Starting phenix.real_space_refine on Sat Feb 7 10:30:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1r_53513/02_2026/9r1r_53513.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1r_53513/02_2026/9r1r_53513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r1r_53513/02_2026/9r1r_53513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1r_53513/02_2026/9r1r_53513.map" model { file = "/net/cci-nas-00/data/ceres_data/9r1r_53513/02_2026/9r1r_53513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1r_53513/02_2026/9r1r_53513.cif" } resolution = 2.65 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= 0.013 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 198 5.16 5 C 19908 2.51 5 N 4881 2.21 5 O 6474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31461 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 9601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1221, 9601 Classifications: {'peptide': 1221} Link IDs: {'PTRANS': 46, 'TRANS': 1174} Chain breaks: 10 Chain: "B" Number of atoms: 9601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1221, 9601 Classifications: {'peptide': 1221} Link IDs: {'PTRANS': 46, 'TRANS': 1174} Chain breaks: 10 Chain: "C" Number of atoms: 9601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1221, 9601 Classifications: {'peptide': 1221} Link IDs: {'PTRANS': 46, 'TRANS': 1174} Chain breaks: 10 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 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: "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: 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: "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: 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: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, '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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: 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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, '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: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 8.39, per 1000 atoms: 0.27 Number of scatterers: 31461 At special positions: 0 Unit cell: (162.184, 158.004, 179.74, 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 198 16.00 O 6474 8.00 N 4881 7.00 C 19908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 12 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 233 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS A 564 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 638 " distance=2.04 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 702 " - pdb=" SG CYS A 754 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS A 815 " - pdb=" SG CYS A 826 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A 888 " - pdb=" SG CYS A 894 " distance=2.03 Simple disulfide: pdb=" SG CYS A1000 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1206 " distance=2.03 Simple disulfide: pdb=" SG CYS A1245 " - pdb=" SG CYS A1313 " distance=2.03 Simple disulfide: pdb=" SG CYS A1264 " - pdb=" SG CYS A1270 " distance=2.02 Simple disulfide: pdb=" SG CYS B 12 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 106 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 222 " - pdb=" SG CYS B 233 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 564 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 638 " distance=2.04 Simple disulfide: pdb=" SG CYS B 586 " - pdb=" SG CYS B 600 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 652 " distance=2.03 Simple disulfide: pdb=" SG CYS B 702 " - pdb=" SG CYS B 754 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 815 " - pdb=" SG CYS B 826 " distance=2.03 Simple disulfide: pdb=" SG CYS B 883 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B 888 " - pdb=" SG CYS B 894 " distance=2.03 Simple disulfide: pdb=" SG CYS B1000 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B1195 " - pdb=" SG CYS B1206 " distance=2.03 Simple disulfide: pdb=" SG CYS B1245 " - pdb=" SG CYS B1313 " distance=2.03 Simple disulfide: pdb=" SG CYS B1264 " - pdb=" SG CYS B1270 " distance=2.02 Simple disulfide: pdb=" SG CYS C 12 " - pdb=" SG CYS C 15 " distance=2.03 Simple disulfide: pdb=" SG CYS C 83 " - pdb=" SG CYS C 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 222 " - pdb=" SG CYS C 233 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 564 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 638 " distance=2.04 Simple disulfide: pdb=" SG CYS C 586 " - pdb=" SG CYS C 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS C 702 " - pdb=" SG CYS C 754 " distance=2.03 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 815 " - pdb=" SG CYS C 826 " distance=2.03 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C 888 " - pdb=" SG CYS C 894 " distance=2.03 Simple disulfide: pdb=" SG CYS C1000 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C1195 " - pdb=" SG CYS C1206 " distance=2.03 Simple disulfide: pdb=" SG CYS C1245 " - pdb=" SG CYS C1313 " distance=2.03 Simple disulfide: pdb=" SG CYS C1264 " - pdb=" SG CYS C1270 " distance=2.02 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 ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 5 3 " - " MAN 5 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " " BMA i 3 " - " MAN i 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 2 3 " - " MAN 2 4 " " BMA 5 3 " - " MAN 5 5 " " BMA K 3 " - " MAN K 4 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 5 " " BMA d 3 " - " MAN d 4 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 5 " " BMA w 3 " - " MAN w 4 " 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 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 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 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 N 2 " - " BMA N 3 " " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG 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 " BETA1-6 " NAG 5 1 " - " FUC 5 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 6 " " NAG m 1 " - " FUC m 6 " NAG-ASN " NAG 0 1 " - " ASN C 944 " " NAG 1 1 " - " ASN C1208 " " NAG 2 1 " - " ASN C1233 " " NAG 3 1 " - " ASN C1247 " " NAG 4 1 " - " ASN C1278 " " NAG 5 1 " - " ASN C1284 " " NAG 6 1 " - " ASN C1314 " " NAG 7 1 " - " ASN C 211 " " NAG A1401 " - " ASN A 17 " " NAG A1402 " - " ASN A 45 " " NAG A1403 " - " ASN A 75 " " NAG A1404 " - " ASN A 88 " " NAG A1405 " - " ASN A 110 " " NAG A1406 " - " ASN A 351 " " NAG A1407 " - " ASN A 417 " " NAG A1408 " - " ASN A 548 " " NAG A1409 " - " ASN A 783 " " NAG A1410 " - " ASN A 67 " " NAG A1411 " - " ASN A 234 " " NAG A1412 " - " ASN A1266 " " NAG B1401 " - " ASN B 17 " " NAG B1402 " - " ASN B 45 " " NAG B1403 " - " ASN B 75 " " NAG B1404 " - " ASN B 88 " " NAG B1405 " - " ASN B 110 " " NAG B1406 " - " ASN B 351 " " NAG B1407 " - " ASN B 417 " " NAG B1408 " - " ASN B 548 " " NAG B1409 " - " ASN B 783 " " NAG B1410 " - " ASN B 67 " " NAG B1411 " - " ASN B 234 " " NAG B1412 " - " ASN B1266 " " NAG C1401 " - " ASN C 17 " " NAG C1402 " - " ASN C 45 " " NAG C1403 " - " ASN C 75 " " NAG C1404 " - " ASN C 88 " " NAG C1405 " - " ASN C 110 " " NAG C1406 " - " ASN C 351 " " NAG C1407 " - " ASN C 417 " " NAG C1408 " - " ASN C 548 " " NAG C1409 " - " ASN C 783 " " NAG C1410 " - " ASN C 67 " " NAG C1411 " - " ASN C 234 " " NAG C1412 " - " ASN C1266 " " NAG D 1 " - " ASN A 24 " " NAG E 1 " - " ASN A 51 " " NAG F 1 " - " ASN A 82 " " NAG G 1 " - " ASN A 176 " " NAG H 1 " - " ASN A 341 " " NAG I 1 " - " ASN A 474 " " NAG J 1 " - " ASN A 536 " " NAG K 1 " - " ASN A 581 " " NAG L 1 " - " ASN A 789 " " NAG M 1 " - " ASN A 843 " " NAG N 1 " - " ASN A 935 " " NAG O 1 " - " ASN A 944 " " NAG P 1 " - " ASN A1208 " " NAG Q 1 " - " ASN A1233 " " NAG R 1 " - " ASN A1247 " " NAG S 1 " - " ASN A1278 " " NAG T 1 " - " ASN A1284 " " NAG U 1 " - " ASN A1314 " " NAG V 1 " - " ASN A 211 " " NAG W 1 " - " ASN B 24 " " NAG X 1 " - " ASN B 51 " " NAG Y 1 " - " ASN B 82 " " NAG Z 1 " - " ASN B 176 " " NAG a 1 " - " ASN B 341 " " NAG b 1 " - " ASN B 474 " " NAG c 1 " - " ASN B 536 " " NAG d 1 " - " ASN B 581 " " NAG e 1 " - " ASN B 789 " " NAG f 1 " - " ASN B 843 " " NAG g 1 " - " ASN B 935 " " NAG h 1 " - " ASN B 944 " " NAG i 1 " - " ASN B1208 " " NAG j 1 " - " ASN B1233 " " NAG k 1 " - " ASN B1247 " " NAG l 1 " - " ASN B1278 " " NAG m 1 " - " ASN B1284 " " NAG n 1 " - " ASN B1314 " " NAG o 1 " - " ASN B 211 " " NAG p 1 " - " ASN C 24 " " NAG q 1 " - " ASN C 51 " " NAG r 1 " - " ASN C 82 " " NAG s 1 " - " ASN C 176 " " NAG t 1 " - " ASN C 341 " " NAG u 1 " - " ASN C 474 " " NAG v 1 " - " ASN C 536 " " NAG w 1 " - " ASN C 581 " " NAG x 1 " - " ASN C 789 " " NAG y 1 " - " ASN C 843 " " NAG z 1 " - " ASN C 935 " Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6828 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 54 sheets defined 24.7% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 30 through 33 removed outlier: 4.018A pdb=" N HIS A 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 33' Processing helix chain 'A' and resid 116 through 126 removed outlier: 4.079A pdb=" N ASN A 125 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 505 through 515 Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'A' and resid 882 through 888 Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 901 through 928 removed outlier: 3.683A pdb=" N CYS A 905 " --> pdb=" O TYR A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 946 Processing helix chain 'A' and resid 954 through 958 removed outlier: 3.665A pdb=" N LYS A 957 " --> pdb=" O GLY A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 985 removed outlier: 3.924A pdb=" N VAL A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1008 through 1015 Processing helix chain 'A' and resid 1026 through 1044 Processing helix chain 'A' and resid 1052 through 1067 removed outlier: 4.492A pdb=" N GLN A1057 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1065 " --> pdb=" O ARG A1061 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A1066 " --> pdb=" O VAL A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1093 Processing helix chain 'A' and resid 1096 through 1101 removed outlier: 4.447A pdb=" N ALA A1099 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1128 removed outlier: 3.585A pdb=" N LEU A1125 " --> pdb=" O ALA A1121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A1126 " --> pdb=" O LEU A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1131 No H-bonds generated for 'chain 'A' and resid 1129 through 1131' Processing helix chain 'A' and resid 1139 through 1147 Processing helix chain 'A' and resid 1148 through 1196 removed outlier: 3.600A pdb=" N SER A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1277 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1321 through 1325 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 30 through 33 removed outlier: 4.018A pdb=" N HIS B 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 116 through 126 removed outlier: 4.080A pdb=" N ASN B 125 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 505 through 515 Processing helix chain 'B' and resid 596 through 607 Processing helix chain 'B' and resid 778 through 783 Processing helix chain 'B' and resid 882 through 888 Processing helix chain 'B' and resid 891 through 899 Processing helix chain 'B' and resid 901 through 928 removed outlier: 3.683A pdb=" N CYS B 905 " --> pdb=" O TYR B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 946 Processing helix chain 'B' and resid 954 through 958 removed outlier: 3.665A pdb=" N LYS B 957 " --> pdb=" O GLY B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 985 removed outlier: 3.924A pdb=" N VAL B 985 " --> pdb=" O LEU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1002 Processing helix chain 'B' and resid 1008 through 1015 Processing helix chain 'B' and resid 1026 through 1044 Processing helix chain 'B' and resid 1052 through 1067 removed outlier: 4.493A pdb=" N GLN B1057 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B1065 " --> pdb=" O ARG B1061 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B1066 " --> pdb=" O VAL B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1093 Processing helix chain 'B' and resid 1096 through 1101 removed outlier: 4.448A pdb=" N ALA B1099 " --> pdb=" O SER B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1128 removed outlier: 3.585A pdb=" N LEU B1125 " --> pdb=" O ALA B1121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B1126 " --> pdb=" O LEU B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1131 No H-bonds generated for 'chain 'B' and resid 1129 through 1131' Processing helix chain 'B' and resid 1139 through 1147 Processing helix chain 'B' and resid 1148 through 1196 removed outlier: 3.599A pdb=" N SER B1183 " --> pdb=" O SER B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1273 through 1277 Processing helix chain 'B' and resid 1303 through 1305 No H-bonds generated for 'chain 'B' and resid 1303 through 1305' Processing helix chain 'B' and resid 1321 through 1325 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 30 through 33 removed outlier: 4.018A pdb=" N HIS C 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 116 through 126 removed outlier: 4.079A pdb=" N ASN C 125 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 505 through 515 Processing helix chain 'C' and resid 596 through 607 Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 882 through 888 Processing helix chain 'C' and resid 891 through 899 Processing helix chain 'C' and resid 901 through 928 removed outlier: 3.683A pdb=" N CYS C 905 " --> pdb=" O TYR C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 946 Processing helix chain 'C' and resid 954 through 958 removed outlier: 3.664A pdb=" N LYS C 957 " --> pdb=" O GLY C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 985 removed outlier: 3.924A pdb=" N VAL C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1002 Processing helix chain 'C' and resid 1008 through 1015 Processing helix chain 'C' and resid 1026 through 1044 Processing helix chain 'C' and resid 1052 through 1067 removed outlier: 4.492A pdb=" N GLN C1057 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C1065 " --> pdb=" O ARG C1061 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C1066 " --> pdb=" O VAL C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1093 Processing helix chain 'C' and resid 1096 through 1101 removed outlier: 4.447A pdb=" N ALA C1099 " --> pdb=" O SER C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1128 removed outlier: 3.585A pdb=" N LEU C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C1126 " --> pdb=" O LEU C1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1131 No H-bonds generated for 'chain 'C' and resid 1129 through 1131' Processing helix chain 'C' and resid 1139 through 1147 Processing helix chain 'C' and resid 1148 through 1196 removed outlier: 3.601A pdb=" N SER C1183 " --> pdb=" O SER C1179 " (cutoff:3.500A) Processing helix chain 'C' and resid 1273 through 1277 Processing helix chain 'C' and resid 1303 through 1305 No H-bonds generated for 'chain 'C' and resid 1303 through 1305' Processing helix chain 'C' and resid 1321 through 1325 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 3.517A pdb=" N GLY A 181 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 41 removed outlier: 6.496A pdb=" N LEU A 188 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ARG A 81 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE A 186 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 127 " --> pdb=" O TRP A 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 155 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 169 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.807A pdb=" N ILE A 215 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 219 through 223 removed outlier: 5.847A pdb=" N GLN A 220 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP A 310 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS A 222 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 364 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A 338 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 362 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE A 371 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.618A pdb=" N LYS A 482 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 12.156A pdb=" N VAL A 321 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 10.943A pdb=" N ASP A 444 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 12.621A pdb=" N ARG A 323 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N ILE A 442 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N GLU A 325 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP A 440 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 450 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 251 through 253 removed outlier: 3.743A pdb=" N VAL B 741 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA B 740 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 703 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASP B 704 " --> pdb=" O ASN B 536 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 257 through 260 removed outlier: 6.571A pdb=" N LEU A 487 " --> pdb=" O VAL A 498 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 498 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 489 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA9, first strand: chain 'A' and resid 380 through 382 removed outlier: 3.626A pdb=" N CYS A 420 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 529 removed outlier: 8.584A pdb=" N VAL A 758 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 770 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA A 764 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 540 removed outlier: 5.152A pdb=" N ASP A 704 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS A 703 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA A 740 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 741 " --> pdb=" O MET A 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 546 through 555 removed outlier: 7.700A pdb=" N LEU A 551 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR A 582 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 553 " --> pdb=" O TYR A 582 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A 584 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL A 555 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS A 586 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY A 678 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N GLN A 644 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 12.006A pdb=" N ILE A 680 " --> pdb=" O TYR A 642 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N TYR A 642 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N TYR A 682 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N GLY A 640 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 11.285A pdb=" N PHE A 684 " --> pdb=" O CYS A 638 " (cutoff:3.500A) removed outlier: 11.480A pdb=" N CYS A 638 " --> pdb=" O PHE A 684 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR A 686 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LYS A 636 " --> pdb=" O THR A 686 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 632 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ILE A 637 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N CYS A 571 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE A 639 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 641 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 546 through 555 removed outlier: 7.700A pdb=" N LEU A 551 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR A 582 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 553 " --> pdb=" O TYR A 582 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A 584 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL A 555 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS A 586 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 662 through 664 removed outlier: 6.480A pdb=" N VAL A 670 " --> pdb=" O PHE A 663 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 815 through 821 removed outlier: 5.743A pdb=" N LEU A 819 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 825 " --> pdb=" O MET A 821 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 856 through 860 removed outlier: 4.850A pdb=" N TYR A1239 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A1261 " --> pdb=" O ILE A1241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 863 through 872 removed outlier: 3.542A pdb=" N ILE A1213 " --> pdb=" O PHE A1228 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A1230 " --> pdb=" O HIS A1211 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS A1211 " --> pdb=" O LEU A1230 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 878 through 881 removed outlier: 4.388A pdb=" N LYS A 878 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.749A pdb=" N VAL A1253 " --> pdb=" O GLN A1308 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.516A pdb=" N GLY B 181 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 37 through 41 removed outlier: 6.826A pdb=" N VAL B 79 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ARG B 190 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG B 81 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 188 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 127 " --> pdb=" O TRP B 155 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP B 155 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 169 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.807A pdb=" N ILE B 215 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 219 through 223 removed outlier: 5.846A pdb=" N GLN B 220 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP B 310 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N CYS B 222 " --> pdb=" O ASP B 310 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B 364 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 338 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE B 362 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE B 371 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 235 through 237 removed outlier: 6.619A pdb=" N LYS B 482 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 12.156A pdb=" N VAL B 321 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 10.944A pdb=" N ASP B 444 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 12.621A pdb=" N ARG B 323 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N ILE B 442 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 10.701A pdb=" N GLU B 325 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP B 440 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU B 450 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.325A pdb=" N ARG B 252 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 741 " --> pdb=" O MET C 732 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA C 740 " --> pdb=" O VAL C 751 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS C 703 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP C 704 " --> pdb=" O ASN C 536 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 257 through 260 removed outlier: 6.571A pdb=" N LEU B 487 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL B 498 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR B 489 " --> pdb=" O ARG B 496 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AD1, first strand: chain 'B' and resid 380 through 382 removed outlier: 3.626A pdb=" N CYS B 420 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 522 through 529 removed outlier: 8.584A pdb=" N VAL B 758 " --> pdb=" O PRO B 774 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 770 " --> pdb=" O ALA B 762 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 764 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 546 through 555 removed outlier: 7.701A pdb=" N LEU B 551 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 582 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 553 " --> pdb=" O TYR B 582 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR B 584 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 555 " --> pdb=" O TYR B 584 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS B 586 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY B 678 " --> pdb=" O GLN B 644 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N GLN B 644 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 12.006A pdb=" N ILE B 680 " --> pdb=" O TYR B 642 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N TYR B 642 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N TYR B 682 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N GLY B 640 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 11.284A pdb=" N PHE B 684 " --> pdb=" O CYS B 638 " (cutoff:3.500A) removed outlier: 11.480A pdb=" N CYS B 638 " --> pdb=" O PHE B 684 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR B 686 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LYS B 636 " --> pdb=" O THR B 686 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B 632 " --> pdb=" O ASN B 690 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ILE B 637 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N CYS B 571 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE B 639 " --> pdb=" O TYR B 569 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 641 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 546 through 555 removed outlier: 7.701A pdb=" N LEU B 551 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 582 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 553 " --> pdb=" O TYR B 582 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR B 584 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 555 " --> pdb=" O TYR B 584 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS B 586 " --> pdb=" O VAL B 555 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 662 through 664 removed outlier: 6.480A pdb=" N VAL B 670 " --> pdb=" O PHE B 663 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 815 through 821 removed outlier: 5.743A pdb=" N LEU B 819 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS B 825 " --> pdb=" O MET B 821 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 856 through 860 removed outlier: 4.850A pdb=" N TYR B1239 " --> pdb=" O LYS B1263 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B1261 " --> pdb=" O ILE B1241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 863 through 872 removed outlier: 3.542A pdb=" N ILE B1213 " --> pdb=" O PHE B1228 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B1230 " --> pdb=" O HIS B1211 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS B1211 " --> pdb=" O LEU B1230 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 878 through 881 removed outlier: 4.389A pdb=" N LYS B 878 " --> pdb=" O LEU B1021 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1307 through 1310 removed outlier: 3.749A pdb=" N VAL B1253 " --> pdb=" O GLN B1308 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 25 through 28 removed outlier: 3.517A pdb=" N GLY C 181 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.827A pdb=" N VAL C 79 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ARG C 190 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG C 81 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 188 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 127 " --> pdb=" O TRP C 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP C 155 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 169 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 37 through 41 removed outlier: 3.807A pdb=" N ILE C 215 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 219 through 223 removed outlier: 5.847A pdb=" N GLN C 220 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP C 310 " --> pdb=" O GLN C 220 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS C 222 " --> pdb=" O ASP C 310 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA C 364 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 338 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE C 362 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE C 371 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 235 through 237 removed outlier: 6.619A pdb=" N LYS C 482 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 12.156A pdb=" N VAL C 321 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 10.943A pdb=" N ASP C 444 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 12.621A pdb=" N ARG C 323 " --> pdb=" O ILE C 442 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N ILE C 442 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N GLU C 325 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP C 440 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU C 450 " --> pdb=" O VAL C 457 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 257 through 260 removed outlier: 6.571A pdb=" N LEU C 487 " --> pdb=" O VAL C 498 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 498 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR C 489 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 343 through 344 Processing sheet with id=AE9, first strand: chain 'C' and resid 380 through 382 removed outlier: 3.626A pdb=" N CYS C 420 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 522 through 529 removed outlier: 8.584A pdb=" N VAL C 758 " --> pdb=" O PRO C 774 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY C 770 " --> pdb=" O ALA C 762 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA C 764 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ALA C 768 " --> pdb=" O ALA C 764 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 546 through 555 removed outlier: 7.701A pdb=" N LEU C 551 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR C 582 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 553 " --> pdb=" O TYR C 582 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR C 584 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL C 555 " --> pdb=" O TYR C 584 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS C 586 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY C 678 " --> pdb=" O GLN C 644 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N GLN C 644 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 12.006A pdb=" N ILE C 680 " --> pdb=" O TYR C 642 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N TYR C 642 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N TYR C 682 " --> pdb=" O GLY C 640 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N GLY C 640 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 11.284A pdb=" N PHE C 684 " --> pdb=" O CYS C 638 " (cutoff:3.500A) removed outlier: 11.481A pdb=" N CYS C 638 " --> pdb=" O PHE C 684 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR C 686 " --> pdb=" O LYS C 636 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LYS C 636 " --> pdb=" O THR C 686 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 632 " --> pdb=" O ASN C 690 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ILE C 637 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N CYS C 571 " --> pdb=" O ILE C 637 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE C 639 " --> pdb=" O TYR C 569 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR C 569 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 641 " --> pdb=" O LYS C 567 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 546 through 555 removed outlier: 7.701A pdb=" N LEU C 551 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR C 582 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 553 " --> pdb=" O TYR C 582 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR C 584 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL C 555 " --> pdb=" O TYR C 584 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS C 586 " --> pdb=" O VAL C 555 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 662 through 664 removed outlier: 6.479A pdb=" N VAL C 670 " --> pdb=" O PHE C 663 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 815 through 821 removed outlier: 5.744A pdb=" N LEU C 819 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS C 825 " --> pdb=" O MET C 821 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 856 through 860 removed outlier: 4.850A pdb=" N TYR C1239 " --> pdb=" O LYS C1263 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE C1261 " --> pdb=" O ILE C1241 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 863 through 872 removed outlier: 3.543A pdb=" N ILE C1213 " --> pdb=" O PHE C1228 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C1230 " --> pdb=" O HIS C1211 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N HIS C1211 " --> pdb=" O LEU C1230 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 878 through 881 removed outlier: 4.388A pdb=" N LYS C 878 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1307 through 1310 removed outlier: 3.749A pdb=" N VAL C1253 " --> pdb=" O GLN C1308 " (cutoff:3.500A) 1163 hydrogen bonds defined for protein. 3159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.33 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9511 1.34 - 1.46: 8700 1.46 - 1.59: 13634 1.59 - 1.71: 0 1.71 - 1.84: 279 Bond restraints: 32124 Sorted by residual: bond pdb=" C ASN A1208 " pdb=" N GLY A1209 " ideal model delta sigma weight residual 1.331 1.298 0.033 1.46e-02 4.69e+03 5.06e+00 bond pdb=" C ASN B1208 " pdb=" N GLY B1209 " ideal model delta sigma weight residual 1.331 1.298 0.032 1.46e-02 4.69e+03 4.94e+00 bond pdb=" C ASN C1208 " pdb=" N GLY C1209 " ideal model delta sigma weight residual 1.331 1.298 0.032 1.46e-02 4.69e+03 4.86e+00 bond pdb=" CA ASN B1208 " pdb=" C ASN B1208 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.48e-02 4.57e+03 4.40e+00 bond pdb=" CA ASN A1208 " pdb=" C ASN A1208 " ideal model delta sigma weight residual 1.524 1.494 0.031 1.48e-02 4.57e+03 4.32e+00 ... (remaining 32119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 42360 2.04 - 4.08: 1131 4.08 - 6.12: 105 6.12 - 8.16: 3 8.16 - 10.20: 9 Bond angle restraints: 43608 Sorted by residual: angle pdb=" C1 BMA 5 3 " pdb=" O5 BMA 5 3 " pdb=" C5 BMA 5 3 " ideal model delta sigma weight residual 118.82 108.62 10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C1 BMA T 3 " pdb=" O5 BMA T 3 " pdb=" C5 BMA T 3 " ideal model delta sigma weight residual 118.82 108.65 10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C1 BMA m 3 " pdb=" O5 BMA m 3 " pdb=" C5 BMA m 3 " ideal model delta sigma weight residual 118.82 108.66 10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C2 NAG A1409 " pdb=" N2 NAG A1409 " pdb=" C7 NAG A1409 " ideal model delta sigma weight residual 124.56 134.06 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C2 NAG C1409 " pdb=" N2 NAG C1409 " pdb=" C7 NAG C1409 " ideal model delta sigma weight residual 124.56 134.05 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 43603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 20041 21.83 - 43.67: 1097 43.67 - 65.50: 108 65.50 - 87.34: 198 87.34 - 109.17: 126 Dihedral angle restraints: 21570 sinusoidal: 10917 harmonic: 10653 Sorted by residual: dihedral pdb=" CB CYS C 571 " pdb=" SG CYS C 571 " pdb=" SG CYS C 638 " pdb=" CB CYS C 638 " ideal model delta sinusoidal sigma weight residual 93.00 45.03 47.97 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CB CYS A 571 " pdb=" SG CYS A 571 " pdb=" SG CYS A 638 " pdb=" CB CYS A 638 " ideal model delta sinusoidal sigma weight residual 93.00 45.07 47.93 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CB CYS B 571 " pdb=" SG CYS B 571 " pdb=" SG CYS B 638 " pdb=" CB CYS B 638 " ideal model delta sinusoidal sigma weight residual 93.00 45.09 47.91 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 21567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 5367 0.208 - 0.416: 51 0.416 - 0.624: 3 0.624 - 0.832: 6 0.832 - 1.040: 6 Chirality restraints: 5433 Sorted by residual: chirality pdb=" C1 BMA 5 3 " pdb=" O4 NAG 5 2 " pdb=" C2 BMA 5 3 " pdb=" O5 BMA 5 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-02 2.50e+03 2.18e+03 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-02 2.50e+03 2.17e+03 chirality pdb=" C1 BMA m 3 " pdb=" O4 NAG m 2 " pdb=" C2 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-02 2.50e+03 2.15e+03 ... (remaining 5430 not shown) Planarity restraints: 5415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " -0.345 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG b 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " -0.108 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.345 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG I 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.108 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG u 1 " 0.345 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG u 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG u 1 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG u 1 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG u 1 " 0.160 2.00e-02 2.50e+03 ... (remaining 5412 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 392 2.65 - 3.21: 28814 3.21 - 3.78: 49230 3.78 - 4.34: 69541 4.34 - 4.90: 112564 Nonbonded interactions: 260541 Sorted by model distance: nonbonded pdb=" O CYS A 571 " pdb=" OG1 THR C 376 " model vdw 2.092 3.040 nonbonded pdb=" OG1 THR B 376 " pdb=" O CYS C 571 " model vdw 2.105 3.040 nonbonded pdb=" OG1 THR A 376 " pdb=" O CYS B 571 " model vdw 2.132 3.040 nonbonded pdb=" O ASP B 63 " pdb=" N ALA B 65 " model vdw 2.190 3.120 nonbonded pdb=" O ASP A 63 " pdb=" N ALA A 65 " model vdw 2.190 3.120 ... (remaining 260536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'D' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'W' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'p' selection = chain 'v' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '1' selection = chain 'P' selection = chain 'i' } ncs_group { reference = chain '2' selection = chain 'K' selection = chain 'Q' selection = chain 'd' selection = chain 'j' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain '4' selection = chain '6' selection = chain '7' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = chain '5' selection = chain 'T' selection = chain 'm' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.320 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.010 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.004 0.033 32382 Z= 0.228 Angle : 0.726 10.201 44325 Z= 0.320 Chirality : 0.068 1.040 5433 Planarity : 0.023 0.299 5322 Dihedral : 17.317 109.170 14571 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.62 % 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: 0.52 (0.15), residues: 3597 helix: 2.45 (0.20), residues: 729 sheet: 0.66 (0.20), residues: 741 loop : -0.54 (0.14), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1185 TYR 0.024 0.001 TYR B 57 PHE 0.012 0.001 PHE C 904 TRP 0.006 0.001 TRP A 157 HIS 0.006 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00434 (32124) covalent geometry : angle 0.68065 (43608) SS BOND : bond 0.00445 ( 57) SS BOND : angle 1.05441 ( 114) hydrogen bonds : bond 0.19157 ( 1124) hydrogen bonds : angle 7.49442 ( 3159) link_ALPHA1-3 : bond 0.00247 ( 6) link_ALPHA1-3 : angle 0.75252 ( 18) link_ALPHA1-6 : bond 0.00207 ( 12) link_ALPHA1-6 : angle 1.53605 ( 36) link_BETA1-4 : bond 0.00477 ( 87) link_BETA1-4 : angle 2.06528 ( 261) link_BETA1-6 : bond 0.00777 ( 3) link_BETA1-6 : angle 2.58894 ( 9) link_NAG-ASN : bond 0.00641 ( 93) link_NAG-ASN : angle 2.52737 ( 279) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 556 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 25 ASN cc_start: 0.7701 (m110) cc_final: 0.7445 (m110) REVERT: A 50 MET cc_start: 0.7749 (mmm) cc_final: 0.7520 (mmm) REVERT: A 71 TYR cc_start: 0.7788 (m-80) cc_final: 0.7510 (m-80) REVERT: A 142 GLN cc_start: 0.6990 (mp10) cc_final: 0.6417 (mp-120) REVERT: A 215 ILE cc_start: 0.6837 (pt) cc_final: 0.6261 (mp) REVERT: A 325 GLU cc_start: 0.7662 (pm20) cc_final: 0.7413 (pm20) REVERT: A 422 ARG cc_start: 0.7539 (ttp-110) cc_final: 0.7024 (ttm170) REVERT: A 572 VAL cc_start: 0.6707 (m) cc_final: 0.6439 (t) REVERT: A 576 TYR cc_start: 0.8533 (m-80) cc_final: 0.7846 (m-80) REVERT: A 681 ASP cc_start: 0.8278 (t0) cc_final: 0.7915 (m-30) REVERT: A 836 ASN cc_start: 0.7871 (t0) cc_final: 0.7181 (p0) REVERT: A 906 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 1145 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7265 (pt0) REVERT: A 1190 GLU cc_start: 0.7706 (tp30) cc_final: 0.7484 (mt-10) REVERT: B 25 ASN cc_start: 0.7733 (m110) cc_final: 0.7438 (m110) REVERT: B 71 TYR cc_start: 0.7726 (m-80) cc_final: 0.6928 (m-80) REVERT: B 142 GLN cc_start: 0.6978 (mp10) cc_final: 0.6488 (mp-120) REVERT: B 210 MET cc_start: 0.7208 (mmp) cc_final: 0.6895 (mmp) REVERT: B 220 GLN cc_start: 0.5881 (mm-40) cc_final: 0.5673 (mm-40) REVERT: B 325 GLU cc_start: 0.7588 (pm20) cc_final: 0.7359 (pm20) REVERT: B 426 GLU cc_start: 0.7623 (tp30) cc_final: 0.7375 (tp30) REVERT: B 576 TYR cc_start: 0.8603 (m-80) cc_final: 0.7975 (m-80) REVERT: B 836 ASN cc_start: 0.7776 (t0) cc_final: 0.6993 (p0) REVERT: B 906 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7637 (tp30) REVERT: B 925 ASP cc_start: 0.6943 (m-30) cc_final: 0.6731 (m-30) REVERT: B 1021 LEU cc_start: 0.8673 (mt) cc_final: 0.8462 (mt) REVERT: B 1142 GLU cc_start: 0.7196 (pt0) cc_final: 0.6776 (pt0) REVERT: B 1145 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7368 (pt0) REVERT: B 1190 GLU cc_start: 0.7601 (tp30) cc_final: 0.7371 (mt-10) REVERT: B 1321 GLU cc_start: 0.7524 (mp0) cc_final: 0.7304 (tm-30) REVERT: C 71 TYR cc_start: 0.7572 (m-80) cc_final: 0.6847 (m-80) REVERT: C 265 LYS cc_start: 0.8590 (tttm) cc_final: 0.8333 (tttm) REVERT: C 325 GLU cc_start: 0.7619 (pm20) cc_final: 0.7287 (pm20) REVERT: C 437 MET cc_start: 0.8653 (mmm) cc_final: 0.8407 (mmm) REVERT: C 572 VAL cc_start: 0.6689 (m) cc_final: 0.6397 (t) REVERT: C 576 TYR cc_start: 0.8575 (m-80) cc_final: 0.7878 (m-80) REVERT: C 836 ASN cc_start: 0.7845 (t0) cc_final: 0.7076 (p0) REVERT: C 906 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7500 (tp30) REVERT: C 925 ASP cc_start: 0.6972 (m-30) cc_final: 0.6709 (m-30) REVERT: C 1142 GLU cc_start: 0.7453 (pt0) cc_final: 0.6733 (pt0) REVERT: C 1145 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7165 (pt0) REVERT: C 1190 GLU cc_start: 0.7781 (tp30) cc_final: 0.7534 (mt-10) REVERT: C 1321 GLU cc_start: 0.7453 (mp0) cc_final: 0.7226 (tm-30) outliers start: 3 outliers final: 2 residues processed: 557 average time/residue: 0.6705 time to fit residues: 441.9168 Evaluate side-chains 412 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 410 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain C residue 951 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0980 chunk 298 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN A 699 GLN A 753 GLN A1016 ASN A1076 GLN A1221 ASN A1296 GLN A1308 GLN B 527 ASN B 699 GLN B1016 ASN B1070 ASN B1076 GLN B1081 GLN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1296 GLN C 208 ASN C 527 ASN C 699 GLN C 745 ASN C1016 ASN C1076 GLN ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.177495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142933 restraints weight = 29764.312| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.71 r_work: 0.3274 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 32382 Z= 0.212 Angle : 0.808 12.811 44325 Z= 0.372 Chirality : 0.053 0.502 5433 Planarity : 0.004 0.036 5322 Dihedral : 13.740 110.397 8074 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 1.98 % Allowed : 7.25 % Favored : 90.77 % 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: 0.24 (0.14), residues: 3597 helix: 1.91 (0.19), residues: 744 sheet: 0.48 (0.20), residues: 702 loop : -0.58 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 252 TYR 0.022 0.002 TYR B 705 PHE 0.021 0.002 PHE B 746 TRP 0.008 0.001 TRP A 155 HIS 0.010 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00479 (32124) covalent geometry : angle 0.74971 (43608) SS BOND : bond 0.00529 ( 57) SS BOND : angle 1.97710 ( 114) hydrogen bonds : bond 0.05408 ( 1124) hydrogen bonds : angle 5.59937 ( 3159) link_ALPHA1-3 : bond 0.01124 ( 6) link_ALPHA1-3 : angle 2.12864 ( 18) link_ALPHA1-6 : bond 0.00805 ( 12) link_ALPHA1-6 : angle 1.76068 ( 36) link_BETA1-4 : bond 0.00636 ( 87) link_BETA1-4 : angle 2.25343 ( 261) link_BETA1-6 : bond 0.00145 ( 3) link_BETA1-6 : angle 2.42529 ( 9) link_NAG-ASN : bond 0.00762 ( 93) link_NAG-ASN : angle 2.92862 ( 279) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 432 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8405 (mmm) cc_final: 0.8156 (mmm) REVERT: A 142 GLN cc_start: 0.7536 (mp10) cc_final: 0.7207 (mp-120) REVERT: A 188 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8415 (tp) REVERT: A 422 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7901 (ttm170) REVERT: A 576 TYR cc_start: 0.8924 (m-80) cc_final: 0.8645 (m-80) REVERT: A 836 ASN cc_start: 0.8104 (t0) cc_final: 0.7724 (p0) REVERT: A 906 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8231 (tp30) REVERT: A 1041 MET cc_start: 0.8494 (ttm) cc_final: 0.8098 (ttm) REVERT: B 71 TYR cc_start: 0.8016 (m-80) cc_final: 0.7513 (m-80) REVERT: B 142 GLN cc_start: 0.7493 (mp10) cc_final: 0.7171 (mp-120) REVERT: B 188 LEU cc_start: 0.8768 (tp) cc_final: 0.8350 (mt) REVERT: B 210 MET cc_start: 0.7691 (mmp) cc_final: 0.7424 (mmp) REVERT: B 215 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6915 (mp) REVERT: B 422 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.8008 (ttm170) REVERT: B 576 TYR cc_start: 0.8927 (m-80) cc_final: 0.8421 (m-80) REVERT: B 836 ASN cc_start: 0.8054 (t0) cc_final: 0.7541 (p0) REVERT: B 906 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8333 (tp30) REVERT: B 926 PHE cc_start: 0.8390 (t80) cc_final: 0.8152 (t80) REVERT: B 1030 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8433 (mmt) REVERT: B 1145 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7946 (pt0) REVERT: C 71 TYR cc_start: 0.8072 (m-80) cc_final: 0.7594 (m-80) REVERT: C 126 VAL cc_start: 0.3968 (OUTLIER) cc_final: 0.3594 (p) REVERT: C 215 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6744 (mp) REVERT: C 532 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: C 572 VAL cc_start: 0.7202 (m) cc_final: 0.6952 (t) REVERT: C 576 TYR cc_start: 0.8904 (m-80) cc_final: 0.8451 (m-80) REVERT: C 836 ASN cc_start: 0.8130 (t0) cc_final: 0.7650 (p0) REVERT: C 1081 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7748 (mm110) REVERT: C 1142 GLU cc_start: 0.7991 (pt0) cc_final: 0.7538 (pt0) outliers start: 63 outliers final: 26 residues processed: 463 average time/residue: 0.6178 time to fit residues: 339.5796 Evaluate side-chains 430 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 397 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 1030 MET Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1304 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain C residue 934 ASP Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1091 THR Chi-restraints excluded: chain C residue 1304 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 257 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 344 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 247 optimal weight: 0.4980 chunk 87 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 972 GLN A1081 GLN A1120 GLN A1221 ASN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 GLN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.177667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142923 restraints weight = 29750.253| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.75 r_work: 0.3285 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32382 Z= 0.150 Angle : 0.727 13.792 44325 Z= 0.334 Chirality : 0.052 0.513 5433 Planarity : 0.004 0.032 5322 Dihedral : 11.109 103.800 8072 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 2.39 % Allowed : 9.57 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3597 helix: 2.07 (0.19), residues: 723 sheet: 0.30 (0.19), residues: 705 loop : -0.52 (0.14), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 169 TYR 0.015 0.001 TYR B 416 PHE 0.029 0.002 PHE A 904 TRP 0.006 0.001 TRP A 157 HIS 0.006 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00325 (32124) covalent geometry : angle 0.66964 (43608) SS BOND : bond 0.00433 ( 57) SS BOND : angle 1.49637 ( 114) hydrogen bonds : bond 0.04621 ( 1124) hydrogen bonds : angle 5.22127 ( 3159) link_ALPHA1-3 : bond 0.01199 ( 6) link_ALPHA1-3 : angle 2.01656 ( 18) link_ALPHA1-6 : bond 0.00718 ( 12) link_ALPHA1-6 : angle 1.86739 ( 36) link_BETA1-4 : bond 0.00530 ( 87) link_BETA1-4 : angle 2.03750 ( 261) link_BETA1-6 : bond 0.00051 ( 3) link_BETA1-6 : angle 2.34396 ( 9) link_NAG-ASN : bond 0.00631 ( 93) link_NAG-ASN : angle 2.86680 ( 279) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 412 time to evaluate : 1.114 Fit side-chains REVERT: A 50 MET cc_start: 0.8359 (mmm) cc_final: 0.8103 (mmm) REVERT: A 118 MET cc_start: 0.2768 (ppp) cc_final: 0.2566 (ppp) REVERT: A 126 VAL cc_start: 0.4014 (OUTLIER) cc_final: 0.3700 (m) REVERT: A 142 GLN cc_start: 0.7436 (mp10) cc_final: 0.7226 (mp-120) REVERT: A 188 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 190 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7252 (ptm-80) REVERT: A 220 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6844 (tp40) REVERT: A 422 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7784 (ttm170) REVERT: A 467 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7509 (ptp90) REVERT: A 576 TYR cc_start: 0.8886 (m-80) cc_final: 0.8646 (m-80) REVERT: A 836 ASN cc_start: 0.8136 (t0) cc_final: 0.7739 (p0) REVERT: A 848 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8827 (mt0) REVERT: B 71 TYR cc_start: 0.7958 (m-80) cc_final: 0.7477 (m-80) REVERT: B 142 GLN cc_start: 0.7420 (mp10) cc_final: 0.7195 (mp-120) REVERT: B 188 LEU cc_start: 0.8875 (tp) cc_final: 0.8506 (mt) REVERT: B 210 MET cc_start: 0.7630 (mmp) cc_final: 0.7320 (mmp) REVERT: B 215 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6883 (mp) REVERT: B 576 TYR cc_start: 0.8860 (m-80) cc_final: 0.8476 (m-80) REVERT: B 681 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: B 836 ASN cc_start: 0.8019 (t0) cc_final: 0.7533 (p0) REVERT: B 1069 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7861 (mp10) REVERT: B 1145 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7903 (pt0) REVERT: B 1295 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: C 71 TYR cc_start: 0.8042 (m-80) cc_final: 0.7616 (m-80) REVERT: C 126 VAL cc_start: 0.4043 (OUTLIER) cc_final: 0.3706 (m) REVERT: C 422 ARG cc_start: 0.8348 (ttm170) cc_final: 0.7989 (ttm170) REVERT: C 572 VAL cc_start: 0.7169 (m) cc_final: 0.6856 (t) REVERT: C 576 TYR cc_start: 0.8819 (m-80) cc_final: 0.8469 (m-80) REVERT: C 836 ASN cc_start: 0.8124 (t0) cc_final: 0.7678 (p0) REVERT: C 850 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7962 (tt) REVERT: C 906 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: C 1041 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8284 (ttm) REVERT: C 1081 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7743 (mm110) REVERT: C 1274 GLU cc_start: 0.7629 (pm20) cc_final: 0.7284 (pm20) outliers start: 76 outliers final: 24 residues processed: 460 average time/residue: 0.6738 time to fit residues: 368.0844 Evaluate side-chains 433 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 397 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1295 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 934 ASP Chi-restraints excluded: chain C residue 1041 MET Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1091 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 322 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 234 optimal weight: 6.9990 chunk 335 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 GLN A1120 GLN A1221 ASN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 GLN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.177178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142812 restraints weight = 29433.715| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.72 r_work: 0.3285 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32382 Z= 0.158 Angle : 0.722 15.199 44325 Z= 0.336 Chirality : 0.052 0.568 5433 Planarity : 0.004 0.033 5322 Dihedral : 9.562 84.335 8070 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 2.26 % Allowed : 10.95 % Favored : 86.79 % 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: 0.18 (0.14), residues: 3597 helix: 1.98 (0.19), residues: 729 sheet: 0.17 (0.19), residues: 705 loop : -0.55 (0.14), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1185 TYR 0.017 0.002 TYR A 71 PHE 0.022 0.002 PHE A 904 TRP 0.006 0.001 TRP B 155 HIS 0.006 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00350 (32124) covalent geometry : angle 0.66076 (43608) SS BOND : bond 0.00505 ( 57) SS BOND : angle 1.85234 ( 114) hydrogen bonds : bond 0.04561 ( 1124) hydrogen bonds : angle 5.13332 ( 3159) link_ALPHA1-3 : bond 0.01187 ( 6) link_ALPHA1-3 : angle 2.20938 ( 18) link_ALPHA1-6 : bond 0.00748 ( 12) link_ALPHA1-6 : angle 1.83894 ( 36) link_BETA1-4 : bond 0.00550 ( 87) link_BETA1-4 : angle 1.99240 ( 261) link_BETA1-6 : bond 0.00046 ( 3) link_BETA1-6 : angle 2.18627 ( 9) link_NAG-ASN : bond 0.00656 ( 93) link_NAG-ASN : angle 2.91094 ( 279) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 412 time to evaluate : 1.138 Fit side-chains REVERT: A 50 MET cc_start: 0.8387 (mmm) cc_final: 0.8178 (mmm) REVERT: A 126 VAL cc_start: 0.4145 (OUTLIER) cc_final: 0.3793 (m) REVERT: A 182 ILE cc_start: 0.8570 (mt) cc_final: 0.8313 (mt) REVERT: A 188 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8487 (tp) REVERT: A 190 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7354 (ptm-80) REVERT: A 220 GLN cc_start: 0.7129 (mm-40) cc_final: 0.6872 (mm-40) REVERT: A 422 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7748 (ttm170) REVERT: A 576 TYR cc_start: 0.8909 (m-80) cc_final: 0.8663 (m-80) REVERT: A 836 ASN cc_start: 0.8132 (t0) cc_final: 0.7750 (p0) REVERT: A 1074 GLU cc_start: 0.7941 (pm20) cc_final: 0.7649 (pt0) REVERT: A 1142 GLU cc_start: 0.8037 (pt0) cc_final: 0.7309 (mt-10) REVERT: B 71 TYR cc_start: 0.7993 (m-80) cc_final: 0.7523 (m-80) REVERT: B 142 GLN cc_start: 0.7421 (mp10) cc_final: 0.7203 (mp-120) REVERT: B 188 LEU cc_start: 0.8893 (tp) cc_final: 0.8581 (mt) REVERT: B 210 MET cc_start: 0.7647 (mmp) cc_final: 0.7353 (mmp) REVERT: B 220 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6870 (mm-40) REVERT: B 223 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6484 (tpt-90) REVERT: B 467 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7961 (ptp90) REVERT: B 576 TYR cc_start: 0.8848 (m-80) cc_final: 0.8469 (m-80) REVERT: B 681 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8222 (m-30) REVERT: B 700 ASP cc_start: 0.7315 (m-30) cc_final: 0.6888 (m-30) REVERT: B 836 ASN cc_start: 0.8006 (t0) cc_final: 0.7544 (p0) REVERT: B 906 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: B 1030 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8464 (mmt) REVERT: B 1145 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7923 (pt0) REVERT: B 1295 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: C 71 TYR cc_start: 0.8091 (m-80) cc_final: 0.7681 (m-80) REVERT: C 126 VAL cc_start: 0.4113 (OUTLIER) cc_final: 0.3751 (m) REVERT: C 576 TYR cc_start: 0.8786 (m-80) cc_final: 0.8469 (m-80) REVERT: C 836 ASN cc_start: 0.8106 (t0) cc_final: 0.7680 (p0) REVERT: C 850 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7987 (tt) REVERT: C 906 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6839 (tp30) REVERT: C 1081 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7746 (mm110) REVERT: C 1274 GLU cc_start: 0.7605 (pm20) cc_final: 0.7235 (pm20) outliers start: 72 outliers final: 29 residues processed: 452 average time/residue: 0.6382 time to fit residues: 344.3073 Evaluate side-chains 430 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 388 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 1030 MET Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1295 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 934 ASP Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1091 THR Chi-restraints excluded: chain C residue 1137 THR Chi-restraints excluded: chain C residue 1221 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 80 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 234 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 333 optimal weight: 0.0060 chunk 138 optimal weight: 0.9980 chunk 217 optimal weight: 0.0470 chunk 296 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 0.4894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A1081 GLN A1120 GLN A1221 ASN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 GLN B1059 GLN B1070 ASN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.178965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148267 restraints weight = 31202.133| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.51 r_work: 0.3411 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32382 Z= 0.132 Angle : 0.696 15.863 44325 Z= 0.323 Chirality : 0.052 0.706 5433 Planarity : 0.003 0.033 5322 Dihedral : 8.947 81.687 8070 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 2.07 % Allowed : 12.30 % Favored : 85.62 % 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: 0.24 (0.14), residues: 3597 helix: 2.30 (0.19), residues: 711 sheet: 0.16 (0.19), residues: 705 loop : -0.57 (0.14), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 169 TYR 0.017 0.001 TYR A 71 PHE 0.022 0.001 PHE A 904 TRP 0.006 0.001 TRP A 155 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00283 (32124) covalent geometry : angle 0.63056 (43608) SS BOND : bond 0.00436 ( 57) SS BOND : angle 1.54864 ( 114) hydrogen bonds : bond 0.04274 ( 1124) hydrogen bonds : angle 5.02520 ( 3159) link_ALPHA1-3 : bond 0.01217 ( 6) link_ALPHA1-3 : angle 2.14400 ( 18) link_ALPHA1-6 : bond 0.00767 ( 12) link_ALPHA1-6 : angle 1.82347 ( 36) link_BETA1-4 : bond 0.00509 ( 87) link_BETA1-4 : angle 1.86977 ( 261) link_BETA1-6 : bond 0.00041 ( 3) link_BETA1-6 : angle 2.10343 ( 9) link_NAG-ASN : bond 0.00567 ( 93) link_NAG-ASN : angle 3.12955 ( 279) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 409 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.4032 (OUTLIER) cc_final: 0.3700 (m) REVERT: A 182 ILE cc_start: 0.8505 (mt) cc_final: 0.8252 (mt) REVERT: A 188 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8490 (tp) REVERT: A 190 ARG cc_start: 0.7432 (ttp80) cc_final: 0.7174 (ptm-80) REVERT: A 220 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6877 (mm-40) REVERT: A 422 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7623 (ttm170) REVERT: A 428 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8755 (pttp) REVERT: A 576 TYR cc_start: 0.8783 (m-80) cc_final: 0.8337 (m-80) REVERT: A 836 ASN cc_start: 0.8060 (t0) cc_final: 0.7785 (p0) REVERT: A 938 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8669 (mp) REVERT: A 1021 LEU cc_start: 0.8842 (mt) cc_final: 0.8548 (mt) REVERT: A 1142 GLU cc_start: 0.7976 (pt0) cc_final: 0.7336 (mt-10) REVERT: B 71 TYR cc_start: 0.7853 (m-80) cc_final: 0.7432 (m-80) REVERT: B 188 LEU cc_start: 0.8873 (tp) cc_final: 0.8601 (mt) REVERT: B 210 MET cc_start: 0.7573 (mmp) cc_final: 0.7241 (mmt) REVERT: B 220 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6808 (mm-40) REVERT: B 223 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6535 (tpt-90) REVERT: B 467 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7698 (ptp90) REVERT: B 576 TYR cc_start: 0.8743 (m-80) cc_final: 0.8404 (m-80) REVERT: B 681 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: B 700 ASP cc_start: 0.7263 (m-30) cc_final: 0.6862 (m-30) REVERT: B 836 ASN cc_start: 0.7933 (t0) cc_final: 0.7552 (p0) REVERT: B 906 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: B 1019 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8314 (tpp) REVERT: B 1069 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7857 (mp10) REVERT: B 1112 GLN cc_start: 0.8242 (mt0) cc_final: 0.7987 (mt0) REVERT: B 1145 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7876 (pt0) REVERT: B 1295 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: C 71 TYR cc_start: 0.7978 (m-80) cc_final: 0.7662 (m-80) REVERT: C 422 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7810 (ttm170) REVERT: C 428 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8736 (pttp) REVERT: C 576 TYR cc_start: 0.8692 (m-80) cc_final: 0.8436 (m-80) REVERT: C 836 ASN cc_start: 0.8035 (t0) cc_final: 0.7703 (p0) REVERT: C 850 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7980 (tt) REVERT: C 906 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6716 (tp30) REVERT: C 1081 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7573 (mm110) REVERT: C 1274 GLU cc_start: 0.7634 (pm20) cc_final: 0.7291 (pm20) outliers start: 66 outliers final: 29 residues processed: 444 average time/residue: 0.6375 time to fit residues: 337.5733 Evaluate side-chains 431 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 387 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 951 ASP Chi-restraints excluded: chain B residue 1019 MET Chi-restraints excluded: chain B residue 1041 MET Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1266 ASN Chi-restraints excluded: chain B residue 1295 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 934 ASP Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1266 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 278 optimal weight: 0.0470 chunk 247 optimal weight: 3.9990 chunk 326 optimal weight: 0.9980 chunk 202 optimal weight: 0.5980 chunk 327 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 279 optimal weight: 0.6980 chunk 238 optimal weight: 0.8980 chunk 337 optimal weight: 8.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 884 ASN A1081 GLN A1120 GLN A1221 ASN B 142 GLN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 GLN B1081 GLN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 884 ASN C1221 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.178437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147360 restraints weight = 31041.477| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.55 r_work: 0.3394 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32382 Z= 0.143 Angle : 0.693 17.834 44325 Z= 0.324 Chirality : 0.052 0.722 5433 Planarity : 0.003 0.031 5322 Dihedral : 8.555 78.399 8070 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.61 % Rotamer: Outliers : 2.32 % Allowed : 12.84 % Favored : 84.84 % 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: 0.24 (0.14), residues: 3597 helix: 2.31 (0.19), residues: 711 sheet: 0.14 (0.19), residues: 714 loop : -0.56 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 169 TYR 0.016 0.001 TYR A 71 PHE 0.019 0.001 PHE A 904 TRP 0.007 0.001 TRP B 305 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00313 (32124) covalent geometry : angle 0.63078 (43608) SS BOND : bond 0.00382 ( 57) SS BOND : angle 1.44905 ( 114) hydrogen bonds : bond 0.04282 ( 1124) hydrogen bonds : angle 4.98938 ( 3159) link_ALPHA1-3 : bond 0.01229 ( 6) link_ALPHA1-3 : angle 2.16691 ( 18) link_ALPHA1-6 : bond 0.00815 ( 12) link_ALPHA1-6 : angle 1.77996 ( 36) link_BETA1-4 : bond 0.00517 ( 87) link_BETA1-4 : angle 1.77628 ( 261) link_BETA1-6 : bond 0.00056 ( 3) link_BETA1-6 : angle 1.97295 ( 9) link_NAG-ASN : bond 0.00523 ( 93) link_NAG-ASN : angle 3.06251 ( 279) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 395 time to evaluate : 1.369 Fit side-chains REVERT: A 126 VAL cc_start: 0.4135 (OUTLIER) cc_final: 0.3785 (m) REVERT: A 182 ILE cc_start: 0.8505 (mt) cc_final: 0.8246 (mt) REVERT: A 188 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8490 (tp) REVERT: A 190 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7257 (ptm-80) REVERT: A 220 GLN cc_start: 0.7115 (mm-40) cc_final: 0.6897 (mm-40) REVERT: A 422 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7610 (ttm170) REVERT: A 428 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8814 (pttp) REVERT: A 576 TYR cc_start: 0.8812 (m-80) cc_final: 0.8378 (m-80) REVERT: A 836 ASN cc_start: 0.8076 (t0) cc_final: 0.7789 (p0) REVERT: A 938 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 1041 MET cc_start: 0.8468 (ttm) cc_final: 0.8152 (ttm) REVERT: A 1142 GLU cc_start: 0.7987 (pt0) cc_final: 0.7348 (mt-10) REVERT: B 71 TYR cc_start: 0.7888 (m-80) cc_final: 0.7452 (m-80) REVERT: B 188 LEU cc_start: 0.8875 (tp) cc_final: 0.8604 (mt) REVERT: B 210 MET cc_start: 0.7622 (mmp) cc_final: 0.7228 (mmt) REVERT: B 220 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6818 (mm-40) REVERT: B 223 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6540 (tpt-90) REVERT: B 467 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7808 (ptp90) REVERT: B 576 TYR cc_start: 0.8755 (m-80) cc_final: 0.8412 (m-80) REVERT: B 681 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: B 836 ASN cc_start: 0.7944 (t0) cc_final: 0.7565 (p0) REVERT: B 906 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: B 1069 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7906 (mp10) REVERT: B 1074 GLU cc_start: 0.7789 (pm20) cc_final: 0.7512 (pt0) REVERT: B 1112 GLN cc_start: 0.8248 (mt0) cc_final: 0.8029 (mt0) REVERT: B 1295 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: C 71 TYR cc_start: 0.8000 (m-80) cc_final: 0.7668 (m-80) REVERT: C 126 VAL cc_start: 0.3796 (OUTLIER) cc_final: 0.3506 (m) REVERT: C 223 ARG cc_start: 0.7474 (mmm160) cc_final: 0.7086 (mtp85) REVERT: C 576 TYR cc_start: 0.8744 (m-80) cc_final: 0.8431 (m-80) REVERT: C 836 ASN cc_start: 0.8026 (t0) cc_final: 0.7688 (p0) REVERT: C 850 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8003 (tt) REVERT: C 906 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6808 (tp30) REVERT: C 1081 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7545 (mm110) REVERT: C 1112 GLN cc_start: 0.8308 (mt0) cc_final: 0.8046 (mt0) REVERT: C 1274 GLU cc_start: 0.7664 (pm20) cc_final: 0.7305 (pm20) outliers start: 74 outliers final: 33 residues processed: 438 average time/residue: 0.6846 time to fit residues: 356.4984 Evaluate side-chains 430 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 383 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1295 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 934 ASP Chi-restraints excluded: chain C residue 1041 MET Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1091 THR Chi-restraints excluded: chain C residue 1137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 7 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 323 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 329 optimal weight: 0.4980 chunk 351 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A1081 GLN A1120 GLN A1221 ASN B 25 ASN B 142 GLN B 972 GLN B1081 GLN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.176889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145823 restraints weight = 31065.406| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.57 r_work: 0.3372 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32382 Z= 0.168 Angle : 0.711 18.398 44325 Z= 0.336 Chirality : 0.050 0.482 5433 Planarity : 0.004 0.033 5322 Dihedral : 8.277 74.291 8070 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 2.20 % Allowed : 13.15 % Favored : 84.65 % 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: 0.15 (0.14), residues: 3597 helix: 2.23 (0.19), residues: 708 sheet: 0.12 (0.19), residues: 711 loop : -0.63 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 169 TYR 0.016 0.002 TYR A 71 PHE 0.017 0.002 PHE C 40 TRP 0.009 0.001 TRP B 305 HIS 0.007 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00373 (32124) covalent geometry : angle 0.65271 (43608) SS BOND : bond 0.00461 ( 57) SS BOND : angle 1.62583 ( 114) hydrogen bonds : bond 0.04583 ( 1124) hydrogen bonds : angle 5.07682 ( 3159) link_ALPHA1-3 : bond 0.01226 ( 6) link_ALPHA1-3 : angle 2.14893 ( 18) link_ALPHA1-6 : bond 0.00856 ( 12) link_ALPHA1-6 : angle 1.73401 ( 36) link_BETA1-4 : bond 0.00519 ( 87) link_BETA1-4 : angle 1.73644 ( 261) link_BETA1-6 : bond 0.00055 ( 3) link_BETA1-6 : angle 1.81429 ( 9) link_NAG-ASN : bond 0.00743 ( 93) link_NAG-ASN : angle 3.02341 ( 279) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 389 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 126 VAL cc_start: 0.4179 (OUTLIER) cc_final: 0.3807 (m) REVERT: A 182 ILE cc_start: 0.8529 (mt) cc_final: 0.8269 (mt) REVERT: A 188 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8527 (tp) REVERT: A 190 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7402 (ptm-80) REVERT: A 220 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6974 (mm-40) REVERT: A 422 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7622 (ttm170) REVERT: A 576 TYR cc_start: 0.8849 (m-80) cc_final: 0.8648 (m-80) REVERT: A 836 ASN cc_start: 0.8104 (t0) cc_final: 0.7799 (p0) REVERT: A 938 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8699 (mp) REVERT: A 1041 MET cc_start: 0.8487 (ttm) cc_final: 0.8227 (ttm) REVERT: A 1142 GLU cc_start: 0.8016 (pt0) cc_final: 0.7385 (mt-10) REVERT: B 71 TYR cc_start: 0.7980 (m-80) cc_final: 0.7568 (m-80) REVERT: B 188 LEU cc_start: 0.8877 (tp) cc_final: 0.8616 (mt) REVERT: B 210 MET cc_start: 0.7715 (mmp) cc_final: 0.7374 (mmt) REVERT: B 223 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6578 (tpt-90) REVERT: B 467 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7953 (ptp90) REVERT: B 576 TYR cc_start: 0.8789 (m-80) cc_final: 0.8420 (m-80) REVERT: B 681 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: B 836 ASN cc_start: 0.7955 (t0) cc_final: 0.7572 (p0) REVERT: B 906 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7105 (tp30) REVERT: B 1019 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8296 (tpp) REVERT: B 1030 MET cc_start: 0.8461 (mmt) cc_final: 0.8097 (mmt) REVERT: B 1041 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8287 (ttm) REVERT: B 1074 GLU cc_start: 0.7819 (pm20) cc_final: 0.7536 (pt0) REVERT: C 52 TYR cc_start: 0.7945 (m-80) cc_final: 0.7593 (m-80) REVERT: C 71 TYR cc_start: 0.8042 (m-80) cc_final: 0.7728 (m-80) REVERT: C 126 VAL cc_start: 0.3888 (OUTLIER) cc_final: 0.3569 (m) REVERT: C 532 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: C 576 TYR cc_start: 0.8763 (m-80) cc_final: 0.8458 (m-80) REVERT: C 836 ASN cc_start: 0.8021 (t0) cc_final: 0.7664 (p0) REVERT: C 850 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8030 (tt) REVERT: C 906 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6726 (tp30) REVERT: C 1074 GLU cc_start: 0.7708 (pm20) cc_final: 0.7506 (pt0) REVERT: C 1081 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7628 (mm110) REVERT: C 1112 GLN cc_start: 0.8435 (mt0) cc_final: 0.8199 (mt0) REVERT: C 1274 GLU cc_start: 0.7645 (pm20) cc_final: 0.7431 (mp0) outliers start: 70 outliers final: 35 residues processed: 427 average time/residue: 0.6812 time to fit residues: 346.2338 Evaluate side-chains 422 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 373 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1221 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 1019 MET Chi-restraints excluded: chain B residue 1041 MET Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 934 ASP Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 1041 MET Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1091 THR Chi-restraints excluded: chain C residue 1137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 55 optimal weight: 0.0050 chunk 312 optimal weight: 0.3980 chunk 123 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 314 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A1081 GLN A1120 GLN A1221 ASN B 25 ASN B 142 GLN B 972 GLN B1081 GLN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.179284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148100 restraints weight = 31062.434| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.56 r_work: 0.3404 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32382 Z= 0.125 Angle : 0.679 18.400 44325 Z= 0.317 Chirality : 0.052 0.765 5433 Planarity : 0.003 0.030 5322 Dihedral : 7.996 71.628 8070 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 2.17 % Allowed : 13.68 % Favored : 84.15 % 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: 0.22 (0.14), residues: 3597 helix: 2.35 (0.19), residues: 711 sheet: 0.12 (0.19), residues: 714 loop : -0.61 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 169 TYR 0.016 0.001 TYR A 71 PHE 0.019 0.001 PHE A 904 TRP 0.008 0.001 TRP B 305 HIS 0.003 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00265 (32124) covalent geometry : angle 0.62107 (43608) SS BOND : bond 0.00432 ( 57) SS BOND : angle 1.50944 ( 114) hydrogen bonds : bond 0.04062 ( 1124) hydrogen bonds : angle 4.93428 ( 3159) link_ALPHA1-3 : bond 0.01233 ( 6) link_ALPHA1-3 : angle 2.05372 ( 18) link_ALPHA1-6 : bond 0.00845 ( 12) link_ALPHA1-6 : angle 1.72064 ( 36) link_BETA1-4 : bond 0.00501 ( 87) link_BETA1-4 : angle 1.66529 ( 261) link_BETA1-6 : bond 0.00046 ( 3) link_BETA1-6 : angle 1.75672 ( 9) link_NAG-ASN : bond 0.00585 ( 93) link_NAG-ASN : angle 2.95301 ( 279) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 391 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8275 (mmm) cc_final: 0.8072 (mmm) REVERT: A 126 VAL cc_start: 0.4147 (OUTLIER) cc_final: 0.3799 (m) REVERT: A 182 ILE cc_start: 0.8481 (mt) cc_final: 0.8230 (mt) REVERT: A 188 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8506 (tp) REVERT: A 190 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7238 (ptm-80) REVERT: A 220 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6880 (mm-40) REVERT: A 422 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7665 (ttm170) REVERT: A 428 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8668 (pttp) REVERT: A 467 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7405 (ptp90) REVERT: A 576 TYR cc_start: 0.8820 (m-80) cc_final: 0.8378 (m-80) REVERT: A 836 ASN cc_start: 0.8089 (t0) cc_final: 0.7803 (p0) REVERT: A 938 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8664 (mp) REVERT: A 1021 LEU cc_start: 0.8856 (mt) cc_final: 0.8561 (mt) REVERT: A 1041 MET cc_start: 0.8472 (ttm) cc_final: 0.8254 (ttm) REVERT: A 1142 GLU cc_start: 0.7967 (pt0) cc_final: 0.7320 (mt-10) REVERT: B 71 TYR cc_start: 0.7940 (m-80) cc_final: 0.7530 (m-80) REVERT: B 188 LEU cc_start: 0.8863 (tp) cc_final: 0.8601 (mt) REVERT: B 210 MET cc_start: 0.7711 (mmp) cc_final: 0.7277 (mmt) REVERT: B 220 GLN cc_start: 0.6966 (mm-40) cc_final: 0.6317 (tm-30) REVERT: B 223 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6630 (tpt-90) REVERT: B 467 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8010 (ptp90) REVERT: B 576 TYR cc_start: 0.8730 (m-80) cc_final: 0.8416 (m-80) REVERT: B 681 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: B 836 ASN cc_start: 0.7912 (t0) cc_final: 0.7678 (p0) REVERT: B 906 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7054 (tp30) REVERT: B 943 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8486 (tp) REVERT: B 1019 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8311 (tpp) REVERT: B 1041 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8193 (ttm) REVERT: B 1069 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7934 (mp10) REVERT: B 1074 GLU cc_start: 0.7772 (pm20) cc_final: 0.7513 (pt0) REVERT: C 52 TYR cc_start: 0.7889 (m-80) cc_final: 0.7552 (m-80) REVERT: C 71 TYR cc_start: 0.7974 (m-80) cc_final: 0.7648 (m-80) REVERT: C 126 VAL cc_start: 0.3646 (OUTLIER) cc_final: 0.3241 (p) REVERT: C 142 GLN cc_start: 0.7421 (mp10) cc_final: 0.7058 (mp10) REVERT: C 428 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8725 (pttp) REVERT: C 529 LYS cc_start: 0.8346 (mmmm) cc_final: 0.8144 (tptp) REVERT: C 532 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: C 576 TYR cc_start: 0.8727 (m-80) cc_final: 0.8434 (m-80) REVERT: C 836 ASN cc_start: 0.8034 (t0) cc_final: 0.7694 (p0) REVERT: C 850 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8026 (tt) REVERT: C 906 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6776 (tp30) REVERT: C 1074 GLU cc_start: 0.7668 (pm20) cc_final: 0.7465 (pt0) REVERT: C 1081 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7585 (mm110) REVERT: C 1112 GLN cc_start: 0.8433 (mt0) cc_final: 0.8212 (mt0) REVERT: C 1274 GLU cc_start: 0.7679 (pm20) cc_final: 0.7449 (mp0) outliers start: 69 outliers final: 31 residues processed: 432 average time/residue: 0.6805 time to fit residues: 349.6682 Evaluate side-chains 440 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 391 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 906 GLU Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 943 LEU Chi-restraints excluded: chain B residue 1019 MET Chi-restraints excluded: chain B residue 1041 MET Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 934 ASP Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 1041 MET Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain C residue 1081 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 226 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 121 optimal weight: 0.0870 chunk 343 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 209 optimal weight: 5.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A1120 GLN A1221 ASN B 25 ASN B 142 GLN B 972 GLN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.178406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.147624 restraints weight = 31034.571| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.53 r_work: 0.3397 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32382 Z= 0.139 Angle : 0.672 13.506 44325 Z= 0.320 Chirality : 0.050 0.571 5433 Planarity : 0.003 0.033 5322 Dihedral : 7.770 66.927 8070 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 1.76 % Allowed : 14.06 % Favored : 84.18 % 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: 0.19 (0.14), residues: 3597 helix: 2.35 (0.19), residues: 711 sheet: 0.10 (0.19), residues: 711 loop : -0.62 (0.14), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.014 0.001 TYR A1269 PHE 0.018 0.001 PHE A 119 TRP 0.011 0.001 TRP B 305 HIS 0.005 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00301 (32124) covalent geometry : angle 0.62535 (43608) SS BOND : bond 0.00438 ( 57) SS BOND : angle 1.51936 ( 114) hydrogen bonds : bond 0.04191 ( 1124) hydrogen bonds : angle 4.93713 ( 3159) link_ALPHA1-3 : bond 0.01217 ( 6) link_ALPHA1-3 : angle 2.03061 ( 18) link_ALPHA1-6 : bond 0.00865 ( 12) link_ALPHA1-6 : angle 1.67365 ( 36) link_BETA1-4 : bond 0.00507 ( 87) link_BETA1-4 : angle 1.63510 ( 261) link_BETA1-6 : bond 0.00092 ( 3) link_BETA1-6 : angle 1.61818 ( 9) link_NAG-ASN : bond 0.00699 ( 93) link_NAG-ASN : angle 2.53804 ( 279) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 390 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.4087 (OUTLIER) cc_final: 0.3729 (m) REVERT: A 182 ILE cc_start: 0.8491 (mt) cc_final: 0.8239 (mt) REVERT: A 188 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8555 (tp) REVERT: A 190 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7352 (ptm-80) REVERT: A 422 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7679 (ttm170) REVERT: A 428 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8769 (pttp) REVERT: A 576 TYR cc_start: 0.8815 (m-80) cc_final: 0.8370 (m-80) REVERT: A 836 ASN cc_start: 0.8103 (t0) cc_final: 0.7824 (p0) REVERT: A 938 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8729 (mp) REVERT: B 71 TYR cc_start: 0.7944 (m-80) cc_final: 0.7556 (m-80) REVERT: B 188 LEU cc_start: 0.8889 (tp) cc_final: 0.8631 (mt) REVERT: B 210 MET cc_start: 0.7739 (mmp) cc_final: 0.7409 (mmp) REVERT: B 422 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7922 (ttm170) REVERT: B 467 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7853 (ptp90) REVERT: B 576 TYR cc_start: 0.8758 (m-80) cc_final: 0.8407 (m-80) REVERT: B 681 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: B 700 ASP cc_start: 0.7252 (m-30) cc_final: 0.6989 (m-30) REVERT: B 830 LYS cc_start: 0.8340 (mppt) cc_final: 0.7905 (mppt) REVERT: B 943 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8467 (tp) REVERT: B 1019 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8250 (tpp) REVERT: B 1041 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8223 (ttm) REVERT: B 1074 GLU cc_start: 0.7762 (pm20) cc_final: 0.7486 (pt0) REVERT: C 52 TYR cc_start: 0.7924 (m-80) cc_final: 0.7539 (m-80) REVERT: C 71 TYR cc_start: 0.8025 (m-80) cc_final: 0.7645 (m-80) REVERT: C 126 VAL cc_start: 0.3594 (OUTLIER) cc_final: 0.3201 (p) REVERT: C 142 GLN cc_start: 0.7487 (mp10) cc_final: 0.7147 (mp10) REVERT: C 220 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6895 (mm-40) REVERT: C 532 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: C 576 TYR cc_start: 0.8774 (m-80) cc_final: 0.8445 (m-80) REVERT: C 836 ASN cc_start: 0.8036 (t0) cc_final: 0.7722 (p0) REVERT: C 850 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8038 (tt) REVERT: C 906 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: C 1074 GLU cc_start: 0.7679 (pm20) cc_final: 0.7477 (pt0) REVERT: C 1081 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7579 (mm110) REVERT: C 1112 GLN cc_start: 0.8387 (mt0) cc_final: 0.8171 (mt0) REVERT: C 1274 GLU cc_start: 0.7701 (pm20) cc_final: 0.7478 (mp0) outliers start: 56 outliers final: 33 residues processed: 419 average time/residue: 0.6752 time to fit residues: 336.2613 Evaluate side-chains 421 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 374 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 943 LEU Chi-restraints excluded: chain B residue 1019 MET Chi-restraints excluded: chain B residue 1041 MET Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 934 ASP Chi-restraints excluded: chain C residue 1041 MET Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 81 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 232 optimal weight: 0.8980 chunk 9 optimal weight: 0.0770 chunk 165 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 347 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 188 optimal weight: 0.0570 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 148 GLN A1081 GLN A1120 GLN A1221 ASN B 25 ASN B 142 GLN B 972 GLN B1081 GLN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.179049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148360 restraints weight = 31269.287| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.53 r_work: 0.3408 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32382 Z= 0.132 Angle : 0.667 13.441 44325 Z= 0.316 Chirality : 0.050 0.701 5433 Planarity : 0.003 0.034 5322 Dihedral : 7.527 63.143 8070 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 1.66 % Allowed : 14.69 % Favored : 83.65 % 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: 0.13 (0.14), residues: 3597 helix: 2.21 (0.19), residues: 729 sheet: 0.08 (0.19), residues: 711 loop : -0.67 (0.14), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 169 TYR 0.019 0.001 TYR A 71 PHE 0.017 0.001 PHE A 904 TRP 0.011 0.001 TRP B 305 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00287 (32124) covalent geometry : angle 0.61847 (43608) SS BOND : bond 0.00429 ( 57) SS BOND : angle 1.51368 ( 114) hydrogen bonds : bond 0.04073 ( 1124) hydrogen bonds : angle 4.90487 ( 3159) link_ALPHA1-3 : bond 0.01196 ( 6) link_ALPHA1-3 : angle 1.96692 ( 18) link_ALPHA1-6 : bond 0.00867 ( 12) link_ALPHA1-6 : angle 1.66222 ( 36) link_BETA1-4 : bond 0.00508 ( 87) link_BETA1-4 : angle 1.60511 ( 261) link_BETA1-6 : bond 0.00121 ( 3) link_BETA1-6 : angle 1.54263 ( 9) link_NAG-ASN : bond 0.00549 ( 93) link_NAG-ASN : angle 2.60355 ( 279) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 383 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8308 (mmm) cc_final: 0.8098 (mmm) REVERT: A 126 VAL cc_start: 0.4202 (OUTLIER) cc_final: 0.3816 (m) REVERT: A 182 ILE cc_start: 0.8479 (mt) cc_final: 0.8233 (mt) REVERT: A 188 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8546 (tp) REVERT: A 190 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7294 (ptm-80) REVERT: A 422 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7691 (ttm170) REVERT: A 428 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8691 (pttp) REVERT: A 576 TYR cc_start: 0.8800 (m-80) cc_final: 0.8378 (m-80) REVERT: A 836 ASN cc_start: 0.8057 (t0) cc_final: 0.7839 (p0) REVERT: A 938 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8700 (mp) REVERT: B 71 TYR cc_start: 0.7927 (m-80) cc_final: 0.7544 (m-80) REVERT: B 142 GLN cc_start: 0.7563 (mp10) cc_final: 0.6966 (mp10) REVERT: B 188 LEU cc_start: 0.8882 (tp) cc_final: 0.8621 (mt) REVERT: B 210 MET cc_start: 0.7734 (mmp) cc_final: 0.7396 (mmp) REVERT: B 422 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7896 (ttm170) REVERT: B 467 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7822 (ptp90) REVERT: B 576 TYR cc_start: 0.8731 (m-80) cc_final: 0.8405 (m-80) REVERT: B 681 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: B 700 ASP cc_start: 0.7254 (m-30) cc_final: 0.6953 (m-30) REVERT: B 830 LYS cc_start: 0.8321 (mppt) cc_final: 0.7869 (mppt) REVERT: B 943 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8470 (tp) REVERT: B 1019 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8288 (tpp) REVERT: B 1041 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8226 (ttm) REVERT: B 1074 GLU cc_start: 0.7724 (pm20) cc_final: 0.7459 (pt0) REVERT: C 52 TYR cc_start: 0.7864 (m-80) cc_final: 0.7452 (m-80) REVERT: C 71 TYR cc_start: 0.8014 (m-80) cc_final: 0.7628 (m-80) REVERT: C 126 VAL cc_start: 0.3506 (OUTLIER) cc_final: 0.3121 (p) REVERT: C 220 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6867 (mm-40) REVERT: C 428 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8738 (pttp) REVERT: C 532 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7849 (mm-30) REVERT: C 576 TYR cc_start: 0.8743 (m-80) cc_final: 0.8441 (m-80) REVERT: C 836 ASN cc_start: 0.8008 (t0) cc_final: 0.7684 (p0) REVERT: C 850 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8030 (tt) REVERT: C 906 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6802 (tp30) REVERT: C 1112 GLN cc_start: 0.8391 (mt0) cc_final: 0.8177 (mt0) REVERT: C 1274 GLU cc_start: 0.7676 (pm20) cc_final: 0.7461 (mp0) outliers start: 53 outliers final: 32 residues processed: 412 average time/residue: 0.6204 time to fit residues: 303.6404 Evaluate side-chains 421 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 375 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 943 LEU Chi-restraints excluded: chain B residue 1019 MET Chi-restraints excluded: chain B residue 1041 MET Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 934 ASP Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 1041 MET Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain C residue 1137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 130 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 213 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 245 optimal weight: 0.0270 chunk 202 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A1120 GLN A1221 ASN B 25 ASN B 972 GLN ** B1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 142 GLN ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144767 restraints weight = 31130.496| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.54 r_work: 0.3351 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32382 Z= 0.191 Angle : 0.724 13.381 44325 Z= 0.349 Chirality : 0.051 0.684 5433 Planarity : 0.004 0.043 5322 Dihedral : 7.500 59.208 8070 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 1.73 % Allowed : 14.60 % Favored : 83.68 % 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: -0.04 (0.14), residues: 3597 helix: 1.90 (0.19), residues: 744 sheet: 0.02 (0.19), residues: 711 loop : -0.74 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 169 TYR 0.018 0.002 TYR B 705 PHE 0.018 0.002 PHE A 119 TRP 0.016 0.001 TRP B 305 HIS 0.005 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00436 (32124) covalent geometry : angle 0.67848 (43608) SS BOND : bond 0.00521 ( 57) SS BOND : angle 1.79098 ( 114) hydrogen bonds : bond 0.04759 ( 1124) hydrogen bonds : angle 5.11556 ( 3159) link_ALPHA1-3 : bond 0.01152 ( 6) link_ALPHA1-3 : angle 1.98688 ( 18) link_ALPHA1-6 : bond 0.00855 ( 12) link_ALPHA1-6 : angle 1.59656 ( 36) link_BETA1-4 : bond 0.00509 ( 87) link_BETA1-4 : angle 1.67535 ( 261) link_BETA1-6 : bond 0.00191 ( 3) link_BETA1-6 : angle 1.44801 ( 9) link_NAG-ASN : bond 0.00583 ( 93) link_NAG-ASN : angle 2.58619 ( 279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12266.23 seconds wall clock time: 209 minutes 44.06 seconds (12584.06 seconds total)