Starting phenix.real_space_refine on Mon May 4 03:57:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jkg_61554/05_2026/9jkg_61554.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jkg_61554/05_2026/9jkg_61554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jkg_61554/05_2026/9jkg_61554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jkg_61554/05_2026/9jkg_61554.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jkg_61554/05_2026/9jkg_61554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jkg_61554/05_2026/9jkg_61554.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 11123 2.51 5 N 2777 2.21 5 O 3991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17991 Number of models: 1 Model: "" Number of chains: 73 Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1399 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 1, 'TRANS': 168} Chain: "C" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3751 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 22, 'TRANS': 452} Chain: "D" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1159 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "E" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3722 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 22, 'TRANS': 449} Chain: "A" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3780 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 22, 'TRANS': 455} Chain: "F" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1159 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 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: 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: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: 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: "f" 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "m" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "r" 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: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 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: "u" 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "x" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "3" 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: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 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: "6" 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: "7" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "8" 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: "9" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "AA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "BA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "CA" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "DA" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "EA" 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: "FA" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {'83G': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'83G': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'83G': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.50, per 1000 atoms: 0.25 Number of scatterers: 17991 At special positions: 0 Unit cell: (136.95, 146.85, 148.5, 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 100 16.00 O 3991 8.00 N 2777 7.00 C 11123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 Atom "HETATM17156 O5 NAG 3 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 2 4 " - " MAN 2 5 " " MAN 7 4 " - " MAN 7 5 " " MAN Q 4 " - " MAN Q 5 " " MAN l 4 " - " MAN l 5 " " MAN q 4 " - " MAN q 5 " ALPHA1-3 " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 4 " " BMA 6 3 " - " MAN 6 4 " " BMA 7 3 " - " MAN 7 4 " " BMA 9 3 " - " MAN 9 4 " " BMA L 3 " - " MAN L 4 " " BMA Q 3 " - " MAN Q 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " NAG W 2 " - " MAN W 3 " " BMA X 3 " - " MAN X 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA m 3 " - " MAN m 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA w 3 " - " MAN w 4 " ALPHA1-6 " BMA 2 3 " - " MAN 2 6 " " BMA 5 3 " - " MAN 5 4 " " BMA 6 3 " - " MAN 6 5 " " BMA 7 3 " - " MAN 7 6 " " MAN 7 6 " - " MAN 7 7 " " BMA K 3 " - " MAN K 4 " " BMA Q 3 " - " MAN Q 6 " " BMA V 3 " - " MAN V 5 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 4 " " BMA l 3 " - " MAN l 6 " " MAN l 6 " - " MAN l 8 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 6 " " MAN q 6 " - " MAN q 7 " " BMA w 3 " - " MAN w 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 4 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG 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 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 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 r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGFA 1 " - " NAGFA 2 " BETA1-6 " NAG a 1 " - " FUC a 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAGCA 1 " - " FUCCA 4 " " NAGDA 1 " - " FUCDA 3 " " NAGFA 1 " - " FUCFA 3 " NAG-ASN " NAG 0 1 " - " ASN A 234 " " NAG 1 1 " - " ASN A 241 " " NAG 2 1 " - " ASN A 262 " " NAG 3 1 " - " ASN A 276 " " NAG 4 1 " - " ASN A 295 " " NAG 5 1 " - " ASN A 301 " " NAG 6 1 " - " ASN A 332 " " NAG 7 1 " - " ASN A 339 " " NAG 8 1 " - " ASN A 362 " " NAG 9 1 " - " ASN A 386 " " NAG A 802 " - " ASN A 188 " " NAG A 803 " - " ASN A 356 " " NAG A 804 " - " ASN A 401 " " NAG B 801 " - " ASN B 625 " " NAG C 802 " - " ASN C 160 " " NAG C 803 " - " ASN C 356 " " NAG C 804 " - " ASN C 397 " " NAG C 805 " - " ASN C 401 " " NAG D 801 " - " ASN D 625 " " NAG E 802 " - " ASN E 356 " " NAG E 803 " - " ASN E 401 " " NAG G 1 " - " ASN B 611 " " NAG H 1 " - " ASN B 616 " " NAG I 1 " - " ASN B 637 " " NAG J 1 " - " ASN C 88 " " NAG K 1 " - " ASN C 130 " " NAG L 1 " - " ASN C 156 " " NAG M 1 " - " ASN C 188 " " NAG N 1 " - " ASN C 197 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 241 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 276 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 339 " " NAG W 1 " - " ASN C 362 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 392 " " NAG Z 1 " - " ASN C 448 " " NAG a 1 " - " ASN D 611 " " NAG b 1 " - " ASN D 616 " " NAG c 1 " - " ASN D 637 " " NAG d 1 " - " ASN E 88 " " NAG e 1 " - " ASN E 130 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN E 188 " " NAG i 1 " - " ASN E 197 " " NAG j 1 " - " ASN E 234 " " NAG k 1 " - " ASN E 241 " " NAG l 1 " - " ASN E 262 " " NAG m 1 " - " ASN E 276 " " NAG n 1 " - " ASN E 295 " " NAG o 1 " - " ASN E 301 " " NAG p 1 " - " ASN E 332 " " NAG q 1 " - " ASN E 339 " " NAG r 1 " - " ASN E 362 " " NAG s 1 " - " ASN E 386 " " NAG t 1 " - " ASN E 392 " " NAG u 1 " - " ASN E 448 " " NAG v 1 " - " ASN A 88 " " NAG w 1 " - " ASN A 130 " " NAG x 1 " - " ASN A 156 " " NAG y 1 " - " ASN A 160 " " NAG z 1 " - " ASN A 197 " " NAGAA 1 " - " ASN A 392 " " NAGBA 1 " - " ASN A 448 " " NAGCA 1 " - " ASN F 611 " " NAGDA 1 " - " ASN F 616 " " NAGEA 1 " - " ASN F 625 " " NAGFA 1 " - " ASN F 637 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 695.3 milliseconds 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 31 sheets defined 29.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 537 through 563 removed outlier: 3.797A pdb=" N GLN B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.604A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 644 removed outlier: 3.533A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 663 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.786A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.940A pdb=" N ASN C 392 " --> pdb=" O GLN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 484 removed outlier: 3.980A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 564 removed outlier: 3.765A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 634 removed outlier: 4.010A pdb=" N ARG D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 661 removed outlier: 4.532A pdb=" N GLY D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 64 removed outlier: 4.004A pdb=" N TYR E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.158A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 334 through 351 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 459 through 464A Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.687A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.846A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.378A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.644A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.007A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 552 Processing helix chain 'F' and resid 564 through 569 removed outlier: 3.932A pdb=" N LEU F 568 " --> pdb=" O HIS F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 639 through 662 Processing sheet with id=AA1, first strand: chain 'B' and resid 604 through 609 removed outlier: 4.825A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.395A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.650A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 84 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.606A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 175 removed outlier: 3.578A pdb=" N ILE C 161 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP C 172 " --> pdb=" O PHE C 159 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 159 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS C 157 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 132 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.513A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.571A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.138A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 301 through 302 removed outlier: 4.224A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AB3, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AB4, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.230A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 93 through 94 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 175 Processing sheet with id=AB9, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.174A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.055A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.954A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 302 through 308 removed outlier: 6.365A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 374 through 377 Processing sheet with id=AC5, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AC6, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.329A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AC9, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.753A pdb=" N ALA A 433 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 259 through 261 removed outlier: 9.682A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.064A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.578A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 377 through 378 577 hydrogen bonds defined for protein. 1590 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: 2.99 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3298 1.33 - 1.45: 4946 1.45 - 1.57: 9917 1.57 - 1.69: 8 1.69 - 1.82: 140 Bond restraints: 18309 Sorted by residual: bond pdb=" N VAL A 182 " pdb=" CA VAL A 182 " ideal model delta sigma weight residual 1.454 1.493 -0.038 7.70e-03 1.69e+04 2.47e+01 bond pdb=" N GLY A 471 " pdb=" CA GLY A 471 " ideal model delta sigma weight residual 1.442 1.477 -0.035 7.70e-03 1.69e+04 2.03e+01 bond pdb=" N VAL E 182 " pdb=" CA VAL E 182 " ideal model delta sigma weight residual 1.456 1.492 -0.035 8.70e-03 1.32e+04 1.66e+01 bond pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sigma weight residual 1.417 1.496 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 MAN q 4 " pdb=" O5 MAN q 4 " ideal model delta sigma weight residual 1.399 1.475 -0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 18304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 23147 2.86 - 5.73: 1673 5.73 - 8.59: 56 8.59 - 11.46: 5 11.46 - 14.32: 5 Bond angle restraints: 24886 Sorted by residual: angle pdb=" CA GLY A 407 " pdb=" C GLY A 407 " pdb=" O GLY A 407 " ideal model delta sigma weight residual 122.22 118.26 3.96 6.50e-01 2.37e+00 3.71e+01 angle pdb=" CA ARG E 469 " pdb=" C ARG E 469 " pdb=" N PRO E 470 " ideal model delta sigma weight residual 117.67 123.74 -6.07 1.01e+00 9.80e-01 3.62e+01 angle pdb=" CA GLY E 441 " pdb=" C GLY E 441 " pdb=" O GLY E 441 " ideal model delta sigma weight residual 122.45 118.27 4.18 7.20e-01 1.93e+00 3.37e+01 angle pdb=" N ASN A 186 " pdb=" CA ASN A 186 " pdb=" C ASN A 186 " ideal model delta sigma weight residual 113.38 107.05 6.33 1.17e+00 7.31e-01 2.93e+01 angle pdb=" CA GLY C 410 " pdb=" C GLY C 410 " pdb=" O GLY C 410 " ideal model delta sigma weight residual 122.29 118.03 4.26 8.10e-01 1.52e+00 2.76e+01 ... (remaining 24881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.45: 12700 28.45 - 56.90: 571 56.90 - 85.35: 395 85.35 - 113.80: 256 113.80 - 142.26: 22 Dihedral angle restraints: 13944 sinusoidal: 8489 harmonic: 5455 Sorted by residual: dihedral pdb=" CB CYS E 228 " pdb=" SG CYS E 228 " pdb=" SG CYS E 239 " pdb=" CB CYS E 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.83 -70.83 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -130.11 44.11 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -128.24 42.24 1 1.00e+01 1.00e-02 2.49e+01 ... (remaining 13941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 3422 0.286 - 0.572: 47 0.572 - 0.857: 13 0.857 - 1.143: 5 1.143 - 1.429: 6 Chirality restraints: 3493 Sorted by residual: chirality pdb=" C1 MAN 2 5 " pdb=" O2 MAN 2 4 " pdb=" C2 MAN 2 5 " pdb=" O5 MAN 2 5 " both_signs ideal model delta sigma weight residual False 2.40 1.14 1.26 2.00e-02 2.50e+03 3.97e+03 chirality pdb=" C1 MAN V 4 " pdb=" O3 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 1.20 1.20 2.00e-02 2.50e+03 3.63e+03 chirality pdb=" C1 MAN e 4 " pdb=" O3 BMA e 3 " pdb=" C2 MAN e 4 " pdb=" O5 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.40 1.36 1.04 2.00e-02 2.50e+03 2.69e+03 ... (remaining 3490 not shown) Planarity restraints: 2896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG z 2 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG z 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG z 2 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG z 2 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG z 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " -0.330 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG j 2 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " 0.513 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.328 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG L 1 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.508 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.132 2.00e-02 2.50e+03 ... (remaining 2893 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 5834 2.83 - 3.35: 17768 3.35 - 3.87: 31728 3.87 - 4.38: 36101 4.38 - 4.90: 55403 Nonbonded interactions: 146834 Sorted by model distance: nonbonded pdb=" O ILE A 225 " pdb=" OG1 THR A 244 " model vdw 2.318 3.040 nonbonded pdb=" ND1 HIS E 249 " pdb=" OH TYR E 486 " model vdw 2.354 3.120 nonbonded pdb=" OH TYR E 61 " pdb=" O CYS E 74 " model vdw 2.362 3.040 nonbonded pdb=" OD1 ASN E 195 " pdb=" OG1 THR E 198 " model vdw 2.380 3.040 nonbonded pdb=" O5 BMA 7 3 " pdb=" O6 BMA 7 3 " model vdw 2.390 2.432 ... (remaining 146829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 1 through 2) selection = (chain '1' and resid 1 through 2) selection = (chain '4' and resid 1 through 2) selection = (chain '8' and resid 1 through 2) selection = (chain 'AA' and resid 1 through 2) selection = (chain 'BA' and resid 1 through 2) selection = (chain 'DA' and resid 1 through 2) selection = (chain 'FA' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 's' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'u' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) selection = (chain 'y' and resid 1 through 2) selection = (chain 'z' and resid 1 through 2) } ncs_group { reference = (chain '2' and (resid 1 or resid 4 through 6)) selection = (chain '7' and (resid 2 or resid 5 through 7)) selection = (chain 'Q' and (resid 1 or resid 4 through 6)) selection = (chain 'q' and (resid 2 or resid 5 through 7)) } ncs_group { reference = (chain '3' and resid 1 through 2) selection = (chain '5' and resid 1 through 2) selection = (chain '9' and resid 1 through 2) selection = (chain 'CA' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) } ncs_group { reference = chain '6' selection = chain 'V' selection = chain 'e' selection = chain 'f' selection = chain 'w' } ncs_group { reference = (chain 'A' and (resid 33 through 506 or resid 803 through 804)) selection = (chain 'C' and (resid 33 through 506 or resid 804 through 805)) selection = (chain 'E' and (resid 33 through 506 or resid 802 through 803)) } ncs_group { reference = (chain 'D' and resid 519 through 662) selection = chain 'F' } ncs_group { reference = chain 'EA' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'b' selection = chain 'h' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.400 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.173 18569 Z= 0.930 Angle : 1.841 36.350 25636 Z= 1.100 Chirality : 0.134 1.429 3493 Planarity : 0.033 0.295 2823 Dihedral : 25.032 142.256 10322 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.66 % Favored : 90.59 % Rotamer: Outliers : 5.23 % Allowed : 9.76 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.16), residues: 1871 helix: -1.93 (0.20), residues: 491 sheet: -1.73 (0.28), residues: 323 loop : -2.59 (0.15), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 166 TYR 0.014 0.002 TYR E 484 PHE 0.023 0.002 PHE C 383 TRP 0.013 0.002 TRP A 395 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.01312 (18309) covalent geometry : angle 1.58520 (24886) SS BOND : bond 0.00525 ( 30) SS BOND : angle 1.41654 ( 60) hydrogen bonds : bond 0.22176 ( 563) hydrogen bonds : angle 9.71966 ( 1590) link_ALPHA1-2 : bond 0.02934 ( 5) link_ALPHA1-2 : angle 5.32328 ( 15) link_ALPHA1-3 : bond 0.03786 ( 19) link_ALPHA1-3 : angle 5.28973 ( 57) link_ALPHA1-6 : bond 0.02811 ( 17) link_ALPHA1-6 : angle 3.65234 ( 51) link_BETA1-4 : bond 0.02815 ( 112) link_BETA1-4 : angle 5.14972 ( 336) link_BETA1-6 : bond 0.00192 ( 4) link_BETA1-6 : angle 1.31084 ( 12) link_NAG-ASN : bond 0.03059 ( 73) link_NAG-ASN : angle 7.57252 ( 219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 548 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 556 LEU cc_start: 0.8990 (tp) cc_final: 0.8715 (tt) REVERT: B 563 GLN cc_start: 0.8311 (mt0) cc_final: 0.8048 (pt0) REVERT: B 580 VAL cc_start: 0.8596 (t) cc_final: 0.8006 (p) REVERT: B 584 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7359 (mt-10) REVERT: B 605 THR cc_start: 0.8083 (p) cc_final: 0.7062 (t) REVERT: B 617 LYS cc_start: 0.8937 (mttt) cc_final: 0.8489 (mtpp) REVERT: B 628 TRP cc_start: 0.6084 (m100) cc_final: 0.5562 (m100) REVERT: B 644 THR cc_start: 0.6650 (OUTLIER) cc_final: 0.5996 (t) REVERT: B 645 LEU cc_start: 0.8305 (tp) cc_final: 0.8102 (mm) REVERT: B 656 ASN cc_start: 0.4809 (m-40) cc_final: 0.4056 (t0) REVERT: C 35 TRP cc_start: 0.8025 (m-90) cc_final: 0.7478 (m-10) REVERT: C 46 LYS cc_start: 0.9063 (mtmm) cc_final: 0.8515 (mtmm) REVERT: C 133 ASP cc_start: 0.6025 (t70) cc_final: 0.5716 (t0) REVERT: C 189 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8625 (t) REVERT: C 432 LYS cc_start: 0.7799 (mttt) cc_final: 0.7339 (mtmt) REVERT: C 462 HIS cc_start: 0.8260 (m-70) cc_final: 0.7924 (p-80) REVERT: C 492 GLU cc_start: 0.6201 (mm-30) cc_final: 0.5123 (mm-30) REVERT: D 559 ILE cc_start: 0.8638 (mm) cc_final: 0.8215 (mm) REVERT: D 584 GLU cc_start: 0.8564 (pt0) cc_final: 0.8229 (pt0) REVERT: D 588 ARG cc_start: 0.7403 (ttp80) cc_final: 0.7057 (tmm-80) REVERT: D 626 MET cc_start: 0.6986 (tpt) cc_final: 0.6348 (tmm) REVERT: D 630 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8715 (mt-10) REVERT: D 650 GLN cc_start: 0.8916 (tp40) cc_final: 0.8648 (tp40) REVERT: D 654 GLU cc_start: 0.9157 (tt0) cc_final: 0.8241 (mp0) REVERT: D 655 LYS cc_start: 0.9050 (tttt) cc_final: 0.8841 (tppt) REVERT: E 56 SER cc_start: 0.8766 (t) cc_final: 0.8196 (p) REVERT: E 86 LEU cc_start: 0.8629 (mp) cc_final: 0.8374 (mp) REVERT: E 89 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8194 (p) REVERT: E 94 ASN cc_start: 0.7781 (t0) cc_final: 0.6858 (t0) REVERT: E 96 TRP cc_start: 0.8617 (m100) cc_final: 0.8323 (m100) REVERT: E 97 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8474 (mptt) REVERT: E 191 TYR cc_start: 0.7529 (m-80) cc_final: 0.6428 (m-80) REVERT: E 195 ASN cc_start: 0.7602 (t0) cc_final: 0.7136 (t0) REVERT: E 254 VAL cc_start: 0.9110 (t) cc_final: 0.8572 (m) REVERT: E 426 MET cc_start: 0.7941 (mtp) cc_final: 0.7597 (mtp) REVERT: E 430 VAL cc_start: 0.8957 (t) cc_final: 0.8726 (m) REVERT: E 434 MET cc_start: 0.8085 (ttp) cc_final: 0.7399 (tmm) REVERT: E 449 ILE cc_start: 0.9174 (mt) cc_final: 0.8958 (mm) REVERT: E 454 LEU cc_start: 0.7439 (mt) cc_final: 0.7079 (mt) REVERT: E 502 LYS cc_start: 0.8926 (tttt) cc_final: 0.8519 (tttt) REVERT: A 154 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7408 (mt) REVERT: A 196 CYS cc_start: 0.6591 (OUTLIER) cc_final: 0.6098 (t) REVERT: A 249 HIS cc_start: 0.6156 (p-80) cc_final: 0.5936 (p-80) REVERT: A 326 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7683 (pt) REVERT: A 368 ASP cc_start: 0.8520 (m-30) cc_final: 0.8319 (m-30) REVERT: A 381 GLU cc_start: 0.7653 (mm-30) cc_final: 0.6928 (mt-10) REVERT: A 383 PHE cc_start: 0.8016 (m-10) cc_final: 0.7009 (m-10) REVERT: A 449 ILE cc_start: 0.9387 (mt) cc_final: 0.9152 (mm) REVERT: A 496 VAL cc_start: 0.8962 (m) cc_final: 0.8640 (m) REVERT: F 564 HIS cc_start: 0.7172 (OUTLIER) cc_final: 0.6909 (p-80) REVERT: F 583 VAL cc_start: 0.8988 (t) cc_final: 0.8773 (t) REVERT: F 584 GLU cc_start: 0.7773 (pt0) cc_final: 0.7269 (pt0) REVERT: F 629 MET cc_start: 0.8435 (mmm) cc_final: 0.7950 (tpp) REVERT: F 636 ASP cc_start: 0.8838 (m-30) cc_final: 0.8612 (m-30) REVERT: F 654 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8071 (mm-30) outliers start: 88 outliers final: 17 residues processed: 602 average time/residue: 0.1597 time to fit residues: 140.5779 Evaluate side-chains 357 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 333 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 72 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 GLN D 650 GLN E 67 ASN E 374 HIS E 397 ASN A 99 ASN A 246 GLN A 280 ASN A 428 GLN ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN F 591 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.097029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075925 restraints weight = 58052.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078219 restraints weight = 30992.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.079564 restraints weight = 21832.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.080395 restraints weight = 18082.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080898 restraints weight = 16228.761| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 18569 Z= 0.277 Angle : 1.165 12.454 25636 Z= 0.490 Chirality : 0.059 0.473 3493 Planarity : 0.005 0.066 2823 Dihedral : 20.593 139.614 6762 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.76 % Rotamer: Outliers : 4.94 % Allowed : 15.82 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.18), residues: 1871 helix: -0.22 (0.21), residues: 494 sheet: -1.33 (0.26), residues: 381 loop : -1.71 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 315 TYR 0.018 0.002 TYR C 435 PHE 0.021 0.002 PHE A 391 TRP 0.026 0.002 TRP E 395 HIS 0.011 0.002 HIS E 308 Details of bonding type rmsd covalent geometry : bond 0.00599 (18309) covalent geometry : angle 1.05078 (24886) SS BOND : bond 0.01191 ( 30) SS BOND : angle 1.66975 ( 60) hydrogen bonds : bond 0.05961 ( 563) hydrogen bonds : angle 6.95319 ( 1590) link_ALPHA1-2 : bond 0.01588 ( 5) link_ALPHA1-2 : angle 2.72700 ( 15) link_ALPHA1-3 : bond 0.02176 ( 19) link_ALPHA1-3 : angle 2.40187 ( 57) link_ALPHA1-6 : bond 0.00969 ( 17) link_ALPHA1-6 : angle 2.22601 ( 51) link_BETA1-4 : bond 0.00770 ( 112) link_BETA1-4 : angle 3.57044 ( 336) link_BETA1-6 : bond 0.00516 ( 4) link_BETA1-6 : angle 1.61186 ( 12) link_NAG-ASN : bond 0.00688 ( 73) link_NAG-ASN : angle 3.14132 ( 219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 312 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 560 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7056 (mt-10) REVERT: B 580 VAL cc_start: 0.9659 (t) cc_final: 0.8626 (p) REVERT: B 584 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7912 (mt-10) REVERT: B 627 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8639 (p) REVERT: B 647 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6178 (tm-30) REVERT: B 655 LYS cc_start: 0.9410 (mmtt) cc_final: 0.8820 (mttm) REVERT: B 657 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8035 (mt-10) REVERT: C 35 TRP cc_start: 0.7492 (m-90) cc_final: 0.7096 (m-10) REVERT: C 40 TYR cc_start: 0.8685 (t80) cc_final: 0.8183 (t80) REVERT: C 95 MET cc_start: 0.8510 (ttp) cc_final: 0.8189 (ttp) REVERT: C 133 ASP cc_start: 0.6717 (t70) cc_final: 0.6334 (t0) REVERT: D 522 PHE cc_start: 0.7408 (p90) cc_final: 0.7182 (p90) REVERT: D 540 GLN cc_start: 0.8530 (pt0) cc_final: 0.8285 (pt0) REVERT: D 553 ASN cc_start: 0.8216 (m110) cc_final: 0.7787 (m110) REVERT: D 554 ASN cc_start: 0.8207 (t0) cc_final: 0.8007 (t0) REVERT: D 626 MET cc_start: 0.8168 (tpt) cc_final: 0.7455 (tmm) REVERT: D 653 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: E 94 ASN cc_start: 0.7838 (t0) cc_final: 0.7224 (t0) REVERT: E 191 TYR cc_start: 0.7885 (m-80) cc_final: 0.7620 (m-80) REVERT: E 195 ASN cc_start: 0.7868 (t0) cc_final: 0.7621 (t0) REVERT: E 434 MET cc_start: 0.8594 (ttp) cc_final: 0.8200 (tmm) REVERT: A 176 PHE cc_start: 0.8160 (m-10) cc_final: 0.7835 (m-10) REVERT: A 245 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8396 (p) REVERT: A 383 PHE cc_start: 0.8894 (m-10) cc_final: 0.8118 (m-10) REVERT: A 427 TRP cc_start: 0.8421 (m-10) cc_final: 0.8027 (m-10) REVERT: F 603 ILE cc_start: 0.8470 (mt) cc_final: 0.7605 (tt) REVERT: F 626 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8233 (mtt) outliers start: 83 outliers final: 43 residues processed: 361 average time/residue: 0.1449 time to fit residues: 79.0967 Evaluate side-chains 291 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 139 optimal weight: 0.2980 chunk 111 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 591 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.094945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.073635 restraints weight = 57916.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075865 restraints weight = 31258.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077264 restraints weight = 22159.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.078099 restraints weight = 18211.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078504 restraints weight = 16283.686| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18569 Z= 0.196 Angle : 0.968 11.207 25636 Z= 0.403 Chirality : 0.053 0.424 3493 Planarity : 0.004 0.064 2823 Dihedral : 16.820 132.841 6738 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.03 % Rotamer: Outliers : 4.16 % Allowed : 18.32 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.18), residues: 1871 helix: 0.40 (0.22), residues: 500 sheet: -1.15 (0.26), residues: 386 loop : -1.42 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 557 TYR 0.014 0.002 TYR C 435 PHE 0.012 0.001 PHE C 391 TRP 0.027 0.002 TRP B 610 HIS 0.004 0.001 HIS C 462 Details of bonding type rmsd covalent geometry : bond 0.00413 (18309) covalent geometry : angle 0.87400 (24886) SS BOND : bond 0.00808 ( 30) SS BOND : angle 1.09080 ( 60) hydrogen bonds : bond 0.05126 ( 563) hydrogen bonds : angle 6.39125 ( 1590) link_ALPHA1-2 : bond 0.01327 ( 5) link_ALPHA1-2 : angle 2.91647 ( 15) link_ALPHA1-3 : bond 0.02186 ( 19) link_ALPHA1-3 : angle 2.27305 ( 57) link_ALPHA1-6 : bond 0.01038 ( 17) link_ALPHA1-6 : angle 2.02787 ( 51) link_BETA1-4 : bond 0.00687 ( 112) link_BETA1-4 : angle 2.92624 ( 336) link_BETA1-6 : bond 0.00543 ( 4) link_BETA1-6 : angle 1.17874 ( 12) link_NAG-ASN : bond 0.00449 ( 73) link_NAG-ASN : angle 2.53975 ( 219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7103 (mtt180) REVERT: B 580 VAL cc_start: 0.9576 (t) cc_final: 0.8752 (p) REVERT: B 584 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 647 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 655 LYS cc_start: 0.9355 (mmtt) cc_final: 0.8973 (mptt) REVERT: C 35 TRP cc_start: 0.7658 (m-90) cc_final: 0.7114 (m-10) REVERT: C 426 MET cc_start: 0.8337 (tpp) cc_final: 0.7304 (tpp) REVERT: D 540 GLN cc_start: 0.8509 (pt0) cc_final: 0.8189 (pt0) REVERT: D 553 ASN cc_start: 0.7992 (m110) cc_final: 0.7790 (m110) REVERT: D 626 MET cc_start: 0.7948 (tpt) cc_final: 0.7456 (mmm) REVERT: E 94 ASN cc_start: 0.7737 (t0) cc_final: 0.7384 (t0) REVERT: E 191 TYR cc_start: 0.8025 (m-80) cc_final: 0.7557 (m-80) REVERT: E 195 ASN cc_start: 0.7802 (t0) cc_final: 0.7485 (t0) REVERT: E 217 TYR cc_start: 0.8604 (m-80) cc_final: 0.8091 (m-80) REVERT: E 434 MET cc_start: 0.8787 (ttp) cc_final: 0.8297 (tmm) REVERT: A 104 MET cc_start: 0.9337 (ttt) cc_final: 0.8577 (tmt) REVERT: A 167 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: A 176 PHE cc_start: 0.7921 (m-10) cc_final: 0.7638 (m-10) REVERT: A 245 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8734 (p) REVERT: A 269 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: A 288 LEU cc_start: 0.9082 (tp) cc_final: 0.8866 (tp) REVERT: A 373 MET cc_start: 0.8722 (ptm) cc_final: 0.8110 (ptp) REVERT: A 383 PHE cc_start: 0.8826 (m-10) cc_final: 0.8175 (m-10) REVERT: F 546 SER cc_start: 0.9039 (t) cc_final: 0.8521 (p) REVERT: F 626 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: F 638 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7615 (p90) REVERT: F 657 GLU cc_start: 0.8759 (mm-30) cc_final: 0.7823 (tp30) REVERT: F 659 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7105 (pt0) outliers start: 70 outliers final: 41 residues processed: 303 average time/residue: 0.1409 time to fit residues: 65.6302 Evaluate side-chains 268 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 395 ASN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 56 optimal weight: 0.0020 chunk 50 optimal weight: 10.0000 chunk 64 optimal weight: 0.2980 chunk 108 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 GLN B 658 GLN D 552 GLN D 650 GLN D 658 GLN E 141 ASN F 552 GLN ** F 562 GLN ** 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 = 0.3745 r_free = 0.3745 target = 0.095310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.073716 restraints weight = 57861.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.075935 restraints weight = 31309.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077317 restraints weight = 22260.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078136 restraints weight = 18399.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.078547 restraints weight = 16577.144| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18569 Z= 0.151 Angle : 0.872 10.918 25636 Z= 0.363 Chirality : 0.050 0.366 3493 Planarity : 0.004 0.051 2823 Dihedral : 14.240 127.503 6738 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 3.93 % Allowed : 18.80 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.18), residues: 1871 helix: 0.64 (0.22), residues: 495 sheet: -0.95 (0.26), residues: 390 loop : -1.22 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 633 TYR 0.013 0.001 TYR D 638 PHE 0.040 0.001 PHE D 522 TRP 0.013 0.001 TRP D 596 HIS 0.015 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00307 (18309) covalent geometry : angle 0.79218 (24886) SS BOND : bond 0.00493 ( 30) SS BOND : angle 1.12761 ( 60) hydrogen bonds : bond 0.04379 ( 563) hydrogen bonds : angle 6.03132 ( 1590) link_ALPHA1-2 : bond 0.01450 ( 5) link_ALPHA1-2 : angle 2.88151 ( 15) link_ALPHA1-3 : bond 0.02202 ( 19) link_ALPHA1-3 : angle 2.33412 ( 57) link_ALPHA1-6 : bond 0.01012 ( 17) link_ALPHA1-6 : angle 1.94149 ( 51) link_BETA1-4 : bond 0.00659 ( 112) link_BETA1-4 : angle 2.56451 ( 336) link_BETA1-6 : bond 0.00588 ( 4) link_BETA1-6 : angle 1.12564 ( 12) link_NAG-ASN : bond 0.00334 ( 73) link_NAG-ASN : angle 2.10189 ( 219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 253 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7134 (mtt180) REVERT: B 621 MET cc_start: 0.8409 (mtm) cc_final: 0.8149 (mmm) REVERT: B 627 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8714 (p) REVERT: B 655 LYS cc_start: 0.9316 (mmtt) cc_final: 0.9047 (mptt) REVERT: B 662 GLU cc_start: 0.8349 (tp30) cc_final: 0.8039 (tp30) REVERT: C 35 TRP cc_start: 0.7561 (m-90) cc_final: 0.6875 (m-10) REVERT: C 195 ASN cc_start: 0.8418 (m-40) cc_final: 0.7557 (t0) REVERT: C 320 THR cc_start: 0.8659 (m) cc_final: 0.8352 (p) REVERT: D 540 GLN cc_start: 0.8400 (pt0) cc_final: 0.8090 (pt0) REVERT: D 626 MET cc_start: 0.7810 (tpt) cc_final: 0.7402 (mmm) REVERT: D 641 LEU cc_start: 0.9530 (tt) cc_final: 0.9216 (pp) REVERT: E 94 ASN cc_start: 0.7725 (t0) cc_final: 0.7361 (t0) REVERT: E 191 TYR cc_start: 0.7941 (m-80) cc_final: 0.7476 (m-80) REVERT: E 195 ASN cc_start: 0.7891 (t0) cc_final: 0.7501 (t0) REVERT: E 217 TYR cc_start: 0.8590 (m-80) cc_final: 0.8216 (m-80) REVERT: E 255 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8943 (m) REVERT: E 434 MET cc_start: 0.8725 (ttp) cc_final: 0.8343 (tmm) REVERT: A 104 MET cc_start: 0.9228 (ttt) cc_final: 0.8650 (tmt) REVERT: A 176 PHE cc_start: 0.7922 (m-10) cc_final: 0.7641 (m-10) REVERT: A 269 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: A 373 MET cc_start: 0.8861 (ptm) cc_final: 0.8210 (ptp) REVERT: A 383 PHE cc_start: 0.8724 (m-10) cc_final: 0.8150 (m-10) REVERT: F 550 GLN cc_start: 0.8838 (pm20) cc_final: 0.8621 (pm20) REVERT: F 593 LEU cc_start: 0.9097 (mt) cc_final: 0.8896 (mt) REVERT: F 626 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8267 (mtt) REVERT: F 638 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7363 (p90) REVERT: F 657 GLU cc_start: 0.8734 (mm-30) cc_final: 0.7835 (tp30) outliers start: 66 outliers final: 38 residues processed: 294 average time/residue: 0.1381 time to fit residues: 62.4462 Evaluate side-chains 260 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 181 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN A 246 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.092534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.070272 restraints weight = 58106.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.072402 restraints weight = 32080.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.073713 restraints weight = 23220.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.074517 restraints weight = 19434.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.074953 restraints weight = 17554.465| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18569 Z= 0.192 Angle : 0.866 13.228 25636 Z= 0.369 Chirality : 0.048 0.317 3493 Planarity : 0.004 0.056 2823 Dihedral : 12.959 125.909 6736 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 5.18 % Allowed : 18.44 % Favored : 76.38 % 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: -0.90 (0.18), residues: 1871 helix: 0.63 (0.23), residues: 494 sheet: -0.82 (0.27), residues: 376 loop : -1.12 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 557 TYR 0.013 0.001 TYR C 484 PHE 0.016 0.001 PHE C 391 TRP 0.027 0.002 TRP C 400 HIS 0.010 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00411 (18309) covalent geometry : angle 0.78971 (24886) SS BOND : bond 0.00495 ( 30) SS BOND : angle 1.44696 ( 60) hydrogen bonds : bond 0.04537 ( 563) hydrogen bonds : angle 6.02141 ( 1590) link_ALPHA1-2 : bond 0.01200 ( 5) link_ALPHA1-2 : angle 2.94213 ( 15) link_ALPHA1-3 : bond 0.02120 ( 19) link_ALPHA1-3 : angle 2.31725 ( 57) link_ALPHA1-6 : bond 0.01033 ( 17) link_ALPHA1-6 : angle 2.07344 ( 51) link_BETA1-4 : bond 0.00589 ( 112) link_BETA1-4 : angle 2.43432 ( 336) link_BETA1-6 : bond 0.00466 ( 4) link_BETA1-6 : angle 1.26174 ( 12) link_NAG-ASN : bond 0.00409 ( 73) link_NAG-ASN : angle 2.02413 ( 219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 227 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7354 (mtt180) REVERT: B 621 MET cc_start: 0.8270 (mtm) cc_final: 0.7999 (mmm) REVERT: B 627 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8677 (p) REVERT: B 634 GLU cc_start: 0.8572 (pt0) cc_final: 0.7953 (pm20) REVERT: B 662 GLU cc_start: 0.8377 (tp30) cc_final: 0.8108 (tp30) REVERT: C 195 ASN cc_start: 0.8505 (m-40) cc_final: 0.7679 (t0) REVERT: C 426 MET cc_start: 0.8108 (mmm) cc_final: 0.7733 (mtp) REVERT: D 537 LEU cc_start: 0.8626 (mt) cc_final: 0.8278 (mp) REVERT: D 540 GLN cc_start: 0.8411 (pt0) cc_final: 0.8190 (pt0) REVERT: D 585 ARG cc_start: 0.8788 (mtp-110) cc_final: 0.8565 (mtp85) REVERT: D 621 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7664 (ptt) REVERT: D 626 MET cc_start: 0.7921 (tpt) cc_final: 0.7631 (mmm) REVERT: E 94 ASN cc_start: 0.8064 (t0) cc_final: 0.7501 (t0) REVERT: E 191 TYR cc_start: 0.8342 (m-80) cc_final: 0.7710 (m-80) REVERT: E 195 ASN cc_start: 0.7746 (t0) cc_final: 0.7331 (t0) REVERT: E 217 TYR cc_start: 0.8686 (m-80) cc_final: 0.8386 (m-80) REVERT: E 434 MET cc_start: 0.8825 (ttp) cc_final: 0.8443 (tmm) REVERT: A 67 ASN cc_start: 0.6972 (m-40) cc_final: 0.6709 (m110) REVERT: A 104 MET cc_start: 0.9308 (ttt) cc_final: 0.8786 (ttt) REVERT: A 373 MET cc_start: 0.8884 (ptm) cc_final: 0.8310 (ptp) REVERT: A 383 PHE cc_start: 0.8791 (m-10) cc_final: 0.8385 (m-10) REVERT: F 593 LEU cc_start: 0.9217 (mt) cc_final: 0.8991 (mt) REVERT: F 632 GLU cc_start: 0.9179 (tp30) cc_final: 0.8636 (tp30) REVERT: F 638 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.6505 (p90) REVERT: F 657 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7721 (tp30) REVERT: F 659 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7248 (pt0) outliers start: 87 outliers final: 53 residues processed: 282 average time/residue: 0.1373 time to fit residues: 59.9292 Evaluate side-chains 260 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 621 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 395 ASN Chi-restraints excluded: chain E residue 406 ASN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain F residue 552 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 HIS D 552 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.092914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.070616 restraints weight = 57454.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.072748 restraints weight = 31793.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.074054 restraints weight = 23078.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.074833 restraints weight = 19326.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075313 restraints weight = 17523.359| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18569 Z= 0.161 Angle : 0.826 10.373 25636 Z= 0.355 Chirality : 0.047 0.290 3493 Planarity : 0.004 0.056 2823 Dihedral : 12.119 119.804 6736 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.21 % Allowed : 21.00 % Favored : 75.79 % 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: -0.73 (0.19), residues: 1871 helix: 0.65 (0.23), residues: 500 sheet: -0.73 (0.27), residues: 372 loop : -0.94 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 633 TYR 0.016 0.001 TYR B 643 PHE 0.010 0.001 PHE C 391 TRP 0.017 0.001 TRP E 45 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00340 (18309) covalent geometry : angle 0.76122 (24886) SS BOND : bond 0.00520 ( 30) SS BOND : angle 1.25993 ( 60) hydrogen bonds : bond 0.04236 ( 563) hydrogen bonds : angle 5.91196 ( 1590) link_ALPHA1-2 : bond 0.01176 ( 5) link_ALPHA1-2 : angle 2.90921 ( 15) link_ALPHA1-3 : bond 0.02145 ( 19) link_ALPHA1-3 : angle 2.33702 ( 57) link_ALPHA1-6 : bond 0.01054 ( 17) link_ALPHA1-6 : angle 1.95517 ( 51) link_BETA1-4 : bond 0.00581 ( 112) link_BETA1-4 : angle 2.21027 ( 336) link_BETA1-6 : bond 0.00462 ( 4) link_BETA1-6 : angle 1.23243 ( 12) link_NAG-ASN : bond 0.00298 ( 73) link_NAG-ASN : angle 1.78908 ( 219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 537 LEU cc_start: 0.9032 (tt) cc_final: 0.8797 (tp) REVERT: B 542 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7445 (mtt180) REVERT: B 589 ASP cc_start: 0.8198 (m-30) cc_final: 0.7959 (m-30) REVERT: B 621 MET cc_start: 0.8345 (mtm) cc_final: 0.8070 (mmm) REVERT: B 627 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8629 (p) REVERT: B 634 GLU cc_start: 0.8540 (pt0) cc_final: 0.7877 (pm20) REVERT: B 662 GLU cc_start: 0.8371 (tp30) cc_final: 0.8152 (tp30) REVERT: C 35 TRP cc_start: 0.7834 (m-90) cc_final: 0.7592 (m100) REVERT: C 426 MET cc_start: 0.8017 (mmm) cc_final: 0.7629 (mtp) REVERT: D 535 MET cc_start: 0.8254 (ppp) cc_final: 0.8054 (tmm) REVERT: D 632 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8168 (mm-30) REVERT: D 641 LEU cc_start: 0.9533 (tt) cc_final: 0.9127 (pp) REVERT: E 94 ASN cc_start: 0.8074 (t0) cc_final: 0.7467 (t0) REVERT: E 195 ASN cc_start: 0.7722 (t0) cc_final: 0.7284 (t0) REVERT: E 434 MET cc_start: 0.8775 (ttp) cc_final: 0.8350 (tmm) REVERT: A 104 MET cc_start: 0.9349 (ttt) cc_final: 0.8833 (ttt) REVERT: A 176 PHE cc_start: 0.8699 (m-80) cc_final: 0.8490 (m-80) REVERT: A 373 MET cc_start: 0.8860 (ptm) cc_final: 0.8224 (ptp) REVERT: A 383 PHE cc_start: 0.8746 (m-10) cc_final: 0.8371 (m-10) REVERT: F 593 LEU cc_start: 0.9216 (mt) cc_final: 0.8998 (mt) REVERT: F 633 ARG cc_start: 0.8955 (ttm110) cc_final: 0.8741 (ttm-80) REVERT: F 638 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.6814 (p90) REVERT: F 657 GLU cc_start: 0.8664 (mm-30) cc_final: 0.7753 (tp30) REVERT: F 659 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7339 (pt0) outliers start: 54 outliers final: 40 residues processed: 257 average time/residue: 0.1427 time to fit residues: 55.8818 Evaluate side-chains 248 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain F residue 552 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN C 404 GLN D 540 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.093095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.071162 restraints weight = 57465.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.073291 restraints weight = 31524.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.074648 restraints weight = 22708.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075419 restraints weight = 18815.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.075883 restraints weight = 17003.279| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18569 Z= 0.143 Angle : 0.808 11.566 25636 Z= 0.347 Chirality : 0.046 0.276 3493 Planarity : 0.004 0.055 2823 Dihedral : 11.250 115.254 6731 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.21 % Allowed : 21.00 % Favored : 75.79 % 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: -0.66 (0.19), residues: 1871 helix: 0.69 (0.23), residues: 501 sheet: -0.69 (0.27), residues: 374 loop : -0.88 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 633 TYR 0.018 0.001 TYR E 217 PHE 0.008 0.001 PHE C 53 TRP 0.018 0.001 TRP C 400 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00294 (18309) covalent geometry : angle 0.74784 (24886) SS BOND : bond 0.00303 ( 30) SS BOND : angle 1.07645 ( 60) hydrogen bonds : bond 0.04053 ( 563) hydrogen bonds : angle 5.79688 ( 1590) link_ALPHA1-2 : bond 0.01272 ( 5) link_ALPHA1-2 : angle 2.92073 ( 15) link_ALPHA1-3 : bond 0.02115 ( 19) link_ALPHA1-3 : angle 2.36522 ( 57) link_ALPHA1-6 : bond 0.01057 ( 17) link_ALPHA1-6 : angle 1.91434 ( 51) link_BETA1-4 : bond 0.00579 ( 112) link_BETA1-4 : angle 2.11677 ( 336) link_BETA1-6 : bond 0.00466 ( 4) link_BETA1-6 : angle 1.20834 ( 12) link_NAG-ASN : bond 0.00276 ( 73) link_NAG-ASN : angle 1.65804 ( 219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 224 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 589 ASP cc_start: 0.8163 (m-30) cc_final: 0.7910 (m-30) REVERT: B 617 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8764 (mtpp) REVERT: B 621 MET cc_start: 0.8342 (mtm) cc_final: 0.8032 (mmm) REVERT: B 627 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8421 (p) REVERT: B 650 GLN cc_start: 0.8520 (tt0) cc_final: 0.8038 (tp-100) REVERT: C 35 TRP cc_start: 0.7912 (m-90) cc_final: 0.7666 (m100) REVERT: C 86 LEU cc_start: 0.9307 (mt) cc_final: 0.9006 (mp) REVERT: C 195 ASN cc_start: 0.8123 (m-40) cc_final: 0.7498 (t0) REVERT: C 377 ASN cc_start: 0.7922 (t0) cc_final: 0.7595 (t0) REVERT: C 426 MET cc_start: 0.7882 (mmm) cc_final: 0.7588 (mtp) REVERT: D 540 GLN cc_start: 0.8149 (pt0) cc_final: 0.7899 (pt0) REVERT: E 94 ASN cc_start: 0.8073 (t0) cc_final: 0.7631 (t0) REVERT: E 195 ASN cc_start: 0.7750 (t0) cc_final: 0.7270 (t0) REVERT: E 434 MET cc_start: 0.8694 (ttp) cc_final: 0.8345 (tmm) REVERT: A 104 MET cc_start: 0.9374 (ttt) cc_final: 0.8921 (ttt) REVERT: A 176 PHE cc_start: 0.8860 (m-80) cc_final: 0.8573 (m-80) REVERT: A 373 MET cc_start: 0.8860 (ptm) cc_final: 0.8212 (ptp) REVERT: A 383 PHE cc_start: 0.8702 (m-10) cc_final: 0.8366 (m-10) REVERT: F 593 LEU cc_start: 0.9189 (mt) cc_final: 0.8967 (mt) REVERT: F 636 ASP cc_start: 0.8611 (p0) cc_final: 0.8372 (p0) REVERT: F 638 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.6854 (p90) REVERT: F 657 GLU cc_start: 0.8695 (mm-30) cc_final: 0.7768 (tp30) REVERT: F 659 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7361 (pt0) outliers start: 54 outliers final: 37 residues processed: 252 average time/residue: 0.1393 time to fit residues: 54.5178 Evaluate side-chains 243 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 406 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain F residue 552 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 648 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 166 optimal weight: 0.0670 chunk 183 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 175 optimal weight: 0.0770 chunk 177 optimal weight: 0.8980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN A 66 HIS A 72 HIS A 246 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.093711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.071633 restraints weight = 57384.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.073799 restraints weight = 31534.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075121 restraints weight = 22707.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.075903 restraints weight = 18953.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.076303 restraints weight = 17118.346| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18569 Z= 0.142 Angle : 0.808 12.065 25636 Z= 0.349 Chirality : 0.046 0.296 3493 Planarity : 0.004 0.063 2823 Dihedral : 10.837 111.363 6730 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.56 % Allowed : 21.83 % Favored : 75.61 % 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: -0.64 (0.19), residues: 1871 helix: 0.63 (0.23), residues: 499 sheet: -0.66 (0.27), residues: 381 loop : -0.82 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 633 TYR 0.015 0.001 TYR C 217 PHE 0.009 0.001 PHE A 391 TRP 0.020 0.001 TRP C 400 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00288 (18309) covalent geometry : angle 0.75122 (24886) SS BOND : bond 0.00447 ( 30) SS BOND : angle 1.24890 ( 60) hydrogen bonds : bond 0.03997 ( 563) hydrogen bonds : angle 5.75676 ( 1590) link_ALPHA1-2 : bond 0.01145 ( 5) link_ALPHA1-2 : angle 2.88170 ( 15) link_ALPHA1-3 : bond 0.02117 ( 19) link_ALPHA1-3 : angle 2.38584 ( 57) link_ALPHA1-6 : bond 0.01059 ( 17) link_ALPHA1-6 : angle 1.89378 ( 51) link_BETA1-4 : bond 0.00580 ( 112) link_BETA1-4 : angle 2.04337 ( 336) link_BETA1-6 : bond 0.00470 ( 4) link_BETA1-6 : angle 1.18300 ( 12) link_NAG-ASN : bond 0.00259 ( 73) link_NAG-ASN : angle 1.55748 ( 219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 617 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8752 (mtpp) REVERT: B 621 MET cc_start: 0.8358 (mtm) cc_final: 0.8151 (mmm) REVERT: B 627 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8350 (p) REVERT: C 35 TRP cc_start: 0.7941 (m-90) cc_final: 0.7698 (m100) REVERT: C 86 LEU cc_start: 0.9260 (mt) cc_final: 0.8953 (mp) REVERT: C 195 ASN cc_start: 0.8022 (m-40) cc_final: 0.7483 (t0) REVERT: C 377 ASN cc_start: 0.7862 (t0) cc_final: 0.7515 (t0) REVERT: C 426 MET cc_start: 0.7631 (mmm) cc_final: 0.7362 (mtp) REVERT: D 601 LYS cc_start: 0.7698 (pttm) cc_final: 0.7377 (pttm) REVERT: E 94 ASN cc_start: 0.8011 (t0) cc_final: 0.7572 (t0) REVERT: E 195 ASN cc_start: 0.7714 (t0) cc_final: 0.7248 (t0) REVERT: E 434 MET cc_start: 0.8671 (ttp) cc_final: 0.8356 (tmm) REVERT: A 104 MET cc_start: 0.9443 (ttt) cc_final: 0.8990 (ttt) REVERT: A 176 PHE cc_start: 0.8842 (m-80) cc_final: 0.8580 (m-80) REVERT: A 373 MET cc_start: 0.8830 (ptm) cc_final: 0.8208 (ptp) REVERT: A 383 PHE cc_start: 0.8816 (m-10) cc_final: 0.8538 (m-10) REVERT: F 636 ASP cc_start: 0.8502 (p0) cc_final: 0.8160 (p0) REVERT: F 638 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.6900 (p90) REVERT: F 657 GLU cc_start: 0.8639 (mm-30) cc_final: 0.7964 (tp30) outliers start: 43 outliers final: 35 residues processed: 250 average time/residue: 0.1396 time to fit residues: 53.7513 Evaluate side-chains 238 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 406 ASN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain F residue 552 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 648 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 49 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN A 66 HIS A 72 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.092812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070640 restraints weight = 57499.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.072767 restraints weight = 31795.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.074096 restraints weight = 22989.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.074878 restraints weight = 19161.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075315 restraints weight = 17389.399| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18569 Z= 0.150 Angle : 0.814 15.683 25636 Z= 0.353 Chirality : 0.046 0.269 3493 Planarity : 0.004 0.097 2823 Dihedral : 10.522 108.303 6730 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.80 % Allowed : 21.53 % Favored : 75.67 % 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: -0.64 (0.19), residues: 1871 helix: 0.54 (0.23), residues: 500 sheet: -0.57 (0.27), residues: 385 loop : -0.81 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 476 TYR 0.011 0.001 TYR C 217 PHE 0.010 0.001 PHE A 391 TRP 0.022 0.001 TRP E 35 HIS 0.012 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00315 (18309) covalent geometry : angle 0.75930 (24886) SS BOND : bond 0.00333 ( 30) SS BOND : angle 1.21269 ( 60) hydrogen bonds : bond 0.03995 ( 563) hydrogen bonds : angle 5.73822 ( 1590) link_ALPHA1-2 : bond 0.01148 ( 5) link_ALPHA1-2 : angle 2.86022 ( 15) link_ALPHA1-3 : bond 0.02061 ( 19) link_ALPHA1-3 : angle 2.38582 ( 57) link_ALPHA1-6 : bond 0.01042 ( 17) link_ALPHA1-6 : angle 1.92322 ( 51) link_BETA1-4 : bond 0.00561 ( 112) link_BETA1-4 : angle 2.01070 ( 336) link_BETA1-6 : bond 0.00423 ( 4) link_BETA1-6 : angle 1.23765 ( 12) link_NAG-ASN : bond 0.00257 ( 73) link_NAG-ASN : angle 1.56549 ( 219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 559 ILE cc_start: 0.9181 (mm) cc_final: 0.8778 (tp) REVERT: B 617 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8733 (mtpp) REVERT: B 627 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8454 (p) REVERT: C 35 TRP cc_start: 0.8055 (m-90) cc_final: 0.7798 (m100) REVERT: C 86 LEU cc_start: 0.9208 (mt) cc_final: 0.8832 (mp) REVERT: C 195 ASN cc_start: 0.8075 (m-40) cc_final: 0.7536 (t0) REVERT: C 377 ASN cc_start: 0.7950 (t0) cc_final: 0.7619 (t0) REVERT: C 426 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7362 (mtp) REVERT: D 540 GLN cc_start: 0.8221 (pt0) cc_final: 0.7962 (pt0) REVERT: D 601 LYS cc_start: 0.7828 (pttm) cc_final: 0.7413 (pttm) REVERT: D 641 LEU cc_start: 0.9483 (tt) cc_final: 0.8985 (pp) REVERT: E 195 ASN cc_start: 0.7751 (t0) cc_final: 0.7258 (t0) REVERT: E 434 MET cc_start: 0.8634 (ttp) cc_final: 0.8336 (tmm) REVERT: A 104 MET cc_start: 0.9464 (ttt) cc_final: 0.9030 (ttt) REVERT: A 176 PHE cc_start: 0.8938 (m-80) cc_final: 0.8657 (m-80) REVERT: A 373 MET cc_start: 0.8857 (ptm) cc_final: 0.8217 (ptp) REVERT: A 383 PHE cc_start: 0.8803 (m-10) cc_final: 0.8513 (m-10) REVERT: F 636 ASP cc_start: 0.8485 (p0) cc_final: 0.8106 (p0) REVERT: F 638 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.6850 (p90) REVERT: F 657 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7900 (tp30) outliers start: 47 outliers final: 33 residues processed: 236 average time/residue: 0.1398 time to fit residues: 50.4858 Evaluate side-chains 237 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 406 ASN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain F residue 552 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 648 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 183 optimal weight: 0.3980 chunk 137 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 203 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.092359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070401 restraints weight = 57216.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.072514 restraints weight = 31515.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.073810 restraints weight = 22738.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.074594 restraints weight = 19010.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.074984 restraints weight = 17197.998| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18569 Z= 0.153 Angle : 0.823 17.848 25636 Z= 0.360 Chirality : 0.045 0.267 3493 Planarity : 0.004 0.087 2823 Dihedral : 10.333 105.098 6728 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.38 % Allowed : 22.31 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1871 helix: 0.50 (0.23), residues: 501 sheet: -0.52 (0.27), residues: 385 loop : -0.79 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 476 TYR 0.014 0.001 TYR E 217 PHE 0.010 0.001 PHE A 391 TRP 0.021 0.002 TRP C 400 HIS 0.018 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00321 (18309) covalent geometry : angle 0.77109 (24886) SS BOND : bond 0.00357 ( 30) SS BOND : angle 1.06911 ( 60) hydrogen bonds : bond 0.04013 ( 563) hydrogen bonds : angle 5.75539 ( 1590) link_ALPHA1-2 : bond 0.01141 ( 5) link_ALPHA1-2 : angle 2.86129 ( 15) link_ALPHA1-3 : bond 0.01966 ( 19) link_ALPHA1-3 : angle 2.35432 ( 57) link_ALPHA1-6 : bond 0.01029 ( 17) link_ALPHA1-6 : angle 1.92752 ( 51) link_BETA1-4 : bond 0.00561 ( 112) link_BETA1-4 : angle 1.96857 ( 336) link_BETA1-6 : bond 0.00407 ( 4) link_BETA1-6 : angle 1.24753 ( 12) link_NAG-ASN : bond 0.00262 ( 73) link_NAG-ASN : angle 1.55728 ( 219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 627 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8664 (p) REVERT: C 35 TRP cc_start: 0.8087 (m-90) cc_final: 0.7841 (m100) REVERT: C 69 TRP cc_start: 0.6073 (m-90) cc_final: 0.5817 (m-90) REVERT: C 86 LEU cc_start: 0.9198 (mt) cc_final: 0.8841 (mp) REVERT: C 195 ASN cc_start: 0.8140 (m-40) cc_final: 0.7456 (t0) REVERT: C 377 ASN cc_start: 0.8051 (t0) cc_final: 0.7729 (t0) REVERT: C 426 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7366 (mtp) REVERT: D 601 LYS cc_start: 0.7925 (pttm) cc_final: 0.7495 (pttm) REVERT: E 195 ASN cc_start: 0.7755 (t0) cc_final: 0.7258 (t0) REVERT: A 104 MET cc_start: 0.9472 (ttt) cc_final: 0.9032 (ttt) REVERT: A 176 PHE cc_start: 0.8956 (m-80) cc_final: 0.8663 (m-80) REVERT: A 373 MET cc_start: 0.8853 (ptm) cc_final: 0.8230 (ptp) REVERT: A 383 PHE cc_start: 0.8824 (m-10) cc_final: 0.8513 (m-10) REVERT: A 426 MET cc_start: 0.7315 (mmt) cc_final: 0.6937 (mmm) REVERT: F 636 ASP cc_start: 0.8471 (p0) cc_final: 0.8080 (p0) REVERT: F 638 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.6743 (p90) REVERT: F 657 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7996 (tp30) outliers start: 40 outliers final: 35 residues processed: 229 average time/residue: 0.1425 time to fit residues: 50.0691 Evaluate side-chains 233 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 406 ASN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain F residue 552 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 648 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 129 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN A 422 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.089631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067222 restraints weight = 58310.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.069344 restraints weight = 32553.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070599 restraints weight = 23643.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071341 restraints weight = 19912.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.071711 restraints weight = 18093.220| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.7133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18569 Z= 0.215 Angle : 0.872 15.545 25636 Z= 0.387 Chirality : 0.046 0.282 3493 Planarity : 0.004 0.055 2823 Dihedral : 10.347 101.897 6728 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 2.38 % Allowed : 22.25 % Favored : 75.37 % 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: -0.69 (0.19), residues: 1871 helix: 0.46 (0.23), residues: 499 sheet: -0.49 (0.26), residues: 389 loop : -0.88 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 633 TYR 0.022 0.002 TYR B 586 PHE 0.016 0.001 PHE C 391 TRP 0.031 0.002 TRP E 35 HIS 0.017 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00471 (18309) covalent geometry : angle 0.81905 (24886) SS BOND : bond 0.00469 ( 30) SS BOND : angle 1.27199 ( 60) hydrogen bonds : bond 0.04544 ( 563) hydrogen bonds : angle 5.86356 ( 1590) link_ALPHA1-2 : bond 0.01092 ( 5) link_ALPHA1-2 : angle 2.91448 ( 15) link_ALPHA1-3 : bond 0.01901 ( 19) link_ALPHA1-3 : angle 2.33309 ( 57) link_ALPHA1-6 : bond 0.00986 ( 17) link_ALPHA1-6 : angle 2.01062 ( 51) link_BETA1-4 : bond 0.00540 ( 112) link_BETA1-4 : angle 1.99973 ( 336) link_BETA1-6 : bond 0.00305 ( 4) link_BETA1-6 : angle 1.45520 ( 12) link_NAG-ASN : bond 0.00395 ( 73) link_NAG-ASN : angle 1.78470 ( 219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3313.72 seconds wall clock time: 58 minutes 39.21 seconds (3519.21 seconds total)