Starting phenix.real_space_refine on Mon May 4 04:18:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jkf_61553/05_2026/9jkf_61553.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jkf_61553/05_2026/9jkf_61553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jkf_61553/05_2026/9jkf_61553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jkf_61553/05_2026/9jkf_61553.map" model { file = "/net/cci-nas-00/data/ceres_data/9jkf_61553/05_2026/9jkf_61553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jkf_61553/05_2026/9jkf_61553.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 11202 2.51 5 N 2782 2.21 5 O 4044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18127 Number of models: 1 Model: "" Number of chains: 78 Chain: "B" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1206 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 1, 'TRANS': 148} Chain: "C" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3760 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 22, 'TRANS': 453} Chain: "D" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1379 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "E" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3731 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 22, 'TRANS': 450} Chain: "A" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3740 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 22, 'TRANS': 451} Chain: "F" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1159 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" 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: "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: 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: "W" 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: "X" 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: "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: 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: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" 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: "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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 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: 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: "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: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "y" Number of atoms: 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: "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: "0" 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: "1" 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: "2" 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: "3" 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: "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: "5" 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: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 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: "8" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "9" 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: "AA" 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: "BA" 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: "CA" 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: "DA" 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: "EA" 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: "FA" 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: "GA" 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: "HA" 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: "IA" 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: "JA" 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: "KA" 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: "LA" 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: "MA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'83G': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'83G': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'83G': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.32, per 1000 atoms: 0.24 Number of scatterers: 18127 At special positions: 0 Unit cell: (138.6, 150.15, 155.1, 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 99 16.00 O 4044 8.00 N 2782 7.00 C 11202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN X 4 " - " MAN X 5 " " MAN p 4 " - " MAN p 5 " " MAN u 4 " - " MAN u 5 " " MANDA 4 " - " MANDA 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 2 3 " - " MAN 2 4 " " BMA 8 3 " - " MAN 8 6 " " MAN 8 4 " - " MAN 8 5 " " BMA 9 3 " - " MAN 9 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA p 3 " - " MAN p 4 " " MAN p 6 " - " MAN p 7 " " BMA u 3 " - " MAN u 4 " " BMA v 3 " - " MAN v 4 " " BMACA 3 " - " MANCA 4 " " BMADA 3 " - " MANDA 4 " " BMAFA 3 " - " MANFA 4 " " BMAGA 3 " - " MANGA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 8 3 " - " MAN 8 4 " " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 7 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 5 " " BMA p 3 " - " MAN p 6 " " MAN p 6 " - " MAN p 8 " " BMA t 3 " - " MAN t 4 " " BMA u 3 " - " MAN u 6 " " MAN u 6 " - " MAN u 7 " " BMA x 3 " - " MAN x 4 " " BMADA 3 " - " MANDA 6 " " MANDA 6 " - " MANDA 7 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " 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 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG 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 i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " 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 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 u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGGA 2 " - " BMAGA 3 " " NAGHA 1 " - " NAGHA 2 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " " NAGKA 1 " - " NAGKA 2 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " BETA1-6 " NAG O 1 " - " FUC O 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG d 1 " - " FUC d 4 " " NAG y 1 " - " FUC y 4 " " NAGJA 1 " - " FUCJA 4 " NAG-ASN " NAG 0 1 " - " ASN A 88 " " NAG 1 1 " - " ASN A 130 " " NAG 2 1 " - " ASN A 156 " " NAG 3 1 " - " ASN A 160 " " NAG 4 1 " - " ASN A 188 " " NAG 5 1 " - " ASN A 197 " " NAG 6 1 " - " ASN A 234 " " NAG 7 1 " - " ASN A 241 " " NAG 8 1 " - " ASN A 262 " " NAG 9 1 " - " ASN A 276 " " NAG A 802 " - " ASN A 356 " " NAG C 802 " - " ASN C 356 " " NAG C 803 " - " ASN C 397 " " NAG E 802 " - " ASN E 356 " " NAG G 1 " - " ASN B 611 " " NAG H 1 " - " ASN B 616 " " NAG I 1 " - " ASN B 625 " " NAG J 1 " - " ASN B 637 " " NAG K 1 " - " ASN C 88 " " NAG L 1 " - " ASN C 130 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 197 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 241 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 276 " " NAG U 1 " - " ASN C 295 " " NAG V 1 " - " ASN C 301 " " NAG W 1 " - " ASN C 332 " " NAG X 1 " - " ASN C 339 " " NAG Y 1 " - " ASN C 362 " " NAG Z 1 " - " ASN C 386 " " NAG a 1 " - " ASN C 392 " " NAG b 1 " - " ASN C 401 " " NAG c 1 " - " ASN C 448 " " NAG d 1 " - " ASN D 611 " " NAG e 1 " - " ASN D 616 " " NAG f 1 " - " ASN D 625 " " NAG g 1 " - " ASN D 637 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 130 " " NAG j 1 " - " ASN E 156 " " NAG k 1 " - " ASN E 160 " " NAG l 1 " - " ASN E 188 " " NAG m 1 " - " ASN E 197 " " NAG n 1 " - " ASN E 234 " " NAG o 1 " - " ASN E 241 " " NAG p 1 " - " ASN E 262 " " NAG q 1 " - " ASN E 276 " " NAG r 1 " - " ASN E 295 " " NAG s 1 " - " ASN E 301 " " NAG t 1 " - " ASN E 332 " " NAG u 1 " - " ASN E 339 " " NAG v 1 " - " ASN E 362 " " NAG w 1 " - " ASN E 386 " " NAG x 1 " - " ASN E 392 " " NAG y 1 " - " ASN E 401 " " NAG z 1 " - " ASN E 448 " " NAGAA 1 " - " ASN A 295 " " NAGBA 1 " - " ASN A 301 " " NAGCA 1 " - " ASN A 332 " " NAGDA 1 " - " ASN A 339 " " NAGEA 1 " - " ASN A 362 " " NAGFA 1 " - " ASN A 386 " " NAGGA 1 " - " ASN A 392 " " NAGHA 1 " - " ASN A 401 " " NAGIA 1 " - " ASN A 448 " " NAGJA 1 " - " ASN F 611 " " NAGKA 1 " - " ASN F 616 " " NAGLA 1 " - " ASN F 625 " " NAGMA 1 " - " ASN F 637 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 571.8 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3534 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 32 sheets defined 29.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 539 through 564 removed outlier: 3.591A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.604A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 643 removed outlier: 4.974A pdb=" N ASN B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 664 removed outlier: 4.009A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.324A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.872A pdb=" N ASN C 392 " --> pdb=" O GLN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 removed outlier: 3.844A pdb=" N ASN C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 484 removed outlier: 4.123A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 564 removed outlier: 4.044A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 634 removed outlier: 3.897A pdb=" N ARG D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 661 removed outlier: 4.605A pdb=" N GLY D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 674 Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.903A pdb=" N TYR E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.953A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 334 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 409 through 413 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.687A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.826A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.061A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.647A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.011A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 553 removed outlier: 4.154A pdb=" N ASN F 553 " --> pdb=" O VAL F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 569 removed outlier: 4.038A pdb=" N LEU F 568 " --> pdb=" O HIS F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.784A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.653A pdb=" N ARG F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 662 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 4.930A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 498 through 499 removed outlier: 5.305A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.688A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA6, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AA7, first strand: chain 'C' and resid 156 through 162 removed outlier: 3.613A pdb=" N CYS C 157 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 159 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP C 172 " --> pdb=" O PHE C 159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 161 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.513A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.317A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.855A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AB4, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.527A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 93 through 94 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 175 Processing sheet with id=AB9, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.187A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.055A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.489A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.861A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.861A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.489A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 301 through 308 removed outlier: 4.222A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 360 through 361 removed outlier: 3.828A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 374 through 377 Processing sheet with id=AC6, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.643A pdb=" N VAL A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AC9, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AD1, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.621A pdb=" N ALA A 433 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.451A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.077A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.632A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 375 through 378 removed outlier: 3.513A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1557 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: 3.26 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3223 1.33 - 1.45: 5021 1.45 - 1.57: 10055 1.57 - 1.69: 10 1.69 - 1.81: 138 Bond restraints: 18447 Sorted by residual: bond pdb=" N PHE A 353 " pdb=" CA PHE A 353 " ideal model delta sigma weight residual 1.457 1.487 -0.031 6.40e-03 2.44e+04 2.29e+01 bond pdb=" C GLN F 562 " pdb=" N GLN F 563 " ideal model delta sigma weight residual 1.332 1.396 -0.064 1.40e-02 5.10e+03 2.08e+01 bond pdb=" N VAL B 608 " pdb=" CA VAL B 608 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.03e+01 bond pdb=" N VAL E 182 " pdb=" CA VAL E 182 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.00e-03 1.23e+04 1.62e+01 bond pdb=" N ILE A 184 " pdb=" CA ILE A 184 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.60e+01 ... (remaining 18442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 23277 2.85 - 5.69: 1707 5.69 - 8.54: 76 8.54 - 11.38: 9 11.38 - 14.23: 7 Bond angle restraints: 25076 Sorted by residual: angle pdb=" N ASN C 397 " pdb=" CA ASN C 397 " pdb=" C ASN C 397 " ideal model delta sigma weight residual 111.71 103.64 8.07 1.15e+00 7.56e-01 4.93e+01 angle pdb=" N LEU F 556 " pdb=" CA LEU F 556 " pdb=" C LEU F 556 " ideal model delta sigma weight residual 113.01 105.84 7.17 1.20e+00 6.94e-01 3.57e+01 angle pdb=" CA ARG E 469 " pdb=" C ARG E 469 " pdb=" N PRO E 470 " ideal model delta sigma weight residual 117.67 123.68 -6.01 1.01e+00 9.80e-01 3.54e+01 angle pdb=" CA GLY E 441 " pdb=" C GLY E 441 " pdb=" O GLY E 441 " ideal model delta sigma weight residual 122.45 118.25 4.20 7.20e-01 1.93e+00 3.41e+01 angle pdb=" CA GLY A 324 " pdb=" C GLY A 324 " pdb=" O GLY A 324 " ideal model delta sigma weight residual 122.52 118.23 4.29 7.90e-01 1.60e+00 2.95e+01 ... (remaining 25071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.45: 12807 28.45 - 56.89: 653 56.89 - 85.34: 390 85.34 - 113.78: 274 113.78 - 142.23: 22 Dihedral angle restraints: 14146 sinusoidal: 8688 harmonic: 5458 Sorted by residual: dihedral pdb=" CB CYS E 228 " pdb=" SG CYS E 228 " pdb=" SG CYS E 239 " pdb=" CB CYS E 239 " ideal model delta sinusoidal sigma weight residual 93.00 154.69 -61.69 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -129.60 43.60 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.76 41.76 1 1.00e+01 1.00e-02 2.44e+01 ... (remaining 14143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 3472 0.293 - 0.585: 52 0.585 - 0.878: 8 0.878 - 1.171: 8 1.171 - 1.463: 3 Chirality restraints: 3543 Sorted by residual: chirality pdb=" C1 MAN i 4 " pdb=" O3 BMA i 3 " pdb=" C2 MAN i 4 " pdb=" O5 MAN i 4 " both_signs ideal model delta sigma weight residual False 2.40 1.36 1.04 2.00e-02 2.50e+03 2.70e+03 chirality pdb=" C1 MAN 1 4 " pdb=" O3 BMA 1 3 " pdb=" C2 MAN 1 4 " pdb=" O5 MAN 1 4 " both_signs ideal model delta sigma weight residual False 2.40 1.43 0.97 2.00e-02 2.50e+03 2.33e+03 chirality pdb=" C1 NAG 5 2 " pdb=" O4 NAG 5 1 " pdb=" C2 NAG 5 2 " pdb=" O5 NAG 5 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-02 2.50e+03 8.49e+02 ... (remaining 3540 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG 5 2 " 0.342 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG 5 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG 5 2 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG 5 2 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG 5 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " -0.326 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG h 2 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " 0.508 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG y 1 " -0.325 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG y 1 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG y 1 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG y 1 " 0.506 2.00e-02 2.50e+03 pdb=" O7 NAG y 1 " -0.162 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2905 2.79 - 3.31: 19315 3.31 - 3.84: 30462 3.84 - 4.37: 38052 4.37 - 4.90: 56773 Nonbonded interactions: 147507 Sorted by model distance: nonbonded pdb=" OD1 ASN C 401 " pdb=" N LEU C 402 " model vdw 2.257 3.120 nonbonded pdb=" O GLN C 344 " pdb=" OG1 THR C 347 " model vdw 2.315 3.040 nonbonded pdb=" O ILE A 225 " pdb=" OG1 THR A 244 " model vdw 2.318 3.040 nonbonded pdb=" ND1 HIS E 249 " pdb=" OH TYR E 486 " model vdw 2.355 3.120 nonbonded pdb=" O LEU D 641 " pdb=" OG1 THR D 644 " model vdw 2.373 3.040 ... (remaining 147502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 1 through 2) selection = (chain '3' and resid 1 through 2) selection = (chain '5' and resid 1 through 2) selection = (chain '7' and resid 1 through 2) selection = (chain 'AA' and resid 1 through 2) selection = (chain 'BA' and resid 1 through 2) selection = (chain 'EA' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'IA' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) selection = (chain 's' and resid 1 through 2) selection = (chain 'w' and resid 1 through 2) selection = (chain 'z' and resid 1 through 2) } ncs_group { reference = chain '1' selection = chain 'T' selection = chain 'W' selection = chain 'i' selection = chain 'j' } ncs_group { reference = (chain '2' and resid 1 through 3) selection = (chain '9' and resid 1 through 3) selection = (chain 'CA' and resid 1 through 3) selection = (chain 'FA' and resid 1 through 3) selection = (chain 'GA' and resid 1 through 3) selection = (chain 'JA' and resid 1 through 3) selection = (chain 'Y' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) selection = (chain 't' and resid 1 through 3) selection = (chain 'v' and resid 1 through 3) selection = (chain 'x' and resid 1 through 3) selection = (chain 'y' and resid 1 through 3) } ncs_group { reference = chain '4' selection = chain '6' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'KA' selection = chain 'LA' selection = chain 'MA' selection = chain 'N' selection = chain 'U' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'l' selection = chain 'n' } ncs_group { reference = (chain '8' and (resid 1 or resid 4 through 6)) selection = (chain 'DA' and (resid 2 or resid 5 through 7)) selection = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'X' and (resid 2 or resid 5 through 7)) selection = (chain 'u' and (resid 2 or resid 5 through 7)) } ncs_group { reference = (chain 'A' and (resid 33 through 507 or resid 802)) selection = (chain 'C' and (resid 33 through 507 or resid 803)) selection = (chain 'E' and (resid 33 through 507 or resid 802)) } ncs_group { reference = (chain 'B' and resid 520 through 662) selection = (chain 'D' and resid 520 through 662) selection = (chain 'F' and resid 520 through 662) } 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: 0.580 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.070 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 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 : 0.013 0.079 18717 Z= 0.929 Angle : 1.832 27.189 25856 Z= 1.098 Chirality : 0.131 1.463 3543 Planarity : 0.035 0.295 2831 Dihedral : 25.393 142.231 10522 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 1.23 % Allowed : 7.91 % Favored : 90.87 % Rotamer: Outliers : 5.89 % Allowed : 9.34 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.16), residues: 1872 helix: -1.91 (0.21), residues: 462 sheet: -1.76 (0.26), residues: 342 loop : -2.43 (0.16), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.016 0.002 TYR C 435 PHE 0.028 0.002 PHE C 396 TRP 0.016 0.002 TRP D 623 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.01331 (18447) covalent geometry : angle 1.60974 (25076) SS BOND : bond 0.00519 ( 30) SS BOND : angle 1.10822 ( 60) hydrogen bonds : bond 0.21586 ( 541) hydrogen bonds : angle 9.64906 ( 1557) link_ALPHA1-2 : bond 0.02058 ( 6) link_ALPHA1-2 : angle 2.59094 ( 18) link_ALPHA1-3 : bond 0.03064 ( 20) link_ALPHA1-3 : angle 4.86646 ( 60) link_ALPHA1-6 : bond 0.02147 ( 16) link_ALPHA1-6 : angle 3.11547 ( 48) link_BETA1-4 : bond 0.01793 ( 121) link_BETA1-4 : angle 4.48661 ( 363) link_BETA1-6 : bond 0.00167 ( 4) link_BETA1-6 : angle 1.79706 ( 12) link_NAG-ASN : bond 0.01735 ( 73) link_NAG-ASN : angle 7.51111 ( 219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 504 time to evaluate : 0.643 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: B 528 SER cc_start: 0.7437 (m) cc_final: 0.6943 (p) REVERT: B 563 GLN cc_start: 0.7924 (mt0) cc_final: 0.7323 (pt0) REVERT: B 586 TYR cc_start: 0.7941 (t80) cc_final: 0.7693 (t80) REVERT: B 601 LYS cc_start: 0.6837 (tptt) cc_final: 0.6222 (tppt) REVERT: B 602 LEU cc_start: 0.7338 (mt) cc_final: 0.6957 (mp) REVERT: B 629 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7830 (tpp) REVERT: B 630 GLU cc_start: 0.8766 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 635 ILE cc_start: 0.8821 (mm) cc_final: 0.8595 (mt) REVERT: B 636 ASP cc_start: 0.8940 (t0) cc_final: 0.8698 (t0) REVERT: B 655 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7847 (mmmt) REVERT: C 68 VAL cc_start: 0.6668 (OUTLIER) cc_final: 0.6324 (m) REVERT: C 98 ASN cc_start: 0.8394 (t0) cc_final: 0.8091 (t0) REVERT: C 150 MET cc_start: 0.7189 (mpp) cc_final: 0.5636 (mmt) REVERT: C 159 PHE cc_start: 0.9495 (OUTLIER) cc_final: 0.9052 (p90) REVERT: C 217 TYR cc_start: 0.7041 (m-80) cc_final: 0.6829 (m-80) REVERT: C 432 LYS cc_start: 0.7199 (mttt) cc_final: 0.6777 (mmmt) REVERT: C 483 LEU cc_start: 0.8625 (mt) cc_final: 0.8420 (mt) REVERT: C 500 LYS cc_start: 0.8243 (tttt) cc_final: 0.7865 (tptt) REVERT: D 560 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8395 (mt-10) REVERT: D 584 GLU cc_start: 0.7983 (pt0) cc_final: 0.7431 (pt0) REVERT: D 591 GLN cc_start: 0.8091 (tt0) cc_final: 0.7584 (tt0) REVERT: D 621 MET cc_start: 0.9141 (mpp) cc_final: 0.8839 (mtt) REVERT: D 648 GLU cc_start: 0.9428 (tt0) cc_final: 0.9142 (tm-30) REVERT: D 651 ASN cc_start: 0.8164 (t0) cc_final: 0.7822 (t0) REVERT: E 113 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: E 125 LEU cc_start: 0.8788 (tp) cc_final: 0.8565 (tp) REVERT: E 155 LYS cc_start: 0.6596 (mttt) cc_final: 0.6057 (mmtt) REVERT: E 261 LEU cc_start: 0.9164 (mt) cc_final: 0.8849 (mm) REVERT: E 373 MET cc_start: 0.7898 (mtp) cc_final: 0.7626 (ptm) REVERT: E 381 GLU cc_start: 0.8370 (tp30) cc_final: 0.7795 (tp30) REVERT: E 425 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8694 (m-40) REVERT: E 434 MET cc_start: 0.8659 (ttp) cc_final: 0.8418 (ptm) REVERT: E 435 TYR cc_start: 0.7931 (t80) cc_final: 0.7566 (t80) REVERT: A 39 TYR cc_start: 0.8158 (m-80) cc_final: 0.7882 (m-80) REVERT: A 102 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8076 (mm-30) REVERT: A 150 MET cc_start: 0.7803 (mtm) cc_final: 0.7228 (mtm) REVERT: A 191 TYR cc_start: 0.7765 (m-80) cc_final: 0.7213 (m-80) REVERT: A 219 THR cc_start: 0.9105 (p) cc_final: 0.8468 (p) REVERT: A 245 VAL cc_start: 0.8237 (m) cc_final: 0.7648 (p) REVERT: A 289 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6759 (ttpt) REVERT: A 342 LEU cc_start: 0.9070 (mt) cc_final: 0.8867 (mt) REVERT: A 373 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7389 (ptp) REVERT: A 447 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.6285 (m) REVERT: A 453 ILE cc_start: 0.8075 (mt) cc_final: 0.7766 (mt) REVERT: A 475 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8108 (mtp) REVERT: F 534 SER cc_start: 0.8291 (t) cc_final: 0.7603 (p) REVERT: F 584 GLU cc_start: 0.7349 (pt0) cc_final: 0.7117 (pt0) REVERT: F 601 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7912 (ttmm) REVERT: F 636 ASP cc_start: 0.9300 (t0) cc_final: 0.9087 (t0) outliers start: 99 outliers final: 17 residues processed: 560 average time/residue: 0.1507 time to fit residues: 123.3405 Evaluate side-chains 328 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 302 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 400 TRP Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 652 GLN C 66 HIS C 99 ASN C 105 HIS C 246 GLN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 551 GLN D 563 GLN E 82 GLN E 195 ASN E 363 GLN E 374 HIS E 428 GLN F 652 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.098285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.075750 restraints weight = 56254.264| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.33 r_work: 0.3131 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18717 Z= 0.219 Angle : 1.120 20.291 25856 Z= 0.461 Chirality : 0.061 1.322 3543 Planarity : 0.005 0.044 2831 Dihedral : 21.247 137.350 6976 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 4.88 % Allowed : 14.99 % Favored : 80.13 % 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: -1.91 (0.18), residues: 1872 helix: -0.08 (0.22), residues: 474 sheet: -1.52 (0.24), residues: 411 loop : -1.75 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 579 TYR 0.031 0.002 TYR B 638 PHE 0.026 0.002 PHE E 382 TRP 0.022 0.002 TRP A 338 HIS 0.009 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00456 (18447) covalent geometry : angle 0.97683 (25076) SS BOND : bond 0.01004 ( 30) SS BOND : angle 1.39307 ( 60) hydrogen bonds : bond 0.05655 ( 541) hydrogen bonds : angle 6.82287 ( 1557) link_ALPHA1-2 : bond 0.00740 ( 6) link_ALPHA1-2 : angle 1.94305 ( 18) link_ALPHA1-3 : bond 0.02379 ( 20) link_ALPHA1-3 : angle 3.04823 ( 60) link_ALPHA1-6 : bond 0.00690 ( 16) link_ALPHA1-6 : angle 1.78784 ( 48) link_BETA1-4 : bond 0.00912 ( 121) link_BETA1-4 : angle 3.38512 ( 363) link_BETA1-6 : bond 0.00326 ( 4) link_BETA1-6 : angle 1.61319 ( 12) link_NAG-ASN : bond 0.00579 ( 73) link_NAG-ASN : angle 3.94639 ( 219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 297 time to evaluate : 0.619 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: B 535 MET cc_start: 0.7959 (ptp) cc_final: 0.7627 (tmm) REVERT: B 617 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9103 (mttp) REVERT: B 648 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8387 (mt-10) REVERT: B 652 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8903 (tp-100) REVERT: B 655 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8957 (mmmt) REVERT: C 173 TYR cc_start: 0.7802 (p90) cc_final: 0.7572 (p90) REVERT: C 318 TYR cc_start: 0.8896 (m-80) cc_final: 0.8628 (m-80) REVERT: C 426 MET cc_start: 0.7842 (tpp) cc_final: 0.7121 (tpp) REVERT: C 435 TYR cc_start: 0.9362 (t80) cc_final: 0.9135 (t80) REVERT: C 500 LYS cc_start: 0.8424 (tttt) cc_final: 0.8025 (tptt) REVERT: D 535 MET cc_start: 0.8856 (mtm) cc_final: 0.8526 (mtp) REVERT: D 553 ASN cc_start: 0.8993 (t0) cc_final: 0.8627 (t0) REVERT: D 560 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8646 (mt-10) REVERT: D 591 GLN cc_start: 0.8862 (tt0) cc_final: 0.8362 (tt0) REVERT: D 621 MET cc_start: 0.9144 (mpp) cc_final: 0.8939 (mtt) REVERT: D 626 MET cc_start: 0.8677 (tpp) cc_final: 0.8059 (mpp) REVERT: E 39 TYR cc_start: 0.8366 (m-80) cc_final: 0.8049 (m-10) REVERT: E 195 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6491 (t0) REVERT: E 260 LEU cc_start: 0.8953 (mt) cc_final: 0.8703 (mp) REVERT: E 381 GLU cc_start: 0.8668 (tp30) cc_final: 0.8294 (tp30) REVERT: A 82 GLN cc_start: 0.7459 (mm110) cc_final: 0.7040 (mt0) REVERT: A 104 MET cc_start: 0.9096 (ttt) cc_final: 0.8373 (ttt) REVERT: A 191 TYR cc_start: 0.8923 (m-80) cc_final: 0.8471 (m-80) REVERT: A 342 LEU cc_start: 0.9454 (mt) cc_final: 0.9228 (mt) REVERT: A 447 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8026 (m) REVERT: A 494 LEU cc_start: 0.9606 (tp) cc_final: 0.9308 (mt) REVERT: F 542 ARG cc_start: 0.9288 (ptm-80) cc_final: 0.8595 (ptm160) REVERT: F 601 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8615 (ttmm) REVERT: F 636 ASP cc_start: 0.9354 (t0) cc_final: 0.9139 (t0) REVERT: F 647 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8483 (mp0) outliers start: 82 outliers final: 43 residues processed: 352 average time/residue: 0.1405 time to fit residues: 74.0488 Evaluate side-chains 267 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 400 TRP Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 0.6980 chunk 154 optimal weight: 0.0470 chunk 3 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 652 GLN C 136 ASN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 553 ASN D 575 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN F 550 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.097667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.075062 restraints weight = 56056.241| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.36 r_work: 0.3114 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18717 Z= 0.165 Angle : 0.978 19.447 25856 Z= 0.402 Chirality : 0.055 0.789 3543 Planarity : 0.004 0.048 2831 Dihedral : 17.315 130.034 6949 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 4.46 % Allowed : 17.37 % Favored : 78.17 % 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: -1.29 (0.18), residues: 1872 helix: 0.73 (0.23), residues: 474 sheet: -1.33 (0.25), residues: 397 loop : -1.43 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 557 TYR 0.017 0.001 TYR B 638 PHE 0.033 0.001 PHE D 522 TRP 0.026 0.001 TRP B 610 HIS 0.012 0.001 HIS E 462 Details of bonding type rmsd covalent geometry : bond 0.00334 (18447) covalent geometry : angle 0.85789 (25076) SS BOND : bond 0.00284 ( 30) SS BOND : angle 1.12500 ( 60) hydrogen bonds : bond 0.04913 ( 541) hydrogen bonds : angle 6.13834 ( 1557) link_ALPHA1-2 : bond 0.00589 ( 6) link_ALPHA1-2 : angle 2.23301 ( 18) link_ALPHA1-3 : bond 0.02285 ( 20) link_ALPHA1-3 : angle 3.11868 ( 60) link_ALPHA1-6 : bond 0.00689 ( 16) link_ALPHA1-6 : angle 1.61665 ( 48) link_BETA1-4 : bond 0.00791 ( 121) link_BETA1-4 : angle 2.91625 ( 363) link_BETA1-6 : bond 0.00393 ( 4) link_BETA1-6 : angle 1.40397 ( 12) link_NAG-ASN : bond 0.00502 ( 73) link_NAG-ASN : angle 3.23680 ( 219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 255 time to evaluate : 0.700 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: B 535 MET cc_start: 0.7593 (ptp) cc_final: 0.7197 (tmm) REVERT: B 564 HIS cc_start: 0.6783 (t-90) cc_final: 0.6559 (m-70) REVERT: B 586 TYR cc_start: 0.9182 (t80) cc_final: 0.8421 (t80) REVERT: B 626 MET cc_start: 0.8355 (mtp) cc_final: 0.6536 (mtp) REVERT: B 648 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8556 (mt-10) REVERT: B 655 LYS cc_start: 0.9294 (mmtt) cc_final: 0.9073 (mptt) REVERT: B 658 GLN cc_start: 0.8324 (mp10) cc_final: 0.8024 (mp10) REVERT: D 537 LEU cc_start: 0.7814 (mp) cc_final: 0.7404 (tp) REVERT: D 550 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8822 (pp30) REVERT: D 560 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8442 (mt-10) REVERT: D 591 GLN cc_start: 0.8753 (tt0) cc_final: 0.8208 (tt0) REVERT: D 657 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6921 (pt0) REVERT: D 659 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8528 (pp20) REVERT: E 39 TYR cc_start: 0.8454 (m-80) cc_final: 0.7949 (m-10) REVERT: E 150 MET cc_start: 0.6655 (tpt) cc_final: 0.4998 (tpt) REVERT: E 195 ASN cc_start: 0.7851 (t0) cc_final: 0.7143 (t0) REVERT: E 373 MET cc_start: 0.8906 (ptm) cc_final: 0.8461 (ptm) REVERT: E 381 GLU cc_start: 0.8563 (tp30) cc_final: 0.8322 (tp30) REVERT: A 82 GLN cc_start: 0.7506 (mm110) cc_final: 0.6947 (mt0) REVERT: A 104 MET cc_start: 0.9173 (ttt) cc_final: 0.8563 (ttt) REVERT: A 109 ILE cc_start: 0.9573 (mt) cc_final: 0.9357 (mt) REVERT: A 191 TYR cc_start: 0.8960 (m-80) cc_final: 0.8428 (m-80) REVERT: A 342 LEU cc_start: 0.9478 (mt) cc_final: 0.9164 (mt) REVERT: A 494 LEU cc_start: 0.9547 (tp) cc_final: 0.9281 (mt) REVERT: F 542 ARG cc_start: 0.9273 (ptm-80) cc_final: 0.8907 (ptm160) REVERT: F 601 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8832 (ttmm) REVERT: F 603 ILE cc_start: 0.9296 (mt) cc_final: 0.9079 (mt) REVERT: F 632 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: F 647 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8724 (mp0) outliers start: 75 outliers final: 43 residues processed: 306 average time/residue: 0.1324 time to fit residues: 61.2899 Evaluate side-chains 258 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 559 ILE Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 GLU Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 42 optimal weight: 0.0170 chunk 138 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 overall best weight: 1.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN A 195 ASN F 550 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.094869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071673 restraints weight = 56112.711| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.38 r_work: 0.3031 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 18717 Z= 0.198 Angle : 0.929 18.729 25856 Z= 0.388 Chirality : 0.052 0.695 3543 Planarity : 0.004 0.054 2831 Dihedral : 14.815 131.989 6943 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 4.82 % Allowed : 17.91 % Favored : 77.28 % 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: -1.15 (0.19), residues: 1872 helix: 0.76 (0.23), residues: 476 sheet: -1.14 (0.25), residues: 413 loop : -1.36 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 166 TYR 0.015 0.002 TYR B 638 PHE 0.037 0.002 PHE D 522 TRP 0.017 0.001 TRP D 672 HIS 0.008 0.001 HIS E 462 Details of bonding type rmsd covalent geometry : bond 0.00424 (18447) covalent geometry : angle 0.81528 (25076) SS BOND : bond 0.00574 ( 30) SS BOND : angle 1.15770 ( 60) hydrogen bonds : bond 0.04811 ( 541) hydrogen bonds : angle 5.82528 ( 1557) link_ALPHA1-2 : bond 0.00474 ( 6) link_ALPHA1-2 : angle 2.21309 ( 18) link_ALPHA1-3 : bond 0.02208 ( 20) link_ALPHA1-3 : angle 3.22616 ( 60) link_ALPHA1-6 : bond 0.00738 ( 16) link_ALPHA1-6 : angle 1.59912 ( 48) link_BETA1-4 : bond 0.00731 ( 121) link_BETA1-4 : angle 2.77899 ( 363) link_BETA1-6 : bond 0.00211 ( 4) link_BETA1-6 : angle 1.54511 ( 12) link_NAG-ASN : bond 0.00481 ( 73) link_NAG-ASN : angle 2.93677 ( 219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 219 time to evaluate : 0.658 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: B 535 MET cc_start: 0.7149 (ptp) cc_final: 0.6879 (tmm) REVERT: B 557 ARG cc_start: 0.7528 (ptm-80) cc_final: 0.7314 (ptm-80) REVERT: B 564 HIS cc_start: 0.6745 (t-90) cc_final: 0.6431 (m-70) REVERT: B 567 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8640 (mtmm) REVERT: B 596 TRP cc_start: 0.9317 (m-10) cc_final: 0.8814 (m-10) REVERT: C 61 TYR cc_start: 0.5809 (t80) cc_final: 0.5608 (t80) REVERT: C 154 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 404 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7237 (pp30) REVERT: D 621 MET cc_start: 0.9172 (mtt) cc_final: 0.8912 (ptp) REVERT: D 636 ASP cc_start: 0.8482 (t0) cc_final: 0.8194 (p0) REVERT: D 647 GLU cc_start: 0.9337 (pp20) cc_final: 0.8853 (pp20) REVERT: D 654 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: D 655 LYS cc_start: 0.9016 (ptpp) cc_final: 0.8787 (mttp) REVERT: E 355 ASN cc_start: 0.9189 (t0) cc_final: 0.8549 (p0) REVERT: E 373 MET cc_start: 0.8921 (ptm) cc_final: 0.8601 (ptm) REVERT: E 381 GLU cc_start: 0.8635 (tp30) cc_final: 0.8389 (tp30) REVERT: E 429 GLU cc_start: 0.8780 (tp30) cc_final: 0.8503 (tp30) REVERT: A 66 HIS cc_start: 0.8723 (t-90) cc_final: 0.8414 (t-90) REVERT: A 104 MET cc_start: 0.9251 (ttt) cc_final: 0.8583 (ttt) REVERT: A 191 TYR cc_start: 0.9161 (m-80) cc_final: 0.8511 (m-80) REVERT: A 474 ASP cc_start: 0.8622 (t70) cc_final: 0.8278 (t0) REVERT: F 601 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8914 (ttmm) REVERT: F 629 MET cc_start: 0.8838 (tpp) cc_final: 0.8555 (tpp) REVERT: F 632 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: F 633 ARG cc_start: 0.8825 (ttm-80) cc_final: 0.8614 (ttm110) REVERT: F 647 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8413 (mp0) outliers start: 81 outliers final: 49 residues processed: 272 average time/residue: 0.1329 time to fit residues: 54.9717 Evaluate side-chains 252 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 559 ILE Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 GLU Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 15 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 140 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.095364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.072145 restraints weight = 55624.869| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 4.40 r_work: 0.3050 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18717 Z= 0.149 Angle : 0.875 18.306 25856 Z= 0.364 Chirality : 0.050 0.651 3543 Planarity : 0.004 0.051 2831 Dihedral : 13.736 129.456 6941 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 3.87 % Allowed : 19.33 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 1872 helix: 0.91 (0.24), residues: 474 sheet: -1.03 (0.26), residues: 392 loop : -1.26 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 633 TYR 0.014 0.001 TYR A 486 PHE 0.011 0.001 PHE E 382 TRP 0.017 0.001 TRP D 672 HIS 0.006 0.001 HIS E 462 Details of bonding type rmsd covalent geometry : bond 0.00301 (18447) covalent geometry : angle 0.76938 (25076) SS BOND : bond 0.00294 ( 30) SS BOND : angle 0.90445 ( 60) hydrogen bonds : bond 0.04384 ( 541) hydrogen bonds : angle 5.59969 ( 1557) link_ALPHA1-2 : bond 0.00492 ( 6) link_ALPHA1-2 : angle 2.30601 ( 18) link_ALPHA1-3 : bond 0.02212 ( 20) link_ALPHA1-3 : angle 3.30278 ( 60) link_ALPHA1-6 : bond 0.00757 ( 16) link_ALPHA1-6 : angle 1.51806 ( 48) link_BETA1-4 : bond 0.00698 ( 121) link_BETA1-4 : angle 2.56445 ( 363) link_BETA1-6 : bond 0.00312 ( 4) link_BETA1-6 : angle 1.36274 ( 12) link_NAG-ASN : bond 0.00424 ( 73) link_NAG-ASN : angle 2.73136 ( 219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 0.776 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: B 567 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8723 (mppt) REVERT: B 574 LYS cc_start: 0.9372 (mmmt) cc_final: 0.9145 (mttm) REVERT: B 596 TRP cc_start: 0.9421 (m-10) cc_final: 0.8908 (m-10) REVERT: B 632 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8812 (mm-30) REVERT: D 557 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.7006 (mtp-110) REVERT: D 591 GLN cc_start: 0.8649 (tt0) cc_final: 0.8110 (tt0) REVERT: D 621 MET cc_start: 0.9171 (mtt) cc_final: 0.8946 (ptp) REVERT: D 647 GLU cc_start: 0.9208 (pp20) cc_final: 0.8588 (pp20) REVERT: D 655 LYS cc_start: 0.8898 (ptpp) cc_final: 0.8684 (ptpp) REVERT: E 195 ASN cc_start: 0.7611 (t0) cc_final: 0.7071 (t0) REVERT: E 226 LEU cc_start: 0.9542 (mt) cc_final: 0.9295 (mp) REVERT: E 355 ASN cc_start: 0.9226 (t0) cc_final: 0.8640 (p0) REVERT: E 373 MET cc_start: 0.8902 (ptm) cc_final: 0.8591 (ptm) REVERT: E 381 GLU cc_start: 0.8655 (tp30) cc_final: 0.8424 (tp30) REVERT: E 429 GLU cc_start: 0.8753 (tp30) cc_final: 0.8482 (tp30) REVERT: A 66 HIS cc_start: 0.8580 (t-90) cc_final: 0.8164 (t70) REVERT: A 104 MET cc_start: 0.9256 (ttt) cc_final: 0.8583 (ttt) REVERT: A 191 TYR cc_start: 0.9138 (m-80) cc_final: 0.8453 (m-80) REVERT: A 474 ASP cc_start: 0.8567 (t70) cc_final: 0.8161 (t0) REVERT: F 542 ARG cc_start: 0.9161 (ptm-80) cc_final: 0.8892 (ptm160) REVERT: F 550 GLN cc_start: 0.7342 (pt0) cc_final: 0.6839 (pm20) REVERT: F 629 MET cc_start: 0.8796 (tpp) cc_final: 0.8527 (tpp) REVERT: F 632 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: F 633 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8350 (ttm110) REVERT: F 634 GLU cc_start: 0.8633 (mp0) cc_final: 0.8381 (pm20) REVERT: F 647 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8392 (mp0) outliers start: 65 outliers final: 43 residues processed: 270 average time/residue: 0.1413 time to fit residues: 57.9705 Evaluate side-chains 250 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 559 ILE Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 GLU Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 76 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 136 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN D 554 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.092587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069081 restraints weight = 55705.085| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.39 r_work: 0.2980 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 18717 Z= 0.200 Angle : 0.885 17.802 25856 Z= 0.375 Chirality : 0.050 0.615 3543 Planarity : 0.004 0.050 2831 Dihedral : 12.627 128.711 6939 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 4.88 % Allowed : 18.20 % Favored : 76.92 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 1872 helix: 0.89 (0.23), residues: 480 sheet: -0.90 (0.26), residues: 396 loop : -1.19 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 633 TYR 0.030 0.002 TYR B 643 PHE 0.017 0.002 PHE C 382 TRP 0.046 0.002 TRP D 678 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00441 (18447) covalent geometry : angle 0.78425 (25076) SS BOND : bond 0.00467 ( 30) SS BOND : angle 1.05408 ( 60) hydrogen bonds : bond 0.04464 ( 541) hydrogen bonds : angle 5.50794 ( 1557) link_ALPHA1-2 : bond 0.00370 ( 6) link_ALPHA1-2 : angle 2.21843 ( 18) link_ALPHA1-3 : bond 0.02136 ( 20) link_ALPHA1-3 : angle 3.29689 ( 60) link_ALPHA1-6 : bond 0.00781 ( 16) link_ALPHA1-6 : angle 1.66531 ( 48) link_BETA1-4 : bond 0.00685 ( 121) link_BETA1-4 : angle 2.50395 ( 363) link_BETA1-6 : bond 0.00164 ( 4) link_BETA1-6 : angle 1.57218 ( 12) link_NAG-ASN : bond 0.00451 ( 73) link_NAG-ASN : angle 2.69839 ( 219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 213 time to evaluate : 0.681 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: B 567 LYS cc_start: 0.9060 (mtmm) cc_final: 0.8601 (mppt) REVERT: B 596 TRP cc_start: 0.9371 (m-10) cc_final: 0.8840 (m-10) REVERT: B 632 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8763 (mm-30) REVERT: B 648 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8599 (mt-10) REVERT: C 426 MET cc_start: 0.8094 (tpt) cc_final: 0.7787 (tpt) REVERT: D 556 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8758 (tt) REVERT: D 557 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7182 (mtp-110) REVERT: D 560 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8469 (mp0) REVERT: D 589 ASP cc_start: 0.8879 (m-30) cc_final: 0.8647 (p0) REVERT: D 621 MET cc_start: 0.9208 (mtt) cc_final: 0.8949 (ptp) REVERT: D 626 MET cc_start: 0.9127 (tpp) cc_final: 0.7974 (mtp) REVERT: D 634 GLU cc_start: 0.8958 (pm20) cc_final: 0.8412 (pm20) REVERT: D 647 GLU cc_start: 0.9247 (pp20) cc_final: 0.8783 (pp20) REVERT: D 654 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: D 655 LYS cc_start: 0.9152 (ptpp) cc_final: 0.8894 (ptpp) REVERT: E 99 ASN cc_start: 0.9360 (t0) cc_final: 0.8903 (t0) REVERT: E 355 ASN cc_start: 0.9202 (t0) cc_final: 0.8787 (t0) REVERT: E 373 MET cc_start: 0.8960 (ptm) cc_final: 0.8694 (ptm) REVERT: E 381 GLU cc_start: 0.8746 (tp30) cc_final: 0.8493 (tp30) REVERT: A 66 HIS cc_start: 0.8647 (t-90) cc_final: 0.8178 (t70) REVERT: A 104 MET cc_start: 0.9299 (ttt) cc_final: 0.8693 (ttt) REVERT: A 191 TYR cc_start: 0.9042 (m-80) cc_final: 0.8516 (m-80) REVERT: A 390 LEU cc_start: 0.9174 (mt) cc_final: 0.8845 (tp) REVERT: A 474 ASP cc_start: 0.8533 (t70) cc_final: 0.8126 (t0) REVERT: F 622 ILE cc_start: 0.9372 (mm) cc_final: 0.9155 (mm) REVERT: F 632 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8484 (mp0) outliers start: 82 outliers final: 53 residues processed: 268 average time/residue: 0.1485 time to fit residues: 59.8848 Evaluate side-chains 255 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 559 ILE Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 GLU Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 145 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN D 564 HIS A 330 HIS F 550 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.092916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069363 restraints weight = 56287.564| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 4.39 r_work: 0.2985 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18717 Z= 0.167 Angle : 0.861 17.589 25856 Z= 0.363 Chirality : 0.048 0.603 3543 Planarity : 0.004 0.072 2831 Dihedral : 11.956 124.425 6939 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 4.28 % Allowed : 19.16 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.19), residues: 1872 helix: 0.86 (0.23), residues: 479 sheet: -0.86 (0.26), residues: 409 loop : -1.16 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 633 TYR 0.020 0.001 TYR B 643 PHE 0.017 0.001 PHE B 522 TRP 0.047 0.001 TRP D 678 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00356 (18447) covalent geometry : angle 0.76326 (25076) SS BOND : bond 0.00376 ( 30) SS BOND : angle 1.09915 ( 60) hydrogen bonds : bond 0.04344 ( 541) hydrogen bonds : angle 5.46976 ( 1557) link_ALPHA1-2 : bond 0.00384 ( 6) link_ALPHA1-2 : angle 2.30884 ( 18) link_ALPHA1-3 : bond 0.02154 ( 20) link_ALPHA1-3 : angle 3.35735 ( 60) link_ALPHA1-6 : bond 0.00745 ( 16) link_ALPHA1-6 : angle 1.51806 ( 48) link_BETA1-4 : bond 0.00674 ( 121) link_BETA1-4 : angle 2.40998 ( 363) link_BETA1-6 : bond 0.00224 ( 4) link_BETA1-6 : angle 1.43166 ( 12) link_NAG-ASN : bond 0.00406 ( 73) link_NAG-ASN : angle 2.58971 ( 219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 208 time to evaluate : 0.628 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: B 535 MET cc_start: 0.7714 (tmm) cc_final: 0.7508 (tmm) REVERT: B 538 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8433 (m) REVERT: B 564 HIS cc_start: 0.6724 (t-90) cc_final: 0.6405 (m-70) REVERT: B 567 LYS cc_start: 0.9088 (mtmm) cc_final: 0.8664 (mppt) REVERT: B 577 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: B 587 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9411 (mm) REVERT: B 596 TRP cc_start: 0.9321 (m-10) cc_final: 0.8834 (m-10) REVERT: B 632 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8849 (mm-30) REVERT: B 650 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8712 (tp40) REVERT: B 658 GLN cc_start: 0.8319 (mp10) cc_final: 0.8083 (mp10) REVERT: C 61 TYR cc_start: 0.7166 (t80) cc_final: 0.6887 (t80) REVERT: C 426 MET cc_start: 0.7883 (tpt) cc_final: 0.7631 (tpt) REVERT: D 554 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8731 (p0) REVERT: D 557 ARG cc_start: 0.7548 (mtp-110) cc_final: 0.6954 (mtp180) REVERT: D 560 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8541 (mp0) REVERT: D 589 ASP cc_start: 0.8862 (m-30) cc_final: 0.8648 (p0) REVERT: D 621 MET cc_start: 0.9215 (mtt) cc_final: 0.8972 (ptp) REVERT: D 626 MET cc_start: 0.8980 (tpp) cc_final: 0.7842 (mtp) REVERT: D 634 GLU cc_start: 0.8956 (pm20) cc_final: 0.8404 (pm20) REVERT: D 647 GLU cc_start: 0.9238 (pp20) cc_final: 0.8714 (pp20) REVERT: D 654 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8217 (pt0) REVERT: E 226 LEU cc_start: 0.9589 (mt) cc_final: 0.9325 (mp) REVERT: E 355 ASN cc_start: 0.9210 (t0) cc_final: 0.8785 (t0) REVERT: E 373 MET cc_start: 0.8898 (ptm) cc_final: 0.8630 (ptm) REVERT: E 381 GLU cc_start: 0.8711 (tp30) cc_final: 0.8481 (tp30) REVERT: E 390 LEU cc_start: 0.9255 (mp) cc_final: 0.9030 (mt) REVERT: E 429 GLU cc_start: 0.8837 (tp30) cc_final: 0.8518 (tp30) REVERT: A 47 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8854 (mm-30) REVERT: A 66 HIS cc_start: 0.8640 (t-90) cc_final: 0.8157 (t70) REVERT: A 104 MET cc_start: 0.9271 (ttt) cc_final: 0.8671 (ttt) REVERT: A 191 TYR cc_start: 0.9158 (m-80) cc_final: 0.8453 (m-80) REVERT: A 474 ASP cc_start: 0.8490 (t70) cc_final: 0.8062 (t0) REVERT: F 632 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8461 (mp0) outliers start: 72 outliers final: 52 residues processed: 257 average time/residue: 0.1381 time to fit residues: 54.2299 Evaluate side-chains 260 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 201 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 559 ILE Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 632 GLU Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 66 optimal weight: 0.0070 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS E 99 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395AASN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.093072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.069688 restraints weight = 56050.479| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.38 r_work: 0.2993 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18717 Z= 0.156 Angle : 0.857 17.416 25856 Z= 0.363 Chirality : 0.048 0.595 3543 Planarity : 0.004 0.051 2831 Dihedral : 11.361 123.425 6939 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 3.99 % Allowed : 19.45 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.19), residues: 1872 helix: 0.89 (0.23), residues: 479 sheet: -0.84 (0.26), residues: 406 loop : -1.15 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 504 TYR 0.020 0.001 TYR B 643 PHE 0.021 0.001 PHE B 522 TRP 0.050 0.001 TRP D 678 HIS 0.020 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00331 (18447) covalent geometry : angle 0.76117 (25076) SS BOND : bond 0.00338 ( 30) SS BOND : angle 1.51447 ( 60) hydrogen bonds : bond 0.04277 ( 541) hydrogen bonds : angle 5.38144 ( 1557) link_ALPHA1-2 : bond 0.00384 ( 6) link_ALPHA1-2 : angle 2.32076 ( 18) link_ALPHA1-3 : bond 0.02166 ( 20) link_ALPHA1-3 : angle 3.39663 ( 60) link_ALPHA1-6 : bond 0.00725 ( 16) link_ALPHA1-6 : angle 1.46960 ( 48) link_BETA1-4 : bond 0.00661 ( 121) link_BETA1-4 : angle 2.36001 ( 363) link_BETA1-6 : bond 0.00244 ( 4) link_BETA1-6 : angle 1.39109 ( 12) link_NAG-ASN : bond 0.00389 ( 73) link_NAG-ASN : angle 2.52523 ( 219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 0.701 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: B 535 MET cc_start: 0.7751 (tmm) cc_final: 0.7536 (tmm) REVERT: B 564 HIS cc_start: 0.6769 (t-90) cc_final: 0.6343 (m-70) REVERT: B 567 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8700 (mppt) REVERT: B 577 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: B 587 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9421 (mm) REVERT: B 596 TRP cc_start: 0.9297 (m-10) cc_final: 0.8862 (m-10) REVERT: B 630 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8495 (mt-10) REVERT: B 632 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8880 (mm-30) REVERT: B 650 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8679 (tp40) REVERT: B 658 GLN cc_start: 0.8290 (mp10) cc_final: 0.8026 (mp10) REVERT: D 557 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.6905 (mtp180) REVERT: D 560 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: D 567 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8197 (ptpp) REVERT: D 591 GLN cc_start: 0.8675 (tt0) cc_final: 0.8175 (tt0) REVERT: D 626 MET cc_start: 0.8971 (tpp) cc_final: 0.8156 (mtp) REVERT: D 634 GLU cc_start: 0.8911 (pm20) cc_final: 0.8365 (pm20) REVERT: D 638 TYR cc_start: 0.9124 (m-80) cc_final: 0.8591 (m-80) REVERT: D 647 GLU cc_start: 0.9247 (pp20) cc_final: 0.8809 (pp20) REVERT: E 153 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7743 (mp0) REVERT: E 226 LEU cc_start: 0.9557 (mt) cc_final: 0.9306 (mp) REVERT: E 355 ASN cc_start: 0.9213 (t0) cc_final: 0.8784 (t0) REVERT: E 373 MET cc_start: 0.8895 (ptm) cc_final: 0.8624 (ptm) REVERT: E 381 GLU cc_start: 0.8713 (tp30) cc_final: 0.8488 (tp30) REVERT: E 390 LEU cc_start: 0.9284 (mp) cc_final: 0.9068 (mt) REVERT: E 429 GLU cc_start: 0.8822 (tp30) cc_final: 0.8506 (tp30) REVERT: A 66 HIS cc_start: 0.8598 (t-90) cc_final: 0.8108 (t70) REVERT: A 104 MET cc_start: 0.9273 (ttt) cc_final: 0.8667 (ttt) REVERT: A 191 TYR cc_start: 0.9146 (m-80) cc_final: 0.8442 (m-80) REVERT: A 474 ASP cc_start: 0.8444 (t70) cc_final: 0.8023 (t0) REVERT: F 550 GLN cc_start: 0.7744 (pt0) cc_final: 0.7199 (pm20) REVERT: F 632 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8440 (mp0) outliers start: 67 outliers final: 54 residues processed: 258 average time/residue: 0.1396 time to fit residues: 54.9989 Evaluate side-chains 262 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 204 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 559 ILE Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 GLU Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 168 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN D 564 HIS E 99 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.092995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069871 restraints weight = 55854.964| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.32 r_work: 0.2998 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 18717 Z= 0.155 Angle : 0.848 17.242 25856 Z= 0.360 Chirality : 0.047 0.583 3543 Planarity : 0.004 0.052 2831 Dihedral : 10.935 122.310 6939 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 3.93 % Allowed : 19.33 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.19), residues: 1872 helix: 0.85 (0.24), residues: 480 sheet: -0.82 (0.26), residues: 411 loop : -1.09 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 633 TYR 0.021 0.001 TYR C 61 PHE 0.014 0.001 PHE B 522 TRP 0.044 0.001 TRP D 678 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00330 (18447) covalent geometry : angle 0.75486 (25076) SS BOND : bond 0.00311 ( 30) SS BOND : angle 1.51591 ( 60) hydrogen bonds : bond 0.04250 ( 541) hydrogen bonds : angle 5.39223 ( 1557) link_ALPHA1-2 : bond 0.00394 ( 6) link_ALPHA1-2 : angle 2.31500 ( 18) link_ALPHA1-3 : bond 0.02158 ( 20) link_ALPHA1-3 : angle 3.40753 ( 60) link_ALPHA1-6 : bond 0.00714 ( 16) link_ALPHA1-6 : angle 1.44132 ( 48) link_BETA1-4 : bond 0.00660 ( 121) link_BETA1-4 : angle 2.31029 ( 363) link_BETA1-6 : bond 0.00252 ( 4) link_BETA1-6 : angle 1.36568 ( 12) link_NAG-ASN : bond 0.00382 ( 73) link_NAG-ASN : angle 2.45253 ( 219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 0.631 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: B 530 MET cc_start: 0.8757 (tpt) cc_final: 0.8392 (tpp) REVERT: B 535 MET cc_start: 0.7913 (tmm) cc_final: 0.7677 (tmm) REVERT: B 564 HIS cc_start: 0.6765 (t-90) cc_final: 0.6311 (m-70) REVERT: B 567 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8750 (mppt) REVERT: B 587 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9421 (mm) REVERT: B 596 TRP cc_start: 0.9291 (m-10) cc_final: 0.8866 (m-10) REVERT: B 632 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8900 (mm-30) REVERT: B 650 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8675 (tp40) REVERT: D 557 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7113 (mtp180) REVERT: D 560 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: D 567 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8226 (ptpp) REVERT: D 589 ASP cc_start: 0.8847 (m-30) cc_final: 0.8600 (p0) REVERT: D 591 GLN cc_start: 0.8648 (tt0) cc_final: 0.8173 (tt0) REVERT: D 626 MET cc_start: 0.8962 (tpp) cc_final: 0.8258 (mtp) REVERT: D 634 GLU cc_start: 0.8810 (pm20) cc_final: 0.8411 (pm20) REVERT: D 638 TYR cc_start: 0.9131 (m-80) cc_final: 0.8555 (m-10) REVERT: D 647 GLU cc_start: 0.9220 (pp20) cc_final: 0.8701 (pp20) REVERT: D 654 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: E 153 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7481 (mp0) REVERT: E 226 LEU cc_start: 0.9493 (mt) cc_final: 0.9259 (mp) REVERT: E 355 ASN cc_start: 0.9224 (t0) cc_final: 0.8805 (t0) REVERT: E 373 MET cc_start: 0.8906 (ptm) cc_final: 0.8637 (ptm) REVERT: E 381 GLU cc_start: 0.8719 (tp30) cc_final: 0.8489 (tp30) REVERT: E 390 LEU cc_start: 0.9318 (mp) cc_final: 0.9108 (mt) REVERT: E 429 GLU cc_start: 0.8857 (tp30) cc_final: 0.8539 (tp30) REVERT: A 66 HIS cc_start: 0.8584 (t-90) cc_final: 0.8094 (t70) REVERT: A 104 MET cc_start: 0.9274 (ttt) cc_final: 0.8656 (ttt) REVERT: A 191 TYR cc_start: 0.9149 (m-80) cc_final: 0.8407 (m-80) REVERT: A 474 ASP cc_start: 0.8405 (t70) cc_final: 0.7971 (t0) REVERT: F 550 GLN cc_start: 0.7548 (pt0) cc_final: 0.7081 (pm20) REVERT: F 560 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.5557 (pp20) REVERT: F 584 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8482 (mt-10) REVERT: F 632 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: F 638 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7756 (m-80) outliers start: 66 outliers final: 52 residues processed: 262 average time/residue: 0.1397 time to fit residues: 56.0570 Evaluate side-chains 257 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 559 ILE Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 GLU Chi-restraints excluded: chain F residue 634 GLU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 51 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN F 550 GLN ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.091245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.068035 restraints weight = 56001.951| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 4.30 r_work: 0.2953 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18717 Z= 0.212 Angle : 0.880 17.154 25856 Z= 0.382 Chirality : 0.048 0.568 3543 Planarity : 0.004 0.051 2831 Dihedral : 10.910 126.353 6935 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 3.39 % Allowed : 20.17 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 1872 helix: 0.78 (0.24), residues: 473 sheet: -0.77 (0.26), residues: 412 loop : -1.14 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 633 TYR 0.021 0.002 TYR B 643 PHE 0.016 0.002 PHE C 382 TRP 0.027 0.002 TRP D 678 HIS 0.019 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00469 (18447) covalent geometry : angle 0.78926 (25076) SS BOND : bond 0.00453 ( 30) SS BOND : angle 1.67697 ( 60) hydrogen bonds : bond 0.04623 ( 541) hydrogen bonds : angle 5.52843 ( 1557) link_ALPHA1-2 : bond 0.00342 ( 6) link_ALPHA1-2 : angle 2.24821 ( 18) link_ALPHA1-3 : bond 0.02121 ( 20) link_ALPHA1-3 : angle 3.32563 ( 60) link_ALPHA1-6 : bond 0.00656 ( 16) link_ALPHA1-6 : angle 1.51075 ( 48) link_BETA1-4 : bond 0.00649 ( 121) link_BETA1-4 : angle 2.32334 ( 363) link_BETA1-6 : bond 0.00175 ( 4) link_BETA1-6 : angle 1.52370 ( 12) link_NAG-ASN : bond 0.00424 ( 73) link_NAG-ASN : angle 2.52313 ( 219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.678 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: B 530 MET cc_start: 0.8812 (tpt) cc_final: 0.8318 (tpp) REVERT: B 535 MET cc_start: 0.7970 (tmm) cc_final: 0.7692 (tmm) REVERT: B 564 HIS cc_start: 0.6727 (t-90) cc_final: 0.6246 (m-70) REVERT: B 567 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8717 (mppt) REVERT: B 632 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8904 (mm-30) REVERT: D 557 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.6912 (mtp180) REVERT: D 560 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8586 (mp0) REVERT: D 567 LYS cc_start: 0.8736 (mtmm) cc_final: 0.8418 (ptpp) REVERT: D 589 ASP cc_start: 0.8857 (m-30) cc_final: 0.8608 (p0) REVERT: D 626 MET cc_start: 0.8948 (tpp) cc_final: 0.8220 (mtp) REVERT: D 634 GLU cc_start: 0.8840 (pm20) cc_final: 0.8449 (pm20) REVERT: D 638 TYR cc_start: 0.9121 (m-80) cc_final: 0.8587 (m-10) REVERT: D 647 GLU cc_start: 0.9278 (pp20) cc_final: 0.8855 (pp20) REVERT: E 133 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7210 (t0) REVERT: E 153 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7564 (mp0) REVERT: E 172 ASP cc_start: 0.8747 (t0) cc_final: 0.8362 (t70) REVERT: E 355 ASN cc_start: 0.9274 (t0) cc_final: 0.8889 (t0) REVERT: E 373 MET cc_start: 0.8943 (ptm) cc_final: 0.8690 (ptm) REVERT: E 381 GLU cc_start: 0.8738 (tp30) cc_final: 0.8523 (tp30) REVERT: A 66 HIS cc_start: 0.8519 (t-90) cc_final: 0.8104 (t-90) REVERT: A 104 MET cc_start: 0.9270 (ttt) cc_final: 0.8612 (ttt) REVERT: A 191 TYR cc_start: 0.9171 (m-80) cc_final: 0.8454 (m-80) REVERT: A 474 ASP cc_start: 0.8468 (t70) cc_final: 0.8047 (t0) REVERT: F 550 GLN cc_start: 0.7749 (pt0) cc_final: 0.7252 (pm20) REVERT: F 560 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.5643 (pp20) REVERT: F 584 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8535 (mt-10) REVERT: F 632 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: F 638 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: F 647 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8327 (mm-30) outliers start: 57 outliers final: 49 residues processed: 237 average time/residue: 0.1434 time to fit residues: 51.6015 Evaluate side-chains 246 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 559 ILE Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 GLU Chi-restraints excluded: chain F residue 634 GLU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 37 optimal weight: 0.0000 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 141 optimal weight: 0.0970 chunk 175 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 147 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 GLN D 564 HIS E 99 ASN A 72 HIS A 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.070174 restraints weight = 56349.647| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.33 r_work: 0.3007 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 18717 Z= 0.145 Angle : 0.843 16.829 25856 Z= 0.364 Chirality : 0.047 0.572 3543 Planarity : 0.004 0.052 2831 Dihedral : 10.489 120.884 6935 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.38 % Favored : 95.57 % Rotamer: Outliers : 3.15 % Allowed : 20.52 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 1872 helix: 0.75 (0.24), residues: 479 sheet: -0.80 (0.27), residues: 396 loop : -1.12 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 633 TYR 0.019 0.001 TYR C 61 PHE 0.009 0.001 PHE C 382 TRP 0.032 0.001 TRP D 678 HIS 0.003 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00303 (18447) covalent geometry : angle 0.75795 (25076) SS BOND : bond 0.00246 ( 30) SS BOND : angle 1.46677 ( 60) hydrogen bonds : bond 0.04249 ( 541) hydrogen bonds : angle 5.43557 ( 1557) link_ALPHA1-2 : bond 0.00484 ( 6) link_ALPHA1-2 : angle 2.26113 ( 18) link_ALPHA1-3 : bond 0.02118 ( 20) link_ALPHA1-3 : angle 3.30562 ( 60) link_ALPHA1-6 : bond 0.00714 ( 16) link_ALPHA1-6 : angle 1.39288 ( 48) link_BETA1-4 : bond 0.00654 ( 121) link_BETA1-4 : angle 2.21186 ( 363) link_BETA1-6 : bond 0.00307 ( 4) link_BETA1-6 : angle 1.28817 ( 12) link_NAG-ASN : bond 0.00393 ( 73) link_NAG-ASN : angle 2.33682 ( 219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3908.74 seconds wall clock time: 68 minutes 26.27 seconds (4106.27 seconds total)