Starting phenix.real_space_refine on Fri Mar 6 13:30:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6m_32329/03_2026/7w6m_32329.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6m_32329/03_2026/7w6m_32329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w6m_32329/03_2026/7w6m_32329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6m_32329/03_2026/7w6m_32329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w6m_32329/03_2026/7w6m_32329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6m_32329/03_2026/7w6m_32329.map" } resolution = 4.7 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= 0.001 sd= 0.061 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 123 5.16 5 C 19362 2.51 5 N 4776 2.21 5 O 6495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30756 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9400 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 45, 'TRANS': 1178} Chain: "B" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9400 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 45, 'TRANS': 1178} Chain: "C" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9400 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 45, 'TRANS': 1178} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 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: 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 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: "M" 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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 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: "S" 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: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: "a" 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: "b" 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: "c" 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: "d" 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 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: 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: "h" 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "r" Number of atoms: 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: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 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: 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: "v" 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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 Time building chain proxies: 6.98, per 1000 atoms: 0.23 Number of scatterers: 30756 At special positions: 0 Unit cell: (147, 151.2, 183.4, 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 123 16.00 O 6495 8.00 N 4776 7.00 C 19362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " " BMA Y 3 " - " MAN Y 5 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 5 " " BMA n 3 " - " MAN n 5 " " BMA p 3 " - " MAN p 5 " " BMA q 3 " - " MAN q 5 " " BMA r 3 " - " MAN r 5 " " BMA s 3 " - " MAN s 5 " " BMA u 3 " - " MAN u 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG 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 h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG 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 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 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 4 " " NAG K 1 " - " FUC K 5 " " NAG R 1 " - " FUC R 3 " " NAG S 1 " - " FUC S 4 " " NAG U 1 " - " FUC U 4 " " NAG Z 1 " - " FUC Z 5 " " NAG g 1 " - " FUC g 3 " " NAG h 1 " - " FUC h 4 " " NAG j 1 " - " FUC j 4 " " NAG o 1 " - " FUC o 5 " " NAG v 1 " - " FUC v 3 " NAG-ASN " NAG A1401 " - " ASN A 118 " " NAG A1402 " - " ASN A 425 " " NAG A1403 " - " ASN A 667 " " NAG A1404 " - " ASN A 351 " " NAG A1405 " - " ASN A1249 " " NAG A1406 " - " ASN A1009 " " NAG B1401 " - " ASN B 118 " " NAG B1402 " - " ASN B 425 " " NAG B1403 " - " ASN B 667 " " NAG B1404 " - " ASN B 351 " " NAG B1405 " - " ASN B1249 " " NAG B1406 " - " ASN B1009 " " NAG C1401 " - " ASN C 118 " " NAG C1402 " - " ASN C 425 " " NAG C1403 " - " ASN C 667 " " NAG C1404 " - " ASN C 351 " " NAG C1405 " - " ASN C1249 " " NAG C1406 " - " ASN C1009 " " NAG D 1 " - " ASN A 216 " " NAG E 1 " - " ASN A 264 " " NAG F 1 " - " ASN A 300 " " NAG G 1 " - " ASN A 324 " " NAG H 1 " - " ASN A 344 " " NAG I 1 " - " ASN A 381 " " NAG J 1 " - " ASN A 514 " " NAG K 1 " - " ASN A 556 " " NAG L 1 " - " ASN A 688 " " NAG M 1 " - " ASN A 726 " " NAG N 1 " - " ASN A 781 " " NAG O 1 " - " ASN A 787 " " NAG P 1 " - " ASN A 873 " " NAG Q 1 " - " ASN A1232 " " NAG R 1 " - " ASN A 743 " " NAG S 1 " - " ASN B 216 " " NAG T 1 " - " ASN B 264 " " NAG U 1 " - " ASN B 300 " " NAG V 1 " - " ASN B 324 " " NAG W 1 " - " ASN B 344 " " NAG X 1 " - " ASN B 381 " " NAG Y 1 " - " ASN B 514 " " NAG Z 1 " - " ASN B 556 " " NAG a 1 " - " ASN B 688 " " NAG b 1 " - " ASN B 726 " " NAG c 1 " - " ASN B 781 " " NAG d 1 " - " ASN B 787 " " NAG e 1 " - " ASN B 873 " " NAG f 1 " - " ASN B1232 " " NAG g 1 " - " ASN B 743 " " NAG h 1 " - " ASN C 216 " " NAG i 1 " - " ASN C 264 " " NAG j 1 " - " ASN C 300 " " NAG k 1 " - " ASN C 324 " " NAG l 1 " - " ASN C 344 " " NAG m 1 " - " ASN C 381 " " NAG n 1 " - " ASN C 514 " " NAG o 1 " - " ASN C 556 " " NAG p 1 " - " ASN C 688 " " NAG q 1 " - " ASN C 726 " " NAG r 1 " - " ASN C 781 " " NAG s 1 " - " ASN C 787 " " NAG t 1 " - " ASN C 873 " " NAG u 1 " - " ASN C1232 " " NAG v 1 " - " ASN C 743 " Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 50 sheets defined 24.5% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.798A pdb=" N THR A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 325 through 332 removed outlier: 4.260A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.508A pdb=" N PHE A 360 " --> pdb=" O HIS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 466 through 475 removed outlier: 3.604A pdb=" N GLN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.733A pdb=" N LYS A 820 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 852 removed outlier: 3.659A pdb=" N LEU A 852 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 917 through 923 removed outlier: 3.715A pdb=" N SER A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 removed outlier: 3.622A pdb=" N ALA A 932 " --> pdb=" O ASP A 928 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 933 " --> pdb=" O LEU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 959 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.519A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1014 Processing helix chain 'A' and resid 1016 through 1020 removed outlier: 3.631A pdb=" N ALA A1020 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1047 removed outlier: 3.770A pdb=" N ASN A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1058 removed outlier: 4.101A pdb=" N THR A1053 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1058' Processing helix chain 'A' and resid 1066 through 1072 Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.939A pdb=" N GLU A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A1123 " --> pdb=" O VAL A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1198 removed outlier: 4.382A pdb=" N HIS A1197 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1237 through 1242 Processing helix chain 'A' and resid 1247 through 1254 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.833A pdb=" N THR B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.502A pdb=" N GLY B 292 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 removed outlier: 4.254A pdb=" N ILE B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.513A pdb=" N PHE B 360 " --> pdb=" O HIS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 removed outlier: 3.902A pdb=" N ASP B 433 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP B 434 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.740A pdb=" N LYS B 820 " --> pdb=" O ASN B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 852 removed outlier: 3.750A pdb=" N LEU B 852 " --> pdb=" O VAL B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 862 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.723A pdb=" N SER B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 937 removed outlier: 3.615A pdb=" N ALA B 932 " --> pdb=" O ASP B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 959 Processing helix chain 'B' and resid 973 through 986 removed outlier: 3.527A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1014 Processing helix chain 'B' and resid 1016 through 1020 removed outlier: 3.636A pdb=" N ALA B1020 " --> pdb=" O VAL B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1047 removed outlier: 3.760A pdb=" N ASN B1043 " --> pdb=" O GLN B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1058 removed outlier: 4.098A pdb=" N THR B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B1055 " --> pdb=" O GLN B1051 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B1057 " --> pdb=" O THR B1053 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS B1058 " --> pdb=" O VAL B1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1049 through 1058' Processing helix chain 'B' and resid 1066 through 1072 Processing helix chain 'B' and resid 1075 through 1122 removed outlier: 3.948A pdb=" N GLU B1107 " --> pdb=" O THR B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1198 removed outlier: 4.382A pdb=" N HIS B1197 " --> pdb=" O LEU B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'B' and resid 1237 through 1242 Processing helix chain 'B' and resid 1247 through 1254 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.800A pdb=" N THR C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.673A pdb=" N GLY C 292 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 332 removed outlier: 4.234A pdb=" N ILE C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.502A pdb=" N PHE C 360 " --> pdb=" O HIS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 436 removed outlier: 3.907A pdb=" N ASP C 433 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP C 434 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.723A pdb=" N LYS C 820 " --> pdb=" O ASN C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 852 removed outlier: 3.732A pdb=" N LEU C 852 " --> pdb=" O VAL C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 862 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 917 through 923 removed outlier: 3.723A pdb=" N SER C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 923 " --> pdb=" O ARG C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 937 removed outlier: 3.621A pdb=" N ALA C 932 " --> pdb=" O ASP C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 959 Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.508A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1014 Processing helix chain 'C' and resid 1016 through 1020 removed outlier: 3.624A pdb=" N ALA C1020 " --> pdb=" O VAL C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1047 removed outlier: 3.755A pdb=" N ASN C1043 " --> pdb=" O GLN C1039 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1058 removed outlier: 4.111A pdb=" N THR C1053 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C1054 " --> pdb=" O THR C1050 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN C1055 " --> pdb=" O GLN C1051 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU C1056 " --> pdb=" O LEU C1052 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN C1057 " --> pdb=" O THR C1053 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS C1058 " --> pdb=" O VAL C1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1049 through 1058' Processing helix chain 'C' and resid 1066 through 1072 Processing helix chain 'C' and resid 1075 through 1122 removed outlier: 3.957A pdb=" N GLU C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1194 through 1198 removed outlier: 4.385A pdb=" N HIS C1197 " --> pdb=" O LEU C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1237 through 1242 Processing helix chain 'C' and resid 1247 through 1254 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 removed outlier: 3.596A pdb=" N TYR A 181 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 154 removed outlier: 4.869A pdb=" N LEU A 107 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.337A pdb=" N ASN A 445 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 281 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 443 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS A 283 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 441 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 285 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP A 439 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A 322 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A 441 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 320 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER A 443 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 318 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.337A pdb=" N ASN A 445 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 281 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 443 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS A 283 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 441 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 285 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP A 439 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 462 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A 452 " --> pdb=" O ARG A 460 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 460 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLN A 454 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 298 removed outlier: 4.494A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 388 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 6.987A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 716 " --> pdb=" O HIS A 737 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 4.165A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 532 through 536 removed outlier: 6.737A pdb=" N TYR A 619 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 590 " --> pdb=" O TYR A 619 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 621 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 588 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A 623 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY A 625 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A 584 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 532 through 536 removed outlier: 7.308A pdb=" N LEU A 603 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 617 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 601 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 619 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 599 " --> pdb=" O TYR A 619 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 786 removed outlier: 4.244A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 782 " --> pdb=" O VAL A1166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A1166 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 797 removed outlier: 4.135A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB6, first strand: chain 'A' and resid 1220 through 1223 Processing sheet with id=AB7, first strand: chain 'A' and resid 1187 through 1191 Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 51 Processing sheet with id=AB9, first strand: chain 'B' and resid 181 through 184 removed outlier: 3.757A pdb=" N TYR B 181 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 175 " --> pdb=" O TYR B 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 148 through 154 removed outlier: 4.872A pdb=" N LEU B 107 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 270 through 286 removed outlier: 3.516A pdb=" N SER B 275 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 449 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN B 445 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 281 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 443 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS B 283 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 441 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 285 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP B 439 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 322 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE B 441 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG B 320 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER B 443 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA B 318 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 270 through 286 removed outlier: 3.516A pdb=" N SER B 275 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 449 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN B 445 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 281 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 443 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS B 283 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 441 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 285 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP B 439 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 462 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU B 452 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ARG B 460 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLN B 454 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.502A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 388 " --> pdb=" O CYS B 373 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 483 through 488 removed outlier: 6.993A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 716 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 499 through 502 removed outlier: 4.157A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 532 through 536 removed outlier: 6.739A pdb=" N TYR B 619 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 590 " --> pdb=" O TYR B 619 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 621 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 588 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR B 623 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 625 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER B 584 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 532 through 536 removed outlier: 7.306A pdb=" N LEU B 603 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER B 617 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 601 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 619 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 599 " --> pdb=" O TYR B 619 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD1, first strand: chain 'B' and resid 781 through 786 removed outlier: 3.684A pdb=" N ILE B 782 " --> pdb=" O VAL B1166 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B1166 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 797 removed outlier: 4.131A pdb=" N PHE B1141 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD4, first strand: chain 'B' and resid 880 through 883 removed outlier: 6.491A pdb=" N SER B 881 " --> pdb=" O LYS B 893 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS B 893 " --> pdb=" O SER B 881 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 883 " --> pdb=" O VAL B 891 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1220 through 1223 Processing sheet with id=AD6, first strand: chain 'B' and resid 1187 through 1191 Processing sheet with id=AD7, first strand: chain 'C' and resid 46 through 51 Processing sheet with id=AD8, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.601A pdb=" N TYR C 181 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 148 through 154 removed outlier: 4.880A pdb=" N LEU C 107 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 270 through 286 removed outlier: 3.534A pdb=" N SER C 275 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 449 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN C 445 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 281 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 443 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS C 283 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 441 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 285 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP C 439 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN C 322 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE C 441 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG C 320 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER C 443 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA C 318 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 270 through 286 removed outlier: 3.534A pdb=" N SER C 275 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 449 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN C 445 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 281 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 443 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS C 283 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 441 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 285 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP C 439 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 462 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 452 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ARG C 460 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN C 454 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 295 through 298 removed outlier: 4.501A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 388 " --> pdb=" O CYS C 373 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 483 through 488 removed outlier: 6.802A pdb=" N VAL C 709 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE C 713 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 716 " --> pdb=" O HIS C 737 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 499 through 502 removed outlier: 4.167A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 532 through 536 removed outlier: 6.738A pdb=" N TYR C 619 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL C 590 " --> pdb=" O TYR C 619 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 621 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE C 588 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR C 623 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 625 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER C 584 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 532 through 536 removed outlier: 7.304A pdb=" N LEU C 603 " --> pdb=" O PHE C 615 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER C 617 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE C 601 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR C 619 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS C 599 " --> pdb=" O TYR C 619 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AE9, first strand: chain 'C' and resid 781 through 786 removed outlier: 3.673A pdb=" N ILE C 782 " --> pdb=" O VAL C1166 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C1166 " --> pdb=" O ILE C 782 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 789 through 797 removed outlier: 4.127A pdb=" N PHE C1141 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AF3, first strand: chain 'C' and resid 880 through 883 removed outlier: 6.496A pdb=" N SER C 881 " --> pdb=" O LYS C 893 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS C 893 " --> pdb=" O SER C 881 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 883 " --> pdb=" O VAL C 891 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1220 through 1223 Processing sheet with id=AF5, first strand: chain 'C' and resid 1187 through 1191 1167 hydrogen bonds defined for protein. 3180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.24 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9399 1.34 - 1.46: 7875 1.46 - 1.58: 13959 1.58 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 31386 Sorted by residual: bond pdb=" C1 NAG C1403 " pdb=" O5 NAG C1403 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 NAG B1403 " pdb=" O5 NAG B1403 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 NAG j 2 " pdb=" O5 NAG j 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 31381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 40517 1.58 - 3.16: 1621 3.16 - 4.74: 379 4.74 - 6.32: 222 6.32 - 7.89: 26 Bond angle restraints: 42765 Sorted by residual: angle pdb=" N VAL A 674 " pdb=" CA VAL A 674 " pdb=" C VAL A 674 " ideal model delta sigma weight residual 113.53 109.23 4.30 9.80e-01 1.04e+00 1.93e+01 angle pdb=" N GLN A 993 " pdb=" CA GLN A 993 " pdb=" CB GLN A 993 " ideal model delta sigma weight residual 114.17 109.83 4.34 1.14e+00 7.69e-01 1.45e+01 angle pdb=" N GLN B 993 " pdb=" CA GLN B 993 " pdb=" CB GLN B 993 " ideal model delta sigma weight residual 114.17 109.85 4.32 1.14e+00 7.69e-01 1.43e+01 angle pdb=" N GLN C 993 " pdb=" CA GLN C 993 " pdb=" CB GLN C 993 " ideal model delta sigma weight residual 114.17 109.89 4.28 1.14e+00 7.69e-01 1.41e+01 angle pdb=" C GLY A1135 " pdb=" N ASP A1136 " pdb=" CA ASP A1136 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.42e+00 ... (remaining 42760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.52: 18953 24.52 - 49.04: 1131 49.04 - 73.56: 307 73.56 - 98.08: 351 98.08 - 122.60: 321 Dihedral angle restraints: 21063 sinusoidal: 10419 harmonic: 10644 Sorted by residual: dihedral pdb=" CB CYS B 464 " pdb=" SG CYS B 464 " pdb=" SG CYS B 473 " pdb=" CB CYS B 473 " ideal model delta sinusoidal sigma weight residual 93.00 164.46 -71.46 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS C 464 " pdb=" SG CYS C 464 " pdb=" SG CYS C 473 " pdb=" CB CYS C 473 " 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 464 " pdb=" SG CYS A 464 " pdb=" SG CYS A 473 " pdb=" CB CYS A 473 " ideal model delta sinusoidal sigma weight residual 93.00 162.49 -69.49 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 21060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 5435 0.143 - 0.286: 97 0.286 - 0.429: 12 0.429 - 0.572: 0 0.572 - 0.715: 3 Chirality restraints: 5547 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 726 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN B 726 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN C 726 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 5544 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 902 " -0.010 2.00e-02 2.50e+03 1.21e-02 2.55e+00 pdb=" CG PHE C 902 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 902 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 902 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 902 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 902 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 902 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 902 " 0.010 2.00e-02 2.50e+03 1.19e-02 2.48e+00 pdb=" CG PHE A 902 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 902 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 902 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 902 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 902 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 902 " 0.010 2.00e-02 2.50e+03 1.18e-02 2.43e+00 pdb=" CG PHE B 902 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B 902 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 902 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 902 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 902 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 902 " 0.001 2.00e-02 2.50e+03 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 639 2.67 - 3.22: 29797 3.22 - 3.78: 47305 3.78 - 4.34: 60996 4.34 - 4.90: 96196 Nonbonded interactions: 234933 Sorted by model distance: nonbonded pdb=" OG1 THR A 167 " pdb=" OG1 THR A 174 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR C 167 " pdb=" OG1 THR C 174 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR B 167 " pdb=" OG1 THR B 174 " model vdw 2.157 3.040 nonbonded pdb=" O ASP B 899 " pdb=" ND2 ASN B 903 " model vdw 2.167 3.120 nonbonded pdb=" O ASP C 899 " pdb=" ND2 ASN C 903 " model vdw 2.169 3.120 ... (remaining 234928 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'S' selection = chain 'U' selection = chain 'h' selection = chain 'j' } ncs_group { reference = (chain 'E' and resid 1 through 4) selection = (chain 'J' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) selection = (chain 'M' and resid 1 through 4) selection = (chain 'N' and resid 1 through 4) selection = (chain 'O' and resid 1 through 4) selection = (chain 'Q' and resid 1 through 4) selection = (chain 'T' and resid 1 through 4) selection = (chain 'Y' and resid 1 through 4) selection = (chain 'Z' and resid 1 through 4) selection = (chain 'a' and resid 1 through 4) selection = (chain 'b' and resid 1 through 4) selection = (chain 'c' and resid 1 through 4) selection = (chain 'd' and resid 1 through 4) selection = (chain 'f' and resid 1 through 4) selection = (chain 'i' and resid 1 through 4) selection = (chain 'n' and resid 1 through 4) selection = (chain 'o' and resid 1 through 4) selection = (chain 'p' and resid 1 through 4) selection = (chain 'q' and resid 1 through 4) selection = (chain 'r' and resid 1 through 4) selection = (chain 's' and resid 1 through 4) selection = (chain 'u' and resid 1 through 4) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) } ncs_group { reference = chain 'I' selection = chain 'X' selection = chain 'm' } 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.890 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.005 0.073 31629 Z= 0.259 Angle : 0.904 16.969 43455 Z= 0.375 Chirality : 0.059 0.715 5547 Planarity : 0.003 0.031 5205 Dihedral : 25.500 122.597 14142 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3666 helix: 0.56 (0.19), residues: 783 sheet: 0.46 (0.17), residues: 924 loop : -1.30 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 146 TYR 0.012 0.001 TYR B 291 PHE 0.028 0.001 PHE C 902 TRP 0.006 0.001 TRP C 168 HIS 0.004 0.000 HIS B 737 Details of bonding type rmsd covalent geometry : bond 0.00511 (31386) covalent geometry : angle 0.83378 (42765) SS BOND : bond 0.00198 ( 39) SS BOND : angle 0.73833 ( 78) hydrogen bonds : bond 0.15211 ( 1099) hydrogen bonds : angle 6.81805 ( 3180) link_ALPHA1-3 : bond 0.00720 ( 24) link_ALPHA1-3 : angle 1.90848 ( 72) link_ALPHA1-6 : bond 0.00690 ( 21) link_ALPHA1-6 : angle 1.49858 ( 63) link_BETA1-4 : bond 0.01313 ( 84) link_BETA1-4 : angle 3.03522 ( 252) link_BETA1-6 : bond 0.01028 ( 12) link_BETA1-6 : angle 1.94687 ( 36) link_NAG-ASN : bond 0.00714 ( 63) link_NAG-ASN : angle 3.92554 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.7865 (m-80) cc_final: 0.7658 (m-80) REVERT: A 215 LEU cc_start: 0.9043 (mm) cc_final: 0.8768 (mm) REVERT: A 644 MET cc_start: 0.7555 (ppp) cc_final: 0.6889 (ppp) REVERT: A 1040 GLU cc_start: 0.9336 (tp30) cc_final: 0.9015 (tp30) REVERT: A 1074 LEU cc_start: 0.7872 (tt) cc_final: 0.7621 (tt) REVERT: A 1117 GLN cc_start: 0.9212 (tp-100) cc_final: 0.8944 (tp-100) REVERT: B 204 MET cc_start: 0.8714 (ppp) cc_final: 0.8431 (tmm) REVERT: B 563 TYR cc_start: 0.8965 (m-80) cc_final: 0.8713 (m-80) REVERT: B 644 MET cc_start: 0.7507 (ppp) cc_final: 0.7223 (ppp) REVERT: B 939 MET cc_start: 0.8665 (mmp) cc_final: 0.7927 (mmp) REVERT: B 1040 GLU cc_start: 0.9337 (tp30) cc_final: 0.9088 (tp30) REVERT: B 1074 LEU cc_start: 0.8464 (tt) cc_final: 0.8262 (tt) REVERT: B 1117 GLN cc_start: 0.9272 (tp-100) cc_final: 0.8953 (tp40) REVERT: C 176 PHE cc_start: 0.9038 (m-80) cc_final: 0.8711 (m-80) REVERT: C 180 ILE cc_start: 0.9230 (tp) cc_final: 0.9007 (tp) REVERT: C 181 TYR cc_start: 0.7966 (m-80) cc_final: 0.7732 (m-80) REVERT: C 563 TYR cc_start: 0.8778 (m-80) cc_final: 0.8503 (m-80) REVERT: C 644 MET cc_start: 0.7150 (ppp) cc_final: 0.6886 (ppp) REVERT: C 938 VAL cc_start: 0.9635 (t) cc_final: 0.9425 (t) REVERT: C 939 MET cc_start: 0.8872 (mmp) cc_final: 0.8125 (mmm) REVERT: C 1040 GLU cc_start: 0.9354 (tp30) cc_final: 0.9085 (tp30) REVERT: C 1117 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8775 (tp40) REVERT: C 1220 PHE cc_start: 0.9085 (m-80) cc_final: 0.8854 (m-80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1336 time to fit residues: 51.9704 Evaluate side-chains 154 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0010 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 overall best weight: 3.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN C1061 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.074442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.051580 restraints weight = 179403.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053191 restraints weight = 123064.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054293 restraints weight = 96212.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055057 restraints weight = 81695.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055498 restraints weight = 73149.344| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31629 Z= 0.172 Angle : 0.860 15.347 43455 Z= 0.367 Chirality : 0.053 0.436 5547 Planarity : 0.003 0.025 5205 Dihedral : 23.043 111.063 8019 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.10 % Allowed : 6.39 % Favored : 93.52 % 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 (0.14), residues: 3666 helix: 0.47 (0.18), residues: 807 sheet: 0.35 (0.17), residues: 966 loop : -1.32 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 146 TYR 0.018 0.001 TYR C 413 PHE 0.032 0.001 PHE C 902 TRP 0.007 0.001 TRP A 168 HIS 0.008 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00350 (31386) covalent geometry : angle 0.76652 (42765) SS BOND : bond 0.00244 ( 39) SS BOND : angle 0.95408 ( 78) hydrogen bonds : bond 0.04768 ( 1099) hydrogen bonds : angle 6.00256 ( 3180) link_ALPHA1-3 : bond 0.01273 ( 24) link_ALPHA1-3 : angle 3.11203 ( 72) link_ALPHA1-6 : bond 0.00944 ( 21) link_ALPHA1-6 : angle 2.16729 ( 63) link_BETA1-4 : bond 0.01080 ( 84) link_BETA1-4 : angle 3.39592 ( 252) link_BETA1-6 : bond 0.01388 ( 12) link_BETA1-6 : angle 2.35829 ( 36) link_NAG-ASN : bond 0.00787 ( 63) link_NAG-ASN : angle 3.88557 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9212 (tp) cc_final: 0.8992 (tp) REVERT: A 644 MET cc_start: 0.7771 (ppp) cc_final: 0.7074 (ppp) REVERT: A 939 MET cc_start: 0.8808 (mmp) cc_final: 0.8313 (mmm) REVERT: A 1040 GLU cc_start: 0.9279 (tp30) cc_final: 0.9046 (tp30) REVERT: A 1117 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8650 (tp-100) REVERT: A 1220 PHE cc_start: 0.9096 (m-80) cc_final: 0.8776 (m-80) REVERT: B 644 MET cc_start: 0.7466 (ppp) cc_final: 0.7038 (ppp) REVERT: B 939 MET cc_start: 0.8574 (mmp) cc_final: 0.8042 (mmm) REVERT: B 1040 GLU cc_start: 0.9249 (tp30) cc_final: 0.9026 (tp30) REVERT: B 1074 LEU cc_start: 0.8447 (tt) cc_final: 0.8162 (tt) REVERT: B 1117 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8727 (tp40) REVERT: C 180 ILE cc_start: 0.9142 (tp) cc_final: 0.8912 (tp) REVERT: C 291 TYR cc_start: 0.7334 (m-80) cc_final: 0.6811 (m-80) REVERT: C 563 TYR cc_start: 0.8857 (m-80) cc_final: 0.8565 (m-80) REVERT: C 644 MET cc_start: 0.7500 (ppp) cc_final: 0.7026 (ppp) REVERT: C 939 MET cc_start: 0.8798 (mmp) cc_final: 0.8235 (mmm) REVERT: C 1040 GLU cc_start: 0.9338 (tp30) cc_final: 0.9125 (tp30) REVERT: C 1074 LEU cc_start: 0.8252 (tp) cc_final: 0.7843 (tt) REVERT: C 1117 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8536 (tp-100) REVERT: C 1220 PHE cc_start: 0.9143 (m-80) cc_final: 0.8787 (m-80) outliers start: 3 outliers final: 0 residues processed: 196 average time/residue: 0.1462 time to fit residues: 50.3769 Evaluate side-chains 145 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 362 optimal weight: 4.9990 chunk 352 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 341 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 358 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 313 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1029 ASN A1061 GLN A1095 ASN A1139 HIS A1197 HIS B1061 GLN B1095 ASN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1197 HIS C1029 ASN C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.075272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052341 restraints weight = 178764.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053990 restraints weight = 122164.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055125 restraints weight = 95381.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055909 restraints weight = 80776.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056434 restraints weight = 72354.862| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31629 Z= 0.137 Angle : 0.828 16.117 43455 Z= 0.345 Chirality : 0.053 0.446 5547 Planarity : 0.003 0.032 5205 Dihedral : 20.460 114.034 8019 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3666 helix: 0.54 (0.18), residues: 807 sheet: 0.41 (0.16), residues: 981 loop : -1.36 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 146 TYR 0.012 0.001 TYR A 105 PHE 0.041 0.001 PHE A 902 TRP 0.004 0.001 TRP C 168 HIS 0.004 0.001 HIS B1139 Details of bonding type rmsd covalent geometry : bond 0.00273 (31386) covalent geometry : angle 0.73124 (42765) SS BOND : bond 0.00236 ( 39) SS BOND : angle 0.85872 ( 78) hydrogen bonds : bond 0.04410 ( 1099) hydrogen bonds : angle 5.67330 ( 3180) link_ALPHA1-3 : bond 0.01302 ( 24) link_ALPHA1-3 : angle 2.53972 ( 72) link_ALPHA1-6 : bond 0.00875 ( 21) link_ALPHA1-6 : angle 2.16244 ( 63) link_BETA1-4 : bond 0.01118 ( 84) link_BETA1-4 : angle 3.55118 ( 252) link_BETA1-6 : bond 0.01493 ( 12) link_BETA1-6 : angle 2.36946 ( 36) link_NAG-ASN : bond 0.00741 ( 63) link_NAG-ASN : angle 3.81680 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.046 Fit side-chains REVERT: A 176 PHE cc_start: 0.8917 (m-80) cc_final: 0.8716 (m-80) REVERT: A 644 MET cc_start: 0.7754 (ppp) cc_final: 0.7038 (ppp) REVERT: A 939 MET cc_start: 0.8652 (mmp) cc_final: 0.8194 (mmm) REVERT: A 1040 GLU cc_start: 0.9274 (tp30) cc_final: 0.9057 (tp30) REVERT: A 1074 LEU cc_start: 0.8272 (tp) cc_final: 0.7903 (tt) REVERT: A 1117 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8879 (tp40) REVERT: A 1220 PHE cc_start: 0.9107 (m-80) cc_final: 0.8749 (m-80) REVERT: B 291 TYR cc_start: 0.7942 (m-80) cc_final: 0.7371 (m-80) REVERT: B 644 MET cc_start: 0.7661 (ppp) cc_final: 0.7164 (ppp) REVERT: B 939 MET cc_start: 0.8435 (mmp) cc_final: 0.7950 (mmm) REVERT: B 1040 GLU cc_start: 0.9265 (tp30) cc_final: 0.9030 (tp30) REVERT: B 1074 LEU cc_start: 0.8435 (tt) cc_final: 0.8099 (tt) REVERT: B 1117 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8611 (tp-100) REVERT: B 1158 LEU cc_start: 0.9542 (tt) cc_final: 0.9243 (tt) REVERT: C 180 ILE cc_start: 0.9175 (tp) cc_final: 0.8957 (tp) REVERT: C 181 TYR cc_start: 0.7897 (m-80) cc_final: 0.7672 (m-80) REVERT: C 291 TYR cc_start: 0.7317 (m-10) cc_final: 0.6731 (m-80) REVERT: C 563 TYR cc_start: 0.8825 (m-80) cc_final: 0.8542 (m-80) REVERT: C 644 MET cc_start: 0.7387 (ppp) cc_final: 0.6930 (ppp) REVERT: C 845 SER cc_start: 0.9405 (t) cc_final: 0.9112 (t) REVERT: C 939 MET cc_start: 0.8637 (mmp) cc_final: 0.8027 (mmm) REVERT: C 1074 LEU cc_start: 0.8153 (tp) cc_final: 0.7754 (tt) REVERT: C 1117 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8531 (tp-100) REVERT: C 1220 PHE cc_start: 0.9133 (m-80) cc_final: 0.8726 (m-80) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1499 time to fit residues: 50.9611 Evaluate side-chains 145 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 178 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 152 optimal weight: 40.0000 chunk 346 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 316 optimal weight: 0.4980 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 0.0670 chunk 86 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 overall best weight: 4.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS A1061 GLN B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.073209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.050657 restraints weight = 183749.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052151 restraints weight = 128864.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053208 restraints weight = 102127.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053874 restraints weight = 87503.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054360 restraints weight = 79154.516| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31629 Z= 0.201 Angle : 0.864 16.021 43455 Z= 0.372 Chirality : 0.054 0.431 5547 Planarity : 0.004 0.046 5205 Dihedral : 18.484 110.775 8019 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: -0.83 (0.13), residues: 3666 helix: 0.48 (0.18), residues: 804 sheet: 0.23 (0.16), residues: 951 loop : -1.45 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 146 TYR 0.014 0.001 TYR B 105 PHE 0.044 0.002 PHE C 902 TRP 0.005 0.001 TRP A 168 HIS 0.007 0.001 HIS C1155 Details of bonding type rmsd covalent geometry : bond 0.00415 (31386) covalent geometry : angle 0.77106 (42765) SS BOND : bond 0.00298 ( 39) SS BOND : angle 1.01380 ( 78) hydrogen bonds : bond 0.04485 ( 1099) hydrogen bonds : angle 5.73163 ( 3180) link_ALPHA1-3 : bond 0.01288 ( 24) link_ALPHA1-3 : angle 2.88364 ( 72) link_ALPHA1-6 : bond 0.01091 ( 21) link_ALPHA1-6 : angle 2.24953 ( 63) link_BETA1-4 : bond 0.01076 ( 84) link_BETA1-4 : angle 3.42623 ( 252) link_BETA1-6 : bond 0.01813 ( 12) link_BETA1-6 : angle 2.88171 ( 36) link_NAG-ASN : bond 0.00764 ( 63) link_NAG-ASN : angle 3.80065 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.076 Fit side-chains REVERT: A 176 PHE cc_start: 0.8887 (m-80) cc_final: 0.8636 (m-80) REVERT: A 644 MET cc_start: 0.7948 (ppp) cc_final: 0.7090 (ppp) REVERT: A 939 MET cc_start: 0.8600 (mmp) cc_final: 0.8246 (mmm) REVERT: A 1074 LEU cc_start: 0.8477 (tp) cc_final: 0.8090 (tt) REVERT: A 1117 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8735 (tp40) REVERT: A 1220 PHE cc_start: 0.9138 (m-80) cc_final: 0.8755 (m-80) REVERT: B 291 TYR cc_start: 0.8163 (m-80) cc_final: 0.7258 (m-80) REVERT: B 563 TYR cc_start: 0.8905 (m-80) cc_final: 0.8688 (m-80) REVERT: B 644 MET cc_start: 0.7981 (ppp) cc_final: 0.7349 (ppp) REVERT: B 939 MET cc_start: 0.8381 (mmp) cc_final: 0.8015 (mmm) REVERT: B 1074 LEU cc_start: 0.8473 (tt) cc_final: 0.8147 (tt) REVERT: B 1117 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8422 (tp-100) REVERT: C 149 LEU cc_start: 0.9388 (tp) cc_final: 0.9171 (tp) REVERT: C 180 ILE cc_start: 0.9168 (tp) cc_final: 0.8936 (tp) REVERT: C 291 TYR cc_start: 0.7413 (m-10) cc_final: 0.7006 (m-80) REVERT: C 563 TYR cc_start: 0.8868 (m-80) cc_final: 0.8553 (m-80) REVERT: C 644 MET cc_start: 0.7590 (ppp) cc_final: 0.6934 (ppp) REVERT: C 782 ILE cc_start: 0.9242 (tt) cc_final: 0.8800 (mm) REVERT: C 844 GLU cc_start: 0.9001 (pp20) cc_final: 0.8753 (pp20) REVERT: C 845 SER cc_start: 0.9418 (t) cc_final: 0.9168 (t) REVERT: C 939 MET cc_start: 0.8564 (mmp) cc_final: 0.8124 (mmm) REVERT: C 1074 LEU cc_start: 0.8446 (tp) cc_final: 0.8025 (tt) REVERT: C 1117 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8470 (tp-100) REVERT: C 1220 PHE cc_start: 0.9240 (m-80) cc_final: 0.8868 (m-80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1408 time to fit residues: 45.2599 Evaluate side-chains 139 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 229 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 126 optimal weight: 0.0060 chunk 244 optimal weight: 20.0000 chunk 289 optimal weight: 0.1980 chunk 174 optimal weight: 6.9990 chunk 261 optimal weight: 0.6980 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** 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 = 0.3535 r_free = 0.3535 target = 0.074465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051724 restraints weight = 181843.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053317 restraints weight = 126616.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054401 restraints weight = 99609.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055143 restraints weight = 85020.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.055538 restraints weight = 76499.695| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31629 Z= 0.140 Angle : 0.825 16.243 43455 Z= 0.345 Chirality : 0.053 0.448 5547 Planarity : 0.003 0.034 5205 Dihedral : 17.002 114.681 8019 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 3666 helix: 0.62 (0.18), residues: 804 sheet: 0.39 (0.17), residues: 903 loop : -1.43 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 490 TYR 0.010 0.001 TYR C 206 PHE 0.042 0.001 PHE C 902 TRP 0.004 0.001 TRP A 168 HIS 0.003 0.001 HIS B1139 Details of bonding type rmsd covalent geometry : bond 0.00278 (31386) covalent geometry : angle 0.73189 (42765) SS BOND : bond 0.00244 ( 39) SS BOND : angle 0.91900 ( 78) hydrogen bonds : bond 0.04142 ( 1099) hydrogen bonds : angle 5.49845 ( 3180) link_ALPHA1-3 : bond 0.01362 ( 24) link_ALPHA1-3 : angle 2.65567 ( 72) link_ALPHA1-6 : bond 0.01233 ( 21) link_ALPHA1-6 : angle 2.15485 ( 63) link_BETA1-4 : bond 0.01155 ( 84) link_BETA1-4 : angle 3.36178 ( 252) link_BETA1-6 : bond 0.02034 ( 12) link_BETA1-6 : angle 3.05562 ( 36) link_NAG-ASN : bond 0.00712 ( 63) link_NAG-ASN : angle 3.70843 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 PHE cc_start: 0.8935 (m-80) cc_final: 0.8665 (m-80) REVERT: A 291 TYR cc_start: 0.7897 (m-80) cc_final: 0.7170 (m-80) REVERT: A 644 MET cc_start: 0.7966 (ppp) cc_final: 0.7064 (ppp) REVERT: A 782 ILE cc_start: 0.9130 (tt) cc_final: 0.8802 (mm) REVERT: A 1074 LEU cc_start: 0.8454 (tp) cc_final: 0.8042 (tt) REVERT: A 1117 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8640 (tp-100) REVERT: A 1220 PHE cc_start: 0.9188 (m-80) cc_final: 0.8821 (m-80) REVERT: B 291 TYR cc_start: 0.8034 (m-80) cc_final: 0.7369 (m-80) REVERT: B 563 TYR cc_start: 0.8907 (m-80) cc_final: 0.8695 (m-80) REVERT: B 644 MET cc_start: 0.8053 (ppp) cc_final: 0.7439 (ppp) REVERT: B 1117 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8460 (tp-100) REVERT: C 181 TYR cc_start: 0.8321 (m-10) cc_final: 0.7987 (m-80) REVERT: C 291 TYR cc_start: 0.7396 (m-10) cc_final: 0.7010 (m-80) REVERT: C 563 TYR cc_start: 0.8851 (m-80) cc_final: 0.8549 (m-80) REVERT: C 644 MET cc_start: 0.7635 (ppp) cc_final: 0.6916 (ppp) REVERT: C 782 ILE cc_start: 0.9211 (tt) cc_final: 0.8736 (mm) REVERT: C 844 GLU cc_start: 0.8987 (pp20) cc_final: 0.8724 (pp20) REVERT: C 845 SER cc_start: 0.9432 (t) cc_final: 0.9211 (t) REVERT: C 939 MET cc_start: 0.8464 (mmp) cc_final: 0.8051 (mmm) REVERT: C 1074 LEU cc_start: 0.8440 (tp) cc_final: 0.8002 (tt) REVERT: C 1117 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8526 (tp-100) REVERT: C 1220 PHE cc_start: 0.9285 (m-80) cc_final: 0.8877 (m-80) outliers start: 2 outliers final: 2 residues processed: 193 average time/residue: 0.1360 time to fit residues: 47.6359 Evaluate side-chains 148 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 71 optimal weight: 20.0000 chunk 237 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** 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 = 0.3465 r_free = 0.3465 target = 0.071298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.049012 restraints weight = 179167.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.050468 restraints weight = 124992.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051486 restraints weight = 98661.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052172 restraints weight = 84247.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052639 restraints weight = 75748.622| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31629 Z= 0.237 Angle : 0.896 15.772 43455 Z= 0.396 Chirality : 0.054 0.408 5547 Planarity : 0.004 0.036 5205 Dihedral : 16.085 113.505 8019 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -1.08 (0.13), residues: 3666 helix: 0.29 (0.18), residues: 807 sheet: 0.06 (0.16), residues: 963 loop : -1.62 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 490 TYR 0.014 0.002 TYR A 934 PHE 0.045 0.002 PHE B 902 TRP 0.006 0.001 TRP A 168 HIS 0.009 0.002 HIS C1155 Details of bonding type rmsd covalent geometry : bond 0.00488 (31386) covalent geometry : angle 0.80807 (42765) SS BOND : bond 0.00375 ( 39) SS BOND : angle 0.97535 ( 78) hydrogen bonds : bond 0.04752 ( 1099) hydrogen bonds : angle 5.88069 ( 3180) link_ALPHA1-3 : bond 0.01356 ( 24) link_ALPHA1-3 : angle 2.74245 ( 72) link_ALPHA1-6 : bond 0.01287 ( 21) link_ALPHA1-6 : angle 2.26316 ( 63) link_BETA1-4 : bond 0.01122 ( 84) link_BETA1-4 : angle 3.30915 ( 252) link_BETA1-6 : bond 0.01996 ( 12) link_BETA1-6 : angle 3.47286 ( 36) link_NAG-ASN : bond 0.00824 ( 63) link_NAG-ASN : angle 3.87927 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 91 PHE cc_start: 0.7662 (m-80) cc_final: 0.6686 (m-10) REVERT: A 176 PHE cc_start: 0.8909 (m-80) cc_final: 0.8603 (m-80) REVERT: A 291 TYR cc_start: 0.7801 (m-80) cc_final: 0.7231 (m-80) REVERT: A 644 MET cc_start: 0.8026 (ppp) cc_final: 0.7102 (ppp) REVERT: A 782 ILE cc_start: 0.9073 (tt) cc_final: 0.8523 (mm) REVERT: A 939 MET cc_start: 0.8455 (mmp) cc_final: 0.8056 (mmm) REVERT: A 1074 LEU cc_start: 0.8220 (tp) cc_final: 0.7931 (tt) REVERT: A 1220 PHE cc_start: 0.9182 (m-80) cc_final: 0.8807 (m-80) REVERT: B 91 PHE cc_start: 0.7436 (m-80) cc_final: 0.6769 (m-10) REVERT: B 563 TYR cc_start: 0.8909 (m-80) cc_final: 0.8588 (m-80) REVERT: B 644 MET cc_start: 0.8218 (ppp) cc_final: 0.7515 (ppp) REVERT: C 149 LEU cc_start: 0.9318 (tp) cc_final: 0.9074 (tp) REVERT: C 180 ILE cc_start: 0.9242 (tp) cc_final: 0.8994 (tp) REVERT: C 181 TYR cc_start: 0.8431 (m-10) cc_final: 0.8077 (m-80) REVERT: C 563 TYR cc_start: 0.8837 (m-80) cc_final: 0.8485 (m-80) REVERT: C 644 MET cc_start: 0.7944 (ppp) cc_final: 0.7118 (ppp) REVERT: C 1074 LEU cc_start: 0.8438 (tp) cc_final: 0.8123 (tt) REVERT: C 1117 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8574 (tp-100) REVERT: C 1220 PHE cc_start: 0.9263 (m-80) cc_final: 0.8880 (m-80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1576 time to fit residues: 46.8404 Evaluate side-chains 129 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 308 optimal weight: 6.9990 chunk 285 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 336 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 6 optimal weight: 40.0000 chunk 126 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 GLN A1061 GLN A1095 ASN B1061 GLN B1095 ASN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.071300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048997 restraints weight = 178819.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.050493 restraints weight = 124306.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.051502 restraints weight = 97677.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052204 restraints weight = 83304.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052677 restraints weight = 74807.593| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31629 Z= 0.211 Angle : 0.874 15.764 43455 Z= 0.381 Chirality : 0.053 0.419 5547 Planarity : 0.004 0.043 5205 Dihedral : 15.516 114.333 8019 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -1.19 (0.13), residues: 3666 helix: 0.25 (0.18), residues: 807 sheet: -0.02 (0.16), residues: 963 loop : -1.71 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1235 TYR 0.019 0.001 TYR B 291 PHE 0.035 0.002 PHE B 902 TRP 0.004 0.001 TRP C 189 HIS 0.006 0.001 HIS C1155 Details of bonding type rmsd covalent geometry : bond 0.00436 (31386) covalent geometry : angle 0.78521 (42765) SS BOND : bond 0.00315 ( 39) SS BOND : angle 1.12493 ( 78) hydrogen bonds : bond 0.04606 ( 1099) hydrogen bonds : angle 5.80264 ( 3180) link_ALPHA1-3 : bond 0.01281 ( 24) link_ALPHA1-3 : angle 2.67262 ( 72) link_ALPHA1-6 : bond 0.01297 ( 21) link_ALPHA1-6 : angle 2.34297 ( 63) link_BETA1-4 : bond 0.01130 ( 84) link_BETA1-4 : angle 3.21683 ( 252) link_BETA1-6 : bond 0.02015 ( 12) link_BETA1-6 : angle 3.43011 ( 36) link_NAG-ASN : bond 0.00772 ( 63) link_NAG-ASN : angle 3.89229 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.000 Fit side-chains REVERT: A 91 PHE cc_start: 0.7591 (m-80) cc_final: 0.6744 (m-80) REVERT: A 108 TYR cc_start: 0.8633 (m-80) cc_final: 0.7989 (m-80) REVERT: A 149 LEU cc_start: 0.9492 (tp) cc_final: 0.9289 (tp) REVERT: A 176 PHE cc_start: 0.8735 (m-80) cc_final: 0.8461 (m-80) REVERT: A 291 TYR cc_start: 0.7971 (m-80) cc_final: 0.7369 (m-80) REVERT: A 644 MET cc_start: 0.8112 (ppp) cc_final: 0.7163 (ppp) REVERT: A 939 MET cc_start: 0.8463 (mmp) cc_final: 0.7930 (mmm) REVERT: A 1220 PHE cc_start: 0.9241 (m-80) cc_final: 0.8865 (m-80) REVERT: B 91 PHE cc_start: 0.7314 (m-80) cc_final: 0.6398 (m-80) REVERT: B 291 TYR cc_start: 0.7973 (m-80) cc_final: 0.7190 (m-80) REVERT: B 563 TYR cc_start: 0.8912 (m-80) cc_final: 0.8590 (m-80) REVERT: B 644 MET cc_start: 0.8231 (ppp) cc_final: 0.7412 (ppp) REVERT: B 1102 LEU cc_start: 0.9665 (pp) cc_final: 0.9383 (mp) REVERT: B 1117 GLN cc_start: 0.8939 (tp40) cc_final: 0.8673 (tp40) REVERT: C 180 ILE cc_start: 0.9217 (tp) cc_final: 0.8942 (tp) REVERT: C 181 TYR cc_start: 0.8309 (m-10) cc_final: 0.7942 (m-80) REVERT: C 563 TYR cc_start: 0.8787 (m-80) cc_final: 0.8403 (m-80) REVERT: C 644 MET cc_start: 0.8124 (ppp) cc_final: 0.7245 (ppp) REVERT: C 1220 PHE cc_start: 0.9308 (m-80) cc_final: 0.8916 (m-80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1409 time to fit residues: 42.6016 Evaluate side-chains 131 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 146 optimal weight: 4.9990 chunk 300 optimal weight: 30.0000 chunk 359 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 71 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 355 optimal weight: 0.6980 chunk 202 optimal weight: 6.9990 chunk 155 optimal weight: 0.1980 chunk 90 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 ASN A1061 GLN A1095 ASN B1061 GLN B1095 ASN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.073711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.050969 restraints weight = 179598.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052559 restraints weight = 123241.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053664 restraints weight = 96477.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054405 restraints weight = 81886.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054918 restraints weight = 73649.620| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31629 Z= 0.139 Angle : 0.849 16.122 43455 Z= 0.356 Chirality : 0.053 0.449 5547 Planarity : 0.003 0.036 5205 Dihedral : 14.701 115.070 8019 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -0.92 (0.13), residues: 3666 helix: 0.50 (0.18), residues: 804 sheet: 0.34 (0.17), residues: 888 loop : -1.59 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 490 TYR 0.016 0.001 TYR B 291 PHE 0.019 0.001 PHE A 902 TRP 0.010 0.001 TRP B 189 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00269 (31386) covalent geometry : angle 0.75965 (42765) SS BOND : bond 0.00258 ( 39) SS BOND : angle 1.00230 ( 78) hydrogen bonds : bond 0.04274 ( 1099) hydrogen bonds : angle 5.48423 ( 3180) link_ALPHA1-3 : bond 0.01289 ( 24) link_ALPHA1-3 : angle 2.57946 ( 72) link_ALPHA1-6 : bond 0.01332 ( 21) link_ALPHA1-6 : angle 2.38728 ( 63) link_BETA1-4 : bond 0.01194 ( 84) link_BETA1-4 : angle 3.19712 ( 252) link_BETA1-6 : bond 0.02174 ( 12) link_BETA1-6 : angle 3.22206 ( 36) link_NAG-ASN : bond 0.00680 ( 63) link_NAG-ASN : angle 3.82479 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.127 Fit side-chains REVERT: A 91 PHE cc_start: 0.7516 (m-80) cc_final: 0.6577 (m-80) REVERT: A 176 PHE cc_start: 0.8792 (m-80) cc_final: 0.8540 (m-80) REVERT: A 291 TYR cc_start: 0.7826 (m-80) cc_final: 0.7447 (m-80) REVERT: A 644 MET cc_start: 0.8046 (ppp) cc_final: 0.7017 (ppp) REVERT: A 782 ILE cc_start: 0.8958 (tt) cc_final: 0.8443 (mm) REVERT: A 1074 LEU cc_start: 0.8204 (tp) cc_final: 0.7890 (tt) REVERT: A 1220 PHE cc_start: 0.9191 (m-80) cc_final: 0.8790 (m-80) REVERT: B 91 PHE cc_start: 0.7310 (m-80) cc_final: 0.6449 (m-10) REVERT: B 291 TYR cc_start: 0.7907 (m-80) cc_final: 0.7322 (m-80) REVERT: B 563 TYR cc_start: 0.8834 (m-80) cc_final: 0.8517 (m-80) REVERT: B 644 MET cc_start: 0.8230 (ppp) cc_final: 0.7472 (ppp) REVERT: B 671 LEU cc_start: 0.9231 (pt) cc_final: 0.8766 (mm) REVERT: B 819 CYS cc_start: 0.9163 (m) cc_final: 0.7848 (t) REVERT: B 1102 LEU cc_start: 0.9614 (pp) cc_final: 0.9338 (mp) REVERT: B 1117 GLN cc_start: 0.8782 (tp40) cc_final: 0.8549 (tp-100) REVERT: C 181 TYR cc_start: 0.8068 (m-10) cc_final: 0.7827 (m-80) REVERT: C 291 TYR cc_start: 0.7767 (m-80) cc_final: 0.7547 (m-80) REVERT: C 563 TYR cc_start: 0.8689 (m-80) cc_final: 0.8301 (m-80) REVERT: C 644 MET cc_start: 0.8087 (ppp) cc_final: 0.7299 (ppp) REVERT: C 658 LYS cc_start: 0.9246 (ptpt) cc_final: 0.8738 (pttt) REVERT: C 782 ILE cc_start: 0.9234 (tt) cc_final: 0.8758 (mm) REVERT: C 1074 LEU cc_start: 0.8404 (tp) cc_final: 0.8063 (tt) REVERT: C 1117 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8357 (tp-100) REVERT: C 1220 PHE cc_start: 0.9226 (m-80) cc_final: 0.8790 (m-80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1550 time to fit residues: 51.0616 Evaluate side-chains 150 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 158 optimal weight: 0.0000 chunk 87 optimal weight: 6.9990 chunk 355 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 346 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 362 optimal weight: 9.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A1061 GLN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C1061 GLN C1095 ASN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.073236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050757 restraints weight = 182292.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052287 restraints weight = 126917.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053339 restraints weight = 99985.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054056 restraints weight = 85458.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054512 restraints weight = 76913.827| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31629 Z= 0.143 Angle : 0.843 16.043 43455 Z= 0.355 Chirality : 0.052 0.447 5547 Planarity : 0.003 0.036 5205 Dihedral : 13.811 113.677 8019 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 3666 helix: 0.64 (0.18), residues: 798 sheet: 0.31 (0.16), residues: 948 loop : -1.62 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1235 TYR 0.019 0.001 TYR B 800 PHE 0.021 0.001 PHE B 902 TRP 0.008 0.001 TRP A 168 HIS 0.004 0.001 HIS B1155 Details of bonding type rmsd covalent geometry : bond 0.00288 (31386) covalent geometry : angle 0.75229 (42765) SS BOND : bond 0.00272 ( 39) SS BOND : angle 1.00592 ( 78) hydrogen bonds : bond 0.04058 ( 1099) hydrogen bonds : angle 5.36986 ( 3180) link_ALPHA1-3 : bond 0.01273 ( 24) link_ALPHA1-3 : angle 2.64988 ( 72) link_ALPHA1-6 : bond 0.01226 ( 21) link_ALPHA1-6 : angle 2.45528 ( 63) link_BETA1-4 : bond 0.01172 ( 84) link_BETA1-4 : angle 3.18268 ( 252) link_BETA1-6 : bond 0.02116 ( 12) link_BETA1-6 : angle 3.31046 ( 36) link_NAG-ASN : bond 0.00691 ( 63) link_NAG-ASN : angle 3.83023 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.044 Fit side-chains REVERT: A 91 PHE cc_start: 0.7611 (m-80) cc_final: 0.6639 (m-80) REVERT: A 176 PHE cc_start: 0.8978 (m-80) cc_final: 0.8711 (m-80) REVERT: A 291 TYR cc_start: 0.7947 (m-80) cc_final: 0.7505 (m-80) REVERT: A 644 MET cc_start: 0.8102 (ppp) cc_final: 0.7047 (ppp) REVERT: A 782 ILE cc_start: 0.8897 (tt) cc_final: 0.8367 (mm) REVERT: A 939 MET cc_start: 0.8671 (mmp) cc_final: 0.8056 (mmm) REVERT: A 1074 LEU cc_start: 0.8180 (tp) cc_final: 0.7848 (tt) REVERT: A 1117 GLN cc_start: 0.9105 (tp40) cc_final: 0.8698 (tp-100) REVERT: A 1220 PHE cc_start: 0.9234 (m-80) cc_final: 0.8835 (m-80) REVERT: B 91 PHE cc_start: 0.7405 (m-80) cc_final: 0.6545 (m-10) REVERT: B 291 TYR cc_start: 0.8088 (m-80) cc_final: 0.7402 (m-80) REVERT: B 563 TYR cc_start: 0.8873 (m-80) cc_final: 0.8543 (m-80) REVERT: B 644 MET cc_start: 0.8217 (ppp) cc_final: 0.7458 (ppp) REVERT: B 671 LEU cc_start: 0.9245 (pt) cc_final: 0.8744 (mm) REVERT: B 819 CYS cc_start: 0.9156 (m) cc_final: 0.7852 (t) REVERT: B 1074 LEU cc_start: 0.8610 (tp) cc_final: 0.8062 (tt) REVERT: B 1102 LEU cc_start: 0.9623 (pp) cc_final: 0.9381 (mp) REVERT: B 1117 GLN cc_start: 0.8895 (tp40) cc_final: 0.8633 (tp-100) REVERT: C 149 LEU cc_start: 0.9405 (tp) cc_final: 0.9204 (tp) REVERT: C 181 TYR cc_start: 0.8226 (m-10) cc_final: 0.7943 (m-80) REVERT: C 563 TYR cc_start: 0.8779 (m-80) cc_final: 0.8390 (m-80) REVERT: C 644 MET cc_start: 0.8094 (ppp) cc_final: 0.7295 (ppp) REVERT: C 658 LYS cc_start: 0.9271 (ptpt) cc_final: 0.8859 (pttt) REVERT: C 782 ILE cc_start: 0.9237 (tt) cc_final: 0.8756 (mm) REVERT: C 1074 LEU cc_start: 0.8617 (tp) cc_final: 0.8246 (tt) REVERT: C 1117 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8400 (tp-100) REVERT: C 1220 PHE cc_start: 0.9287 (m-80) cc_final: 0.8843 (m-80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1392 time to fit residues: 47.7358 Evaluate side-chains 146 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 206 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 3 optimal weight: 0.0010 chunk 192 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 287 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 261 optimal weight: 9.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** 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 = 0.3516 r_free = 0.3516 target = 0.073683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.051158 restraints weight = 169272.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052726 restraints weight = 116193.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.053816 restraints weight = 90605.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054583 restraints weight = 76532.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.055088 restraints weight = 68340.774| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31629 Z= 0.135 Angle : 0.836 16.165 43455 Z= 0.352 Chirality : 0.052 0.453 5547 Planarity : 0.003 0.033 5205 Dihedral : 12.882 112.960 8019 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.81 (0.13), residues: 3666 helix: 0.64 (0.18), residues: 801 sheet: 0.44 (0.17), residues: 918 loop : -1.59 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1235 TYR 0.014 0.001 TYR B 291 PHE 0.020 0.001 PHE C 902 TRP 0.009 0.001 TRP B 189 HIS 0.008 0.001 HIS B 270 Details of bonding type rmsd covalent geometry : bond 0.00267 (31386) covalent geometry : angle 0.74624 (42765) SS BOND : bond 0.00266 ( 39) SS BOND : angle 0.96253 ( 78) hydrogen bonds : bond 0.03937 ( 1099) hydrogen bonds : angle 5.25520 ( 3180) link_ALPHA1-3 : bond 0.01300 ( 24) link_ALPHA1-3 : angle 2.59727 ( 72) link_ALPHA1-6 : bond 0.00982 ( 21) link_ALPHA1-6 : angle 2.17732 ( 63) link_BETA1-4 : bond 0.01178 ( 84) link_BETA1-4 : angle 3.17861 ( 252) link_BETA1-6 : bond 0.02144 ( 12) link_BETA1-6 : angle 3.29038 ( 36) link_NAG-ASN : bond 0.00702 ( 63) link_NAG-ASN : angle 3.84836 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.014 Fit side-chains REVERT: A 91 PHE cc_start: 0.7488 (m-80) cc_final: 0.6530 (m-80) REVERT: A 291 TYR cc_start: 0.7829 (m-80) cc_final: 0.7435 (m-80) REVERT: A 465 ASP cc_start: 0.6981 (p0) cc_final: 0.6532 (p0) REVERT: A 644 MET cc_start: 0.8100 (ppp) cc_final: 0.7021 (ppp) REVERT: A 782 ILE cc_start: 0.8856 (tt) cc_final: 0.8258 (mm) REVERT: A 939 MET cc_start: 0.8729 (mmp) cc_final: 0.8142 (mmm) REVERT: A 1074 LEU cc_start: 0.8668 (tp) cc_final: 0.8256 (tt) REVERT: A 1117 GLN cc_start: 0.9122 (tp40) cc_final: 0.8839 (tp40) REVERT: A 1220 PHE cc_start: 0.9183 (m-80) cc_final: 0.8782 (m-80) REVERT: B 91 PHE cc_start: 0.7269 (m-80) cc_final: 0.6465 (m-10) REVERT: B 291 TYR cc_start: 0.7954 (m-80) cc_final: 0.7270 (m-80) REVERT: B 563 TYR cc_start: 0.8766 (m-80) cc_final: 0.8437 (m-80) REVERT: B 644 MET cc_start: 0.8148 (ppp) cc_final: 0.7401 (ppp) REVERT: B 671 LEU cc_start: 0.9209 (pt) cc_final: 0.8727 (mm) REVERT: B 819 CYS cc_start: 0.9126 (m) cc_final: 0.7781 (t) REVERT: B 1074 LEU cc_start: 0.8700 (tp) cc_final: 0.8182 (tt) REVERT: B 1102 LEU cc_start: 0.9605 (pp) cc_final: 0.9298 (mp) REVERT: B 1117 GLN cc_start: 0.9050 (tp40) cc_final: 0.8712 (tp-100) REVERT: C 181 TYR cc_start: 0.8254 (m-10) cc_final: 0.8016 (m-80) REVERT: C 291 TYR cc_start: 0.7372 (m-80) cc_final: 0.7123 (m-80) REVERT: C 563 TYR cc_start: 0.8670 (m-80) cc_final: 0.8293 (m-80) REVERT: C 644 MET cc_start: 0.8025 (ppp) cc_final: 0.7249 (ppp) REVERT: C 658 LYS cc_start: 0.9240 (ptpt) cc_final: 0.8834 (pttt) REVERT: C 782 ILE cc_start: 0.9176 (tt) cc_final: 0.8723 (mp) REVERT: C 950 LEU cc_start: 0.9591 (mm) cc_final: 0.9267 (mt) REVERT: C 1074 LEU cc_start: 0.8551 (tp) cc_final: 0.8178 (tt) REVERT: C 1117 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8426 (tp40) REVERT: C 1220 PHE cc_start: 0.9220 (m-80) cc_final: 0.8757 (m-80) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1436 time to fit residues: 50.1057 Evaluate side-chains 154 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 29 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 357 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 364 optimal weight: 6.9990 chunk 351 optimal weight: 1.9990 chunk 1 optimal weight: 0.0030 chunk 46 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 269 optimal weight: 7.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN B 97 GLN B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.073354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.050825 restraints weight = 171593.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052412 restraints weight = 117547.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053509 restraints weight = 91475.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054259 restraints weight = 77308.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.054782 restraints weight = 68999.367| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31629 Z= 0.135 Angle : 0.824 16.178 43455 Z= 0.348 Chirality : 0.051 0.450 5547 Planarity : 0.003 0.032 5205 Dihedral : 12.105 111.288 8019 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.76 (0.13), residues: 3666 helix: 0.71 (0.18), residues: 801 sheet: 0.45 (0.17), residues: 927 loop : -1.57 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1112 TYR 0.015 0.001 TYR B 291 PHE 0.018 0.001 PHE C 902 TRP 0.008 0.001 TRP B 189 HIS 0.003 0.001 HIS B 270 Details of bonding type rmsd covalent geometry : bond 0.00271 (31386) covalent geometry : angle 0.73118 (42765) SS BOND : bond 0.00269 ( 39) SS BOND : angle 0.94353 ( 78) hydrogen bonds : bond 0.03878 ( 1099) hydrogen bonds : angle 5.20415 ( 3180) link_ALPHA1-3 : bond 0.01246 ( 24) link_ALPHA1-3 : angle 2.46327 ( 72) link_ALPHA1-6 : bond 0.00934 ( 21) link_ALPHA1-6 : angle 1.88013 ( 63) link_BETA1-4 : bond 0.01172 ( 84) link_BETA1-4 : angle 3.21424 ( 252) link_BETA1-6 : bond 0.02167 ( 12) link_BETA1-6 : angle 3.47288 ( 36) link_NAG-ASN : bond 0.00696 ( 63) link_NAG-ASN : angle 3.88204 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3750.16 seconds wall clock time: 66 minutes 45.09 seconds (4005.09 seconds total)