side-chains 635 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 535 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 623 GLN Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1310 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1059 MET Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 329 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 92 optimal weight: 0.0670 chunk 183 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 352 optimal weight: 1.9990 chunk 267 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 321 GLN A1112 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B1112 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 GLN C1066 ASN C1112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.165168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124514 restraints weight = 51086.180| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.75 r_work: 0.3434 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33048 Z= 0.203 Angle : 0.822 13.793 45426 Z= 0.375 Chirality : 0.050 0.354 5778 Planarity : 0.003 0.046 5376 Dihedral : 9.406 71.240 8439 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 4.77 % Allowed : 19.07 % Favored : 76.17 % 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: -2.79 (0.13), residues: 3717 helix: 0.73 (0.20), residues: 744 sheet: -1.92 (0.17), residues: 918 loop : -2.94 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 977 TYR 0.023 0.002 TYR C 204 PHE 0.028 0.001 PHE B 104 TRP 0.031 0.002 TRP B 222 HIS 0.005 0.001 HIS C1237 Details of bonding type rmsd covalent geometry : bond 0.00451 (32790) covalent geometry : angle 0.72881 (44703) SS BOND : bond 0.00541 ( 42) SS BOND : angle 1.48289 ( 84) hydrogen bonds : bond 0.04018 ( 851) hydrogen bonds : angle 5.15120 ( 2427) Misc. bond : bond 0.00137 ( 3) link_ALPHA1-2 : bond 0.02612 ( 6) link_ALPHA1-2 : angle 3.63500 ( 18) link_ALPHA1-3 : bond 0.00915 ( 12) link_ALPHA1-3 : angle 3.14271 ( 36) link_ALPHA1-6 : bond 0.01598 ( 24) link_ALPHA1-6 : angle 2.27172 ( 72) link_BETA1-4 : bond 0.01065 ( 87) link_BETA1-4 : angle 2.86159 ( 261) link_BETA1-6 : bond 0.00314 ( 3) link_BETA1-6 : angle 1.22407 ( 9) link_NAG-ASN : bond 0.00589 ( 81) link_NAG-ASN : angle 3.88302 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 542 time to evaluate : 0.984 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 215 LYS cc_start: 0.8573 (mttt) cc_final: 0.8272 (mttt) REVERT: A 286 ASP cc_start: 0.8556 (t70) cc_final: 0.8272 (t0) REVERT: A 371 ASP cc_start: 0.7225 (p0) cc_final: 0.6429 (m-30) REVERT: A 372 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: A 382 THR cc_start: 0.8054 (m) cc_final: 0.7719 (t) REVERT: A 461 LYS cc_start: 0.8975 (tttt) cc_final: 0.8739 (tttm) REVERT: A 597 GLN cc_start: 0.8537 (mt0) cc_final: 0.8253 (tt0) REVERT: A 663 LYS cc_start: 0.8887 (tptp) cc_final: 0.8655 (tptm) REVERT: A 664 TRP cc_start: 0.6833 (m-10) cc_final: 0.6467 (m100) REVERT: A 702 CYS cc_start: 0.7750 (m) cc_final: 0.7466 (m) REVERT: A 824 ILE cc_start: 0.8831 (mm) cc_final: 0.8609 (tp) REVERT: A 829 PHE cc_start: 0.7494 (m-80) cc_final: 0.7002 (p90) REVERT: A 898 ARG cc_start: 0.8380 (ttp80) cc_final: 0.7629 (tpp80) REVERT: A 1023 VAL cc_start: 0.9496 (OUTLIER) cc_final: 0.9045 (m) REVERT: A 1059 MET cc_start: 0.8736 (ttm) cc_final: 0.8508 (ttm) REVERT: A 1141 LYS cc_start: 0.8890 (mttt) cc_final: 0.8404 (mtpt) REVERT: A 1152 GLU cc_start: 0.8395 (tp30) cc_final: 0.7764 (tp30) REVERT: A 1155 ASN cc_start: 0.8797 (m-40) cc_final: 0.7869 (t0) REVERT: A 1260 TYR cc_start: 0.7809 (m-10) cc_final: 0.7527 (m-10) REVERT: A 1268 ASP cc_start: 0.8835 (m-30) cc_final: 0.8626 (m-30) REVERT: A 1331 MET cc_start: 0.6839 (ttt) cc_final: 0.6344 (tmm) REVERT: B 247 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7374 (mtt180) REVERT: B 286 ASP cc_start: 0.8713 (t70) cc_final: 0.8338 (t0) REVERT: B 382 THR cc_start: 0.8169 (m) cc_final: 0.7839 (t) REVERT: B 592 THR cc_start: 0.8376 (p) cc_final: 0.8109 (t) REVERT: B 603 LEU cc_start: 0.9138 (tp) cc_final: 0.8758 (tp) REVERT: B 633 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8205 (mm-40) REVERT: B 664 TRP cc_start: 0.6926 (m-10) cc_final: 0.6534 (m100) REVERT: B 680 MET cc_start: 0.8514 (mmm) cc_final: 0.8016 (mtp) REVERT: B 702 CYS cc_start: 0.7850 (m) cc_final: 0.7448 (m) REVERT: B 775 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: B 822 SER cc_start: 0.8833 (m) cc_final: 0.8601 (t) REVERT: B 824 ILE cc_start: 0.8767 (mm) cc_final: 0.8516 (tp) REVERT: B 829 PHE cc_start: 0.7333 (m-80) cc_final: 0.7009 (p90) REVERT: B 925 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8316 (tt0) REVERT: B 973 ARG cc_start: 0.7001 (mtt180) cc_final: 0.6738 (mtp85) REVERT: B 1011 ASP cc_start: 0.7267 (t0) cc_final: 0.7053 (t0) REVERT: B 1023 VAL cc_start: 0.9338 (t) cc_final: 0.8969 (m) REVERT: B 1059 MET cc_start: 0.8602 (ttm) cc_final: 0.8318 (ttm) REVERT: B 1066 ASN cc_start: 0.8905 (m110) cc_final: 0.8565 (m110) REVERT: B 1120 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8374 (mttt) REVERT: B 1152 GLU cc_start: 0.8378 (tp30) cc_final: 0.7674 (tp30) REVERT: B 1155 ASN cc_start: 0.8776 (m-40) cc_final: 0.8198 (t0) REVERT: B 1161 GLU cc_start: 0.7446 (pm20) cc_final: 0.7170 (pm20) REVERT: B 1260 TYR cc_start: 0.7812 (m-10) cc_final: 0.7487 (m-10) REVERT: B 1263 LEU cc_start: 0.9029 (tp) cc_final: 0.8810 (tt) REVERT: C 247 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7375 (mtt180) REVERT: C 286 ASP cc_start: 0.8628 (t70) cc_final: 0.8335 (t0) REVERT: C 293 PHE cc_start: 0.8646 (t80) cc_final: 0.8117 (t80) REVERT: C 570 GLU cc_start: 0.7495 (mp0) cc_final: 0.7274 (mp0) REVERT: C 592 THR cc_start: 0.8200 (p) cc_final: 0.7928 (t) REVERT: C 663 LYS cc_start: 0.8922 (tttt) cc_final: 0.8650 (tppp) REVERT: C 664 TRP cc_start: 0.7208 (m100) cc_final: 0.6848 (m100) REVERT: C 680 MET cc_start: 0.8158 (mmt) cc_final: 0.7577 (mtp) REVERT: C 694 ILE cc_start: 0.5470 (OUTLIER) cc_final: 0.4824 (tp) REVERT: C 829 PHE cc_start: 0.7455 (m-80) cc_final: 0.6995 (p90) REVERT: C 883 LYS cc_start: 0.9117 (mttm) cc_final: 0.8829 (mmtp) REVERT: C 898 ARG cc_start: 0.8390 (ttp80) cc_final: 0.7595 (tpp80) REVERT: C 925 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8271 (tt0) REVERT: C 928 MET cc_start: 0.8763 (tpp) cc_final: 0.8118 (tpp) REVERT: C 938 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8179 (tpm-80) REVERT: C 973 ARG cc_start: 0.6996 (mtt180) cc_final: 0.6704 (mtp85) REVERT: C 1141 LYS cc_start: 0.8789 (mttt) cc_final: 0.8327 (mtpt) REVERT: C 1152 GLU cc_start: 0.8344 (tp30) cc_final: 0.7682 (tp30) REVERT: C 1155 ASN cc_start: 0.8886 (m-40) cc_final: 0.8176 (t0) REVERT: C 1331 MET cc_start: 0.7123 (tpp) cc_final: 0.6519 (tpt) outliers start: 156 outliers final: 123 residues processed: 644 average time/residue: 0.1662 time to fit residues: 181.3326 Evaluate side-chains 645 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 516 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 621 GLN Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1318 VAL Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 476 TRP Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1303 GLU Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1318 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 66 optimal weight: 0.4980 chunk 290 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 154 optimal weight: 0.0980 chunk 185 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 ASN C1315 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.167938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.123150 restraints weight = 52530.130| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 4.05 r_work: 0.3413 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 33048 Z= 0.193 Angle : 0.817 13.940 45426 Z= 0.374 Chirality : 0.050 0.350 5778 Planarity : 0.003 0.046 5376 Dihedral : 9.146 67.949 8439 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 4.71 % Allowed : 19.55 % Favored : 75.74 % 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: -2.69 (0.13), residues: 3717 helix: 0.80 (0.20), residues: 753 sheet: -1.86 (0.18), residues: 861 loop : -2.87 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1212 TYR 0.023 0.001 TYR C1278 PHE 0.039 0.001 PHE B 293 TRP 0.033 0.002 TRP B 222 HIS 0.003 0.001 HIS B1221 Details of bonding type rmsd covalent geometry : bond 0.00429 (32790) covalent geometry : angle 0.72461 (44703) SS BOND : bond 0.00628 ( 42) SS BOND : angle 1.98823 ( 84) hydrogen bonds : bond 0.03957 ( 851) hydrogen bonds : angle 5.14839 ( 2427) Misc. bond : bond 0.00110 ( 3) link_ALPHA1-2 : bond 0.02597 ( 6) link_ALPHA1-2 : angle 3.57867 ( 18) link_ALPHA1-3 : bond 0.00893 ( 12) link_ALPHA1-3 : angle 3.03592 ( 36) link_ALPHA1-6 : bond 0.01569 ( 24) link_ALPHA1-6 : angle 2.28072 ( 72) link_BETA1-4 : bond 0.01025 ( 87) link_BETA1-4 : angle 2.76191 ( 261) link_BETA1-6 : bond 0.00322 ( 3) link_BETA1-6 : angle 1.22285 ( 9) link_NAG-ASN : bond 0.00585 ( 81) link_NAG-ASN : angle 3.82985 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 547 time to evaluate : 1.078 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 215 LYS cc_start: 0.8553 (mttt) cc_final: 0.8266 (mttt) REVERT: A 286 ASP cc_start: 0.8625 (t70) cc_final: 0.8315 (t0) REVERT: A 371 ASP cc_start: 0.7204 (p0) cc_final: 0.6409 (m-30) REVERT: A 372 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: A 382 THR cc_start: 0.8005 (m) cc_final: 0.7646 (t) REVERT: A 461 LYS cc_start: 0.8986 (tttt) cc_final: 0.8758 (tttm) REVERT: A 597 GLN cc_start: 0.8526 (mt0) cc_final: 0.8214 (tt0) REVERT: A 663 LYS cc_start: 0.8913 (tptp) cc_final: 0.8680 (tptm) REVERT: A 664 TRP cc_start: 0.6842 (m-10) cc_final: 0.6477 (m100) REVERT: A 680 MET cc_start: 0.8152 (mmt) cc_final: 0.7555 (mtp) REVERT: A 702 CYS cc_start: 0.7825 (m) cc_final: 0.7559 (m) REVERT: A 824 ILE cc_start: 0.8827 (mm) cc_final: 0.8622 (tp) REVERT: A 829 PHE cc_start: 0.7617 (m-80) cc_final: 0.7087 (p90) REVERT: A 898 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7652 (tpp80) REVERT: A 923 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8527 (ttp80) REVERT: A 925 GLU cc_start: 0.8943 (tt0) cc_final: 0.8341 (tt0) REVERT: A 1023 VAL cc_start: 0.9500 (OUTLIER) cc_final: 0.9059 (m) REVERT: A 1059 MET cc_start: 0.8744 (ttm) cc_final: 0.8524 (ttm) REVERT: A 1141 LYS cc_start: 0.8912 (mttt) cc_final: 0.8412 (mtpt) REVERT: A 1152 GLU cc_start: 0.8453 (tp30) cc_final: 0.7839 (tp30) REVERT: A 1155 ASN cc_start: 0.8821 (m-40) cc_final: 0.7899 (t0) REVERT: A 1260 TYR cc_start: 0.7827 (m-10) cc_final: 0.7548 (m-10) REVERT: A 1268 ASP cc_start: 0.8862 (m-30) cc_final: 0.8622 (m-30) REVERT: A 1331 MET cc_start: 0.6735 (ttt) cc_final: 0.6240 (tmm) REVERT: B 247 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7398 (mtt180) REVERT: B 286 ASP cc_start: 0.8750 (t70) cc_final: 0.8362 (t0) REVERT: B 371 ASP cc_start: 0.7265 (p0) cc_final: 0.6729 (m-30) REVERT: B 382 THR cc_start: 0.8228 (m) cc_final: 0.7869 (t) REVERT: B 592 THR cc_start: 0.8352 (p) cc_final: 0.8101 (t) REVERT: B 603 LEU cc_start: 0.9115 (tp) cc_final: 0.8729 (tp) REVERT: B 633 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8198 (mm-40) REVERT: B 664 TRP cc_start: 0.6894 (m-10) cc_final: 0.6492 (m100) REVERT: B 680 MET cc_start: 0.8540 (mmm) cc_final: 0.8123 (mtp) REVERT: B 694 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.4983 (tp) REVERT: B 702 CYS cc_start: 0.7897 (m) cc_final: 0.7525 (m) REVERT: B 775 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: B 822 SER cc_start: 0.8816 (m) cc_final: 0.8573 (t) REVERT: B 824 ILE cc_start: 0.8760 (mm) cc_final: 0.8535 (tp) REVERT: B 829 PHE cc_start: 0.7402 (m-80) cc_final: 0.7043 (p90) REVERT: B 925 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8370 (tt0) REVERT: B 1023 VAL cc_start: 0.9335 (t) cc_final: 0.8968 (m) REVERT: B 1059 MET cc_start: 0.8612 (ttm) cc_final: 0.8342 (ttm) REVERT: B 1066 ASN cc_start: 0.8874 (m110) cc_final: 0.8572 (m110) REVERT: B 1076 GLN cc_start: 0.8167 (mp10) cc_final: 0.7940 (mp10) REVERT: B 1120 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8359 (mttt) REVERT: B 1152 GLU cc_start: 0.8414 (tp30) cc_final: 0.7715 (tp30) REVERT: B 1155 ASN cc_start: 0.8798 (m-40) cc_final: 0.8232 (t0) REVERT: B 1161 GLU cc_start: 0.7525 (pm20) cc_final: 0.7206 (pm20) REVERT: B 1260 TYR cc_start: 0.7780 (m-10) cc_final: 0.7414 (m-10) REVERT: C 286 ASP cc_start: 0.8727 (t70) cc_final: 0.8429 (t0) REVERT: C 293 PHE cc_start: 0.8640 (t80) cc_final: 0.8132 (t80) REVERT: C 371 ASP cc_start: 0.7040 (p0) cc_final: 0.6560 (m-30) REVERT: C 570 GLU cc_start: 0.7546 (mp0) cc_final: 0.7293 (mp0) REVERT: C 663 LYS cc_start: 0.8919 (tttt) cc_final: 0.8651 (tppp) REVERT: C 664 TRP cc_start: 0.7186 (m100) cc_final: 0.6818 (m100) REVERT: C 680 MET cc_start: 0.8161 (mmt) cc_final: 0.7624 (mtp) REVERT: C 694 ILE cc_start: 0.5478 (OUTLIER) cc_final: 0.4832 (tp) REVERT: C 701 GLU cc_start: 0.8269 (pt0) cc_final: 0.7919 (pm20) REVERT: C 829 PHE cc_start: 0.7524 (m-80) cc_final: 0.6995 (p90) REVERT: C 850 ASP cc_start: 0.8530 (t0) cc_final: 0.8246 (t0) REVERT: C 883 LYS cc_start: 0.9146 (mttm) cc_final: 0.8912 (mttm) REVERT: C 898 ARG cc_start: 0.8382 (ttp80) cc_final: 0.7586 (tpp80) REVERT: C 925 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8310 (tt0) REVERT: C 928 MET cc_start: 0.8755 (tpp) cc_final: 0.8187 (tpp) REVERT: C 938 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8270 (tpm-80) REVERT: C 1066 ASN cc_start: 0.8802 (m110) cc_final: 0.8481 (m110) REVERT: C 1067 TYR cc_start: 0.8653 (m-80) cc_final: 0.8393 (m-80) REVERT: C 1076 GLN cc_start: 0.8000 (mp10) cc_final: 0.7116 (tp40) REVERT: C 1141 LYS cc_start: 0.8784 (mttt) cc_final: 0.8331 (mtpt) REVERT: C 1152 GLU cc_start: 0.8429 (tp30) cc_final: 0.7779 (tp30) REVERT: C 1155 ASN cc_start: 0.8927 (m-40) cc_final: 0.8206 (t0) REVERT: C 1293 MET cc_start: 0.8527 (tpt) cc_final: 0.8318 (tpt) REVERT: C 1331 MET cc_start: 0.7133 (tpp) cc_final: 0.6505 (tpt) outliers start: 154 outliers final: 123 residues processed: 649 average time/residue: 0.1613 time to fit residues: 177.5591 Evaluate side-chains 653 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 523 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1303 GLU Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1318 VAL Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1318 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 369 optimal weight: 8.9990 chunk 202 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 322 optimal weight: 4.9990 chunk 354 optimal weight: 0.0870 chunk 311 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 316 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 ASN C1315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.166880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125673 restraints weight = 51542.903| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.01 r_work: 0.3436 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33048 Z= 0.152 Angle : 0.791 13.775 45426 Z= 0.362 Chirality : 0.049 0.346 5778 Planarity : 0.003 0.048 5376 Dihedral : 8.851 64.791 8439 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 4.46 % Allowed : 20.23 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.13), residues: 3717 helix: 0.94 (0.20), residues: 747 sheet: -1.82 (0.18), residues: 867 loop : -2.80 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 977 TYR 0.033 0.001 TYR B1067 PHE 0.035 0.001 PHE B 293 TRP 0.029 0.001 TRP B 222 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00328 (32790) covalent geometry : angle 0.70227 (44703) SS BOND : bond 0.00502 ( 42) SS BOND : angle 1.67090 ( 84) hydrogen bonds : bond 0.03666 ( 851) hydrogen bonds : angle 5.00894 ( 2427) Misc. bond : bond 0.00080 ( 3) link_ALPHA1-2 : bond 0.02545 ( 6) link_ALPHA1-2 : angle 3.49497 ( 18) link_ALPHA1-3 : bond 0.00865 ( 12) link_ALPHA1-3 : angle 2.95679 ( 36) link_ALPHA1-6 : bond 0.01584 ( 24) link_ALPHA1-6 : angle 2.31576 ( 72) link_BETA1-4 : bond 0.01013 ( 87) link_BETA1-4 : angle 2.67424 ( 261) link_BETA1-6 : bond 0.00358 ( 3) link_BETA1-6 : angle 1.21805 ( 9) link_NAG-ASN : bond 0.00604 ( 81) link_NAG-ASN : angle 3.70939 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 551 time to evaluate : 1.072 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 286 ASP cc_start: 0.8601 (t70) cc_final: 0.8262 (t0) REVERT: A 293 PHE cc_start: 0.8667 (t80) cc_final: 0.7753 (t80) REVERT: A 371 ASP cc_start: 0.7094 (p0) cc_final: 0.6287 (m-30) REVERT: A 372 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: A 382 THR cc_start: 0.7963 (m) cc_final: 0.7616 (t) REVERT: A 461 LYS cc_start: 0.8962 (tttt) cc_final: 0.8728 (tttm) REVERT: A 597 GLN cc_start: 0.8524 (mt0) cc_final: 0.8156 (tt0) REVERT: A 623 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: A 641 GLU cc_start: 0.8085 (tp30) cc_final: 0.7779 (tp30) REVERT: A 663 LYS cc_start: 0.8894 (tptp) cc_final: 0.8666 (tptm) REVERT: A 664 TRP cc_start: 0.6725 (m-10) cc_final: 0.6372 (m100) REVERT: A 680 MET cc_start: 0.8090 (mmt) cc_final: 0.7527 (mtp) REVERT: A 702 CYS cc_start: 0.7737 (m) cc_final: 0.7475 (m) REVERT: A 824 ILE cc_start: 0.8803 (mm) cc_final: 0.8594 (tp) REVERT: A 829 PHE cc_start: 0.7564 (m-80) cc_final: 0.7060 (p90) REVERT: A 898 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7573 (tpp80) REVERT: A 923 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8502 (ttp80) REVERT: A 925 GLU cc_start: 0.8977 (tt0) cc_final: 0.8474 (tt0) REVERT: A 1023 VAL cc_start: 0.9481 (t) cc_final: 0.9035 (m) REVERT: A 1059 MET cc_start: 0.8725 (ttm) cc_final: 0.8491 (ttm) REVERT: A 1141 LYS cc_start: 0.8887 (mttt) cc_final: 0.8383 (mtpt) REVERT: A 1152 GLU cc_start: 0.8400 (tp30) cc_final: 0.7716 (tp30) REVERT: A 1155 ASN cc_start: 0.8783 (m-40) cc_final: 0.8047 (t0) REVERT: A 1260 TYR cc_start: 0.7802 (m-10) cc_final: 0.7489 (m-10) REVERT: A 1331 MET cc_start: 0.6694 (ttt) cc_final: 0.6220 (tmm) REVERT: B 286 ASP cc_start: 0.8729 (t70) cc_final: 0.8174 (t0) REVERT: B 371 ASP cc_start: 0.7151 (p0) cc_final: 0.6641 (m-30) REVERT: B 382 THR cc_start: 0.8166 (m) cc_final: 0.7808 (t) REVERT: B 592 THR cc_start: 0.8321 (p) cc_final: 0.8051 (t) REVERT: B 603 LEU cc_start: 0.9079 (tp) cc_final: 0.8688 (tp) REVERT: B 633 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8070 (mm-40) REVERT: B 680 MET cc_start: 0.8497 (mmm) cc_final: 0.8025 (mtp) REVERT: B 702 CYS cc_start: 0.7847 (m) cc_final: 0.7499 (m) REVERT: B 775 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: B 822 SER cc_start: 0.8901 (m) cc_final: 0.8640 (t) REVERT: B 824 ILE cc_start: 0.8769 (mm) cc_final: 0.8523 (tp) REVERT: B 829 PHE cc_start: 0.7382 (m-80) cc_final: 0.7006 (p90) REVERT: B 925 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8367 (tt0) REVERT: B 928 MET cc_start: 0.8277 (tpt) cc_final: 0.8059 (tpt) REVERT: B 1023 VAL cc_start: 0.9298 (t) cc_final: 0.8892 (m) REVERT: B 1059 MET cc_start: 0.8566 (ttm) cc_final: 0.8297 (ttm) REVERT: B 1066 ASN cc_start: 0.8783 (m110) cc_final: 0.8500 (m110) REVERT: B 1076 GLN cc_start: 0.8155 (mp10) cc_final: 0.7937 (mp10) REVERT: B 1120 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8335 (mttt) REVERT: B 1152 GLU cc_start: 0.8375 (tp30) cc_final: 0.7833 (tp30) REVERT: B 1155 ASN cc_start: 0.8767 (m-40) cc_final: 0.8164 (t0) REVERT: B 1158 GLU cc_start: 0.7533 (tt0) cc_final: 0.7325 (tt0) REVERT: B 1161 GLU cc_start: 0.7528 (pm20) cc_final: 0.7186 (pm20) REVERT: B 1260 TYR cc_start: 0.7733 (m-10) cc_final: 0.7387 (m-10) REVERT: C 286 ASP cc_start: 0.8714 (t70) cc_final: 0.8407 (t0) REVERT: C 293 PHE cc_start: 0.8629 (t80) cc_final: 0.8063 (t80) REVERT: C 371 ASP cc_start: 0.6957 (p0) cc_final: 0.6508 (m-30) REVERT: C 570 GLU cc_start: 0.7499 (mp0) cc_final: 0.7290 (mp0) REVERT: C 601 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8495 (pt) REVERT: C 657 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8231 (p) REVERT: C 663 LYS cc_start: 0.8914 (tttt) cc_final: 0.8672 (tppp) REVERT: C 664 TRP cc_start: 0.7170 (m100) cc_final: 0.6919 (m100) REVERT: C 680 MET cc_start: 0.8166 (mmt) cc_final: 0.7596 (mtp) REVERT: C 701 GLU cc_start: 0.8184 (pt0) cc_final: 0.7714 (pm20) REVERT: C 711 GLN cc_start: 0.8779 (tt0) cc_final: 0.8246 (mt0) REVERT: C 805 GLN cc_start: 0.8702 (mt0) cc_final: 0.8323 (mp10) REVERT: C 829 PHE cc_start: 0.7524 (m-80) cc_final: 0.6987 (p90) REVERT: C 850 ASP cc_start: 0.8495 (t0) cc_final: 0.8183 (t0) REVERT: C 883 LYS cc_start: 0.9135 (mttm) cc_final: 0.8862 (mmtp) REVERT: C 898 ARG cc_start: 0.8363 (ttp80) cc_final: 0.7518 (tpp80) REVERT: C 925 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8321 (tt0) REVERT: C 928 MET cc_start: 0.8741 (tpp) cc_final: 0.8231 (tpp) REVERT: C 938 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8292 (tpm-80) REVERT: C 1141 LYS cc_start: 0.8772 (mttt) cc_final: 0.8313 (mtpt) REVERT: C 1152 GLU cc_start: 0.8397 (tp30) cc_final: 0.7720 (tp30) REVERT: C 1155 ASN cc_start: 0.8874 (m-40) cc_final: 0.8200 (t0) REVERT: C 1331 MET cc_start: 0.7161 (tpp) cc_final: 0.6548 (tpt) outliers start: 146 outliers final: 115 residues processed: 642 average time/residue: 0.1628 time to fit residues: 177.4504 Evaluate side-chains 648 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 527 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1318 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 127 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 344 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 348 optimal weight: 0.9990 chunk 21 optimal weight: 0.0470 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN A1187 GLN A1315 GLN B1066 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.170761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126551 restraints weight = 51958.896| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.98 r_work: 0.3452 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33048 Z= 0.139 Angle : 0.782 13.401 45426 Z= 0.358 Chirality : 0.048 0.340 5778 Planarity : 0.003 0.052 5376 Dihedral : 8.626 61.696 8439 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 4.03 % Allowed : 21.14 % Favored : 74.82 % 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: -2.48 (0.14), residues: 3717 helix: 1.04 (0.20), residues: 747 sheet: -1.64 (0.18), residues: 861 loop : -2.79 (0.12), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 977 TYR 0.065 0.001 TYR B1067 PHE 0.020 0.001 PHE B 104 TRP 0.032 0.001 TRP C 222 HIS 0.003 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00291 (32790) covalent geometry : angle 0.69492 (44703) SS BOND : bond 0.00502 ( 42) SS BOND : angle 1.63984 ( 84) hydrogen bonds : bond 0.03519 ( 851) hydrogen bonds : angle 4.94576 ( 2427) Misc. bond : bond 0.00069 ( 3) link_ALPHA1-2 : bond 0.02500 ( 6) link_ALPHA1-2 : angle 3.41000 ( 18) link_ALPHA1-3 : bond 0.00843 ( 12) link_ALPHA1-3 : angle 2.91731 ( 36) link_ALPHA1-6 : bond 0.01612 ( 24) link_ALPHA1-6 : angle 2.32862 ( 72) link_BETA1-4 : bond 0.01019 ( 87) link_BETA1-4 : angle 2.61102 ( 261) link_BETA1-6 : bond 0.00385 ( 3) link_BETA1-6 : angle 1.20993 ( 9) link_NAG-ASN : bond 0.00655 ( 81) link_NAG-ASN : angle 3.66006 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 549 time to evaluate : 0.941 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 286 ASP cc_start: 0.8618 (t70) cc_final: 0.8206 (t0) REVERT: A 293 PHE cc_start: 0.8655 (t80) cc_final: 0.7748 (t80) REVERT: A 371 ASP cc_start: 0.7049 (p0) cc_final: 0.6264 (m-30) REVERT: A 372 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: A 382 THR cc_start: 0.8011 (m) cc_final: 0.7653 (t) REVERT: A 461 LYS cc_start: 0.8931 (tttt) cc_final: 0.8521 (tmtt) REVERT: A 597 GLN cc_start: 0.8546 (mt0) cc_final: 0.8164 (tt0) REVERT: A 623 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: A 641 GLU cc_start: 0.8047 (tp30) cc_final: 0.7760 (tp30) REVERT: A 663 LYS cc_start: 0.8881 (tptp) cc_final: 0.8657 (tptm) REVERT: A 680 MET cc_start: 0.8098 (mmt) cc_final: 0.7432 (mtp) REVERT: A 702 CYS cc_start: 0.7795 (m) cc_final: 0.7559 (m) REVERT: A 711 GLN cc_start: 0.8724 (tt0) cc_final: 0.8218 (mt0) REVERT: A 824 ILE cc_start: 0.8806 (mm) cc_final: 0.8571 (tp) REVERT: A 829 PHE cc_start: 0.7567 (m-80) cc_final: 0.7094 (p90) REVERT: A 898 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7567 (tpp80) REVERT: A 925 GLU cc_start: 0.8961 (tt0) cc_final: 0.8361 (tt0) REVERT: A 1023 VAL cc_start: 0.9474 (t) cc_final: 0.9026 (m) REVERT: A 1059 MET cc_start: 0.8729 (ttm) cc_final: 0.8495 (ttm) REVERT: A 1141 LYS cc_start: 0.8882 (mttt) cc_final: 0.8391 (mtpt) REVERT: A 1152 GLU cc_start: 0.8419 (tp30) cc_final: 0.7732 (tp30) REVERT: A 1155 ASN cc_start: 0.8772 (m-40) cc_final: 0.8107 (t0) REVERT: A 1260 TYR cc_start: 0.7796 (m-10) cc_final: 0.7506 (m-10) REVERT: A 1331 MET cc_start: 0.6720 (ttt) cc_final: 0.6252 (tmm) REVERT: B 286 ASP cc_start: 0.8699 (t70) cc_final: 0.8271 (t0) REVERT: B 371 ASP cc_start: 0.7148 (p0) cc_final: 0.6643 (m-30) REVERT: B 382 THR cc_start: 0.8120 (m) cc_final: 0.7782 (t) REVERT: B 603 LEU cc_start: 0.9066 (tp) cc_final: 0.8656 (tp) REVERT: B 633 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8052 (mm-40) REVERT: B 641 GLU cc_start: 0.8468 (tp30) cc_final: 0.7737 (tp30) REVERT: B 657 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 664 TRP cc_start: 0.7156 (m100) cc_final: 0.6933 (m100) REVERT: B 680 MET cc_start: 0.8489 (mmm) cc_final: 0.8006 (mtp) REVERT: B 702 CYS cc_start: 0.7837 (m) cc_final: 0.7489 (m) REVERT: B 775 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: B 822 SER cc_start: 0.8874 (m) cc_final: 0.8609 (t) REVERT: B 824 ILE cc_start: 0.8744 (mm) cc_final: 0.8506 (tp) REVERT: B 829 PHE cc_start: 0.7364 (m-80) cc_final: 0.6999 (p90) REVERT: B 925 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8412 (tt0) REVERT: B 1023 VAL cc_start: 0.9287 (t) cc_final: 0.8871 (m) REVERT: B 1059 MET cc_start: 0.8560 (ttm) cc_final: 0.8303 (ttm) REVERT: B 1066 ASN cc_start: 0.8797 (m-40) cc_final: 0.8501 (m110) REVERT: B 1076 GLN cc_start: 0.8161 (mp10) cc_final: 0.7946 (mp10) REVERT: B 1120 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8343 (mttt) REVERT: B 1152 GLU cc_start: 0.8323 (tp30) cc_final: 0.7795 (tp30) REVERT: B 1155 ASN cc_start: 0.8762 (m-40) cc_final: 0.8144 (t0) REVERT: B 1158 GLU cc_start: 0.7490 (tt0) cc_final: 0.7225 (tt0) REVERT: B 1161 GLU cc_start: 0.7567 (pm20) cc_final: 0.7243 (pm20) REVERT: B 1260 TYR cc_start: 0.7750 (m-10) cc_final: 0.7350 (m-10) REVERT: C 93 ASN cc_start: 0.8270 (t0) cc_final: 0.8036 (t0) REVERT: C 286 ASP cc_start: 0.8698 (t70) cc_final: 0.8421 (t0) REVERT: C 293 PHE cc_start: 0.8582 (t80) cc_final: 0.7980 (t80) REVERT: C 371 ASP cc_start: 0.6952 (p0) cc_final: 0.6399 (m-30) REVERT: C 529 LYS cc_start: 0.8387 (mmmm) cc_final: 0.7834 (mmmm) REVERT: C 601 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8487 (pt) REVERT: C 657 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8204 (p) REVERT: C 663 LYS cc_start: 0.8847 (tttt) cc_final: 0.8634 (tppp) REVERT: C 664 TRP cc_start: 0.7164 (m100) cc_final: 0.6914 (m100) REVERT: C 680 MET cc_start: 0.8168 (mmt) cc_final: 0.7576 (mtp) REVERT: C 701 GLU cc_start: 0.8127 (pt0) cc_final: 0.7777 (pm20) REVERT: C 711 GLN cc_start: 0.8783 (tt0) cc_final: 0.8242 (mt0) REVERT: C 805 GLN cc_start: 0.8699 (mt0) cc_final: 0.8336 (mp10) REVERT: C 829 PHE cc_start: 0.7543 (m-80) cc_final: 0.6997 (p90) REVERT: C 883 LYS cc_start: 0.9131 (mttm) cc_final: 0.8847 (mmtp) REVERT: C 898 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7511 (tpp80) REVERT: C 925 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8335 (tt0) REVERT: C 928 MET cc_start: 0.8732 (tpp) cc_final: 0.8227 (tpp) REVERT: C 938 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8316 (tpm-80) REVERT: C 1023 VAL cc_start: 0.9525 (OUTLIER) cc_final: 0.9262 (m) REVERT: C 1076 GLN cc_start: 0.7969 (mp10) cc_final: 0.7112 (tp40) REVERT: C 1141 LYS cc_start: 0.8747 (mttt) cc_final: 0.8303 (mtpt) REVERT: C 1152 GLU cc_start: 0.8381 (tp30) cc_final: 0.7850 (tp30) REVERT: C 1155 ASN cc_start: 0.8816 (m-40) cc_final: 0.8068 (t0) REVERT: C 1331 MET cc_start: 0.7216 (tpp) cc_final: 0.6584 (tpt) outliers start: 132 outliers final: 115 residues processed: 637 average time/residue: 0.1619 time to fit residues: 174.9990 Evaluate side-chains 652 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 529 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1303 GLU Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 368 optimal weight: 3.9990 chunk 369 optimal weight: 5.9990 chunk 365 optimal weight: 0.0570 chunk 189 optimal weight: 0.0870 chunk 364 optimal weight: 4.9990 chunk 159 optimal weight: 0.1980 chunk 170 optimal weight: 8.9990 chunk 319 optimal weight: 0.0770 chunk 336 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 overall best weight: 0.8836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1088 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.169403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.128866 restraints weight = 51179.530| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 4.02 r_work: 0.3466 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33048 Z= 0.140 Angle : 0.779 13.032 45426 Z= 0.358 Chirality : 0.048 0.330 5778 Planarity : 0.003 0.050 5376 Dihedral : 8.407 59.853 8439 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 3.82 % Allowed : 21.60 % Favored : 74.58 % 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: -2.42 (0.14), residues: 3717 helix: 1.13 (0.20), residues: 741 sheet: -1.60 (0.18), residues: 861 loop : -2.76 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 977 TYR 0.028 0.001 TYR B1067 PHE 0.029 0.001 PHE C1272 TRP 0.042 0.001 TRP A 222 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00298 (32790) covalent geometry : angle 0.69372 (44703) SS BOND : bond 0.00605 ( 42) SS BOND : angle 1.77853 ( 84) hydrogen bonds : bond 0.03451 ( 851) hydrogen bonds : angle 4.89018 ( 2427) Misc. bond : bond 0.00051 ( 3) link_ALPHA1-2 : bond 0.02508 ( 6) link_ALPHA1-2 : angle 3.35141 ( 18) link_ALPHA1-3 : bond 0.00816 ( 12) link_ALPHA1-3 : angle 2.89923 ( 36) link_ALPHA1-6 : bond 0.01572 ( 24) link_ALPHA1-6 : angle 2.31180 ( 72) link_BETA1-4 : bond 0.01015 ( 87) link_BETA1-4 : angle 2.56684 ( 261) link_BETA1-6 : bond 0.00350 ( 3) link_BETA1-6 : angle 1.31732 ( 9) link_NAG-ASN : bond 0.00627 ( 81) link_NAG-ASN : angle 3.59659 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 541 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8600 (t70) cc_final: 0.8170 (t0) REVERT: A 293 PHE cc_start: 0.8646 (t80) cc_final: 0.7700 (t80) REVERT: A 371 ASP cc_start: 0.7027 (p0) cc_final: 0.6254 (m-30) REVERT: A 372 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: A 382 THR cc_start: 0.8004 (m) cc_final: 0.7643 (t) REVERT: A 477 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7721 (p) REVERT: A 597 GLN cc_start: 0.8510 (mt0) cc_final: 0.8149 (tt0) REVERT: A 623 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: A 664 TRP cc_start: 0.6815 (m-10) cc_final: 0.6328 (m100) REVERT: A 702 CYS cc_start: 0.7718 (m) cc_final: 0.7496 (m) REVERT: A 711 GLN cc_start: 0.8725 (tt0) cc_final: 0.8213 (mt0) REVERT: A 824 ILE cc_start: 0.8770 (mm) cc_final: 0.8535 (tp) REVERT: A 829 PHE cc_start: 0.7547 (m-80) cc_final: 0.7091 (p90) REVERT: A 898 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7522 (tpp80) REVERT: A 925 GLU cc_start: 0.8950 (tt0) cc_final: 0.8372 (tt0) REVERT: A 999 ASP cc_start: 0.8218 (t0) cc_final: 0.7999 (t0) REVERT: A 1023 VAL cc_start: 0.9473 (t) cc_final: 0.9031 (m) REVERT: A 1059 MET cc_start: 0.8740 (ttm) cc_final: 0.8508 (ttm) REVERT: A 1141 LYS cc_start: 0.8870 (mttt) cc_final: 0.8393 (mtpt) REVERT: A 1152 GLU cc_start: 0.8409 (tp30) cc_final: 0.7748 (tp30) REVERT: A 1155 ASN cc_start: 0.8744 (m-40) cc_final: 0.7951 (t0) REVERT: A 1260 TYR cc_start: 0.7763 (m-10) cc_final: 0.7490 (m-10) REVERT: A 1331 MET cc_start: 0.6715 (ttt) cc_final: 0.6245 (tmm) REVERT: B 286 ASP cc_start: 0.8701 (t70) cc_final: 0.8247 (t0) REVERT: B 371 ASP cc_start: 0.7079 (p0) cc_final: 0.6571 (m-30) REVERT: B 382 THR cc_start: 0.8121 (m) cc_final: 0.7771 (t) REVERT: B 603 LEU cc_start: 0.9038 (tp) cc_final: 0.8651 (tp) REVERT: B 633 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8017 (mm-40) REVERT: B 657 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8172 (p) REVERT: B 664 TRP cc_start: 0.7156 (m100) cc_final: 0.6835 (m100) REVERT: B 680 MET cc_start: 0.8471 (mmm) cc_final: 0.7961 (mtp) REVERT: B 702 CYS cc_start: 0.7746 (m) cc_final: 0.7404 (m) REVERT: B 775 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: B 805 GLN cc_start: 0.8738 (mt0) cc_final: 0.8422 (mp10) REVERT: B 822 SER cc_start: 0.8850 (m) cc_final: 0.8547 (t) REVERT: B 824 ILE cc_start: 0.8721 (mm) cc_final: 0.8489 (tp) REVERT: B 829 PHE cc_start: 0.7355 (m-80) cc_final: 0.7002 (p90) REVERT: B 925 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8436 (tt0) REVERT: B 1023 VAL cc_start: 0.9292 (t) cc_final: 0.8868 (m) REVERT: B 1059 MET cc_start: 0.8576 (ttm) cc_final: 0.8298 (ttm) REVERT: B 1076 GLN cc_start: 0.8161 (mp10) cc_final: 0.7955 (mp10) REVERT: B 1120 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8344 (mttt) REVERT: B 1152 GLU cc_start: 0.8298 (tp30) cc_final: 0.7765 (tp30) REVERT: B 1155 ASN cc_start: 0.8745 (m-40) cc_final: 0.8134 (t0) REVERT: B 1158 GLU cc_start: 0.7459 (tt0) cc_final: 0.7179 (tt0) REVERT: B 1161 GLU cc_start: 0.7581 (pm20) cc_final: 0.7233 (pm20) REVERT: B 1199 MET cc_start: 0.8042 (mtt) cc_final: 0.7764 (mtm) REVERT: B 1260 TYR cc_start: 0.7719 (m-10) cc_final: 0.7343 (m-10) REVERT: C 93 ASN cc_start: 0.8295 (t0) cc_final: 0.8002 (t0) REVERT: C 184 PHE cc_start: 0.6967 (m-80) cc_final: 0.6665 (m-80) REVERT: C 286 ASP cc_start: 0.8705 (t70) cc_final: 0.8435 (t0) REVERT: C 293 PHE cc_start: 0.8557 (t80) cc_final: 0.7922 (t80) REVERT: C 371 ASP cc_start: 0.6905 (p0) cc_final: 0.6286 (m-30) REVERT: C 529 LYS cc_start: 0.8360 (mmmm) cc_final: 0.7797 (mmmm) REVERT: C 601 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8486 (pt) REVERT: C 657 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8236 (p) REVERT: C 664 TRP cc_start: 0.7176 (m100) cc_final: 0.6919 (m100) REVERT: C 701 GLU cc_start: 0.8095 (pt0) cc_final: 0.7651 (pm20) REVERT: C 711 GLN cc_start: 0.8795 (tt0) cc_final: 0.8263 (mt0) REVERT: C 805 GLN cc_start: 0.8699 (mt0) cc_final: 0.8330 (mp10) REVERT: C 829 PHE cc_start: 0.7542 (m-80) cc_final: 0.6981 (p90) REVERT: C 883 LYS cc_start: 0.9122 (mttm) cc_final: 0.8892 (mmtp) REVERT: C 898 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7493 (tpp80) REVERT: C 925 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8344 (tt0) REVERT: C 928 MET cc_start: 0.8724 (tpp) cc_final: 0.8229 (tpp) REVERT: C 938 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8363 (tpm-80) REVERT: C 1023 VAL cc_start: 0.9518 (OUTLIER) cc_final: 0.9179 (m) REVERT: C 1141 LYS cc_start: 0.8769 (mttt) cc_final: 0.8310 (mtpt) REVERT: C 1152 GLU cc_start: 0.8362 (tp30) cc_final: 0.7829 (tp30) REVERT: C 1155 ASN cc_start: 0.8785 (m-40) cc_final: 0.8082 (t0) REVERT: C 1244 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8218 (mp0) REVERT: C 1331 MET cc_start: 0.7219 (tpp) cc_final: 0.6596 (tpt) outliers start: 125 outliers final: 111 residues processed: 623 average time/residue: 0.1620 time to fit residues: 171.6641 Evaluate side-chains 647 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 527 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 286 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 209 optimal weight: 0.5980 chunk 250 optimal weight: 0.0270 chunk 216 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.171952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.128052 restraints weight = 52157.383| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.97 r_work: 0.3475 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33048 Z= 0.136 Angle : 0.766 12.707 45426 Z= 0.351 Chirality : 0.048 0.325 5778 Planarity : 0.003 0.048 5376 Dihedral : 8.141 59.875 8439 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 3.61 % Allowed : 21.85 % Favored : 74.55 % 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: -2.38 (0.14), residues: 3717 helix: 1.17 (0.20), residues: 741 sheet: -1.61 (0.18), residues: 861 loop : -2.73 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 977 TYR 0.030 0.001 TYR B1067 PHE 0.028 0.001 PHE C1272 TRP 0.037 0.001 TRP A 222 HIS 0.003 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00287 (32790) covalent geometry : angle 0.68312 (44703) SS BOND : bond 0.00492 ( 42) SS BOND : angle 1.63428 ( 84) hydrogen bonds : bond 0.03358 ( 851) hydrogen bonds : angle 4.83366 ( 2427) Misc. bond : bond 0.00063 ( 3) link_ALPHA1-2 : bond 0.02543 ( 6) link_ALPHA1-2 : angle 3.31925 ( 18) link_ALPHA1-3 : bond 0.00794 ( 12) link_ALPHA1-3 : angle 2.84821 ( 36) link_ALPHA1-6 : bond 0.01585 ( 24) link_ALPHA1-6 : angle 2.28833 ( 72) link_BETA1-4 : bond 0.01013 ( 87) link_BETA1-4 : angle 2.52574 ( 261) link_BETA1-6 : bond 0.00401 ( 3) link_BETA1-6 : angle 1.23054 ( 9) link_NAG-ASN : bond 0.00620 ( 81) link_NAG-ASN : angle 3.52502 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7881.85 seconds wall clock time: 136 minutes 2.75 seconds (8162.75 seconds total)