Starting phenix.real_space_refine on Fri Feb 6 14:19:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ofq_70442/02_2026/9ofq_70442.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ofq_70442/02_2026/9ofq_70442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ofq_70442/02_2026/9ofq_70442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ofq_70442/02_2026/9ofq_70442.map" model { file = "/net/cci-nas-00/data/ceres_data/9ofq_70442/02_2026/9ofq_70442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ofq_70442/02_2026/9ofq_70442.cif" } resolution = 2.88 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= 0.003 sd= 1.080 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 111 5.16 5 C 15790 2.51 5 N 3944 2.21 5 O 5307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25152 Number of models: 1 Model: "" Number of chains: 60 Chain: "C" Number of atoms: 6694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6694 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 28, 'TRANS': 844} Chain breaks: 1 Chain: "A" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7768 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 36, 'TRANS': 975} Chain: "H" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "B" Number of atoms: 6688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6688 Classifications: {'peptide': 872} Link IDs: {'PTRANS': 28, 'TRANS': 843} Chain breaks: 1 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "1" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "2" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "3" Number of atoms: 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: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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 Time building chain proxies: 6.12, per 1000 atoms: 0.24 Number of scatterers: 25152 At special positions: 0 Unit cell: (130.68, 135, 194.4, 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 111 16.00 O 5307 8.00 N 3944 7.00 C 15790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 229 " distance=2.02 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 254 " - pdb=" SG CYS C 263 " distance=2.03 Simple disulfide: pdb=" SG CYS C 444 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 554 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 628 " distance=2.03 Simple disulfide: pdb=" SG CYS C 611 " - pdb=" SG CYS C 617 " distance=2.04 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 724 " distance=2.03 Simple disulfide: pdb=" SG CYS C 915 " - pdb=" SG CYS C 926 " distance=2.03 Simple disulfide: pdb=" SG CYS C 965 " - pdb=" SG CYS C1012 " distance=2.04 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 554 " distance=2.04 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 628 " distance=2.03 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS A 713 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A 915 " - pdb=" SG CYS A 926 " distance=2.04 Simple disulfide: pdb=" SG CYS A 965 " - pdb=" SG CYS A1012 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 229 " distance=2.02 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 444 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 628 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 713 " - pdb=" SG CYS B 724 " distance=2.03 Simple disulfide: pdb=" SG CYS B 915 " - pdb=" SG CYS B 926 " distance=2.03 Simple disulfide: pdb=" SG CYS B 965 " - pdb=" SG CYS B1012 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA D 3 " - " MAN D 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 6 " " MAN X 4 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 4 " " BMA j 3 " - " MAN j 4 " " BMA k 3 " - " MAN k 4 " " BMA o 3 " - " MAN o 4 " " BMA t 3 " - " MAN t 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 4 " " BMA 1 3 " - " MAN 1 5 " " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 5 " " BMA D 3 " - " MAN D 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 4 " " BMA k 3 " - " MAN k 5 " " BMA l 3 " - " MAN l 4 " " BMA o 3 " - " MAN o 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " 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 e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN B 669 " " NAG 1 1 " - " ASN B 928 " " NAG 2 1 " - " ASN B1013 " " NAG 3 1 " - " ASN B1018 " " NAG 4 1 " - " ASN B1035 " " NAG A1201 " - " ASN A 111 " " NAG A1202 " - " ASN A 147 " " NAG A1203 " - " ASN A 176 " " NAG A1204 " - " ASN A 462 " " NAG A1205 " - " ASN A 486 " " NAG A1206 " - " ASN A 540 " " NAG A1207 " - " ASN A 661 " " NAG A1208 " - " ASN A 332 " " NAG B1201 " - " ASN B 111 " " NAG B1202 " - " ASN B 438 " " NAG B1203 " - " ASN B 486 " " NAG B1204 " - " ASN B 540 " " NAG B1205 " - " ASN B 661 " " NAG C1201 " - " ASN C 111 " " NAG C1202 " - " ASN C 147 " " NAG C1203 " - " ASN C 176 " " NAG C1204 " - " ASN C 486 " " NAG C1205 " - " ASN C 540 " " NAG D 1 " - " ASN C 62 " " NAG E 1 " - " ASN C 98 " " NAG F 1 " - " ASN C 171 " " NAG G 1 " - " ASN C 220 " " NAG I 1 " - " ASN C 242 " " NAG J 1 " - " ASN C 438 " " NAG K 1 " - " ASN C 462 " " NAG M 1 " - " ASN C 516 " " NAG N 1 " - " ASN C 536 " " NAG O 1 " - " ASN C 566 " " NAG P 1 " - " ASN C 579 " " NAG Q 1 " - " ASN C 585 " " NAG R 1 " - " ASN C 661 " " NAG S 1 " - " ASN C 669 " " NAG T 1 " - " ASN C 928 " " NAG U 1 " - " ASN C1013 " " NAG V 1 " - " ASN C1018 " " NAG W 1 " - " ASN C1035 " " NAG X 1 " - " ASN A 62 " " NAG Y 1 " - " ASN A 98 " " NAG Z 1 " - " ASN A 171 " " NAG a 1 " - " ASN A 220 " " NAG b 1 " - " ASN A 242 " " NAG c 1 " - " ASN A 325 " " NAG d 1 " - " ASN A 438 " " NAG e 1 " - " ASN A 516 " " NAG f 1 " - " ASN A 536 " " NAG g 1 " - " ASN A 566 " " NAG h 1 " - " ASN A 579 " " NAG i 1 " - " ASN A 585 " " NAG j 1 " - " ASN A 669 " " NAG k 1 " - " ASN A 928 " " NAG l 1 " - " ASN A1013 " " NAG m 1 " - " ASN A1018 " " NAG n 1 " - " ASN A1035 " " NAG o 1 " - " ASN B 62 " " NAG p 1 " - " ASN B 98 " " NAG q 1 " - " ASN B 147 " " NAG r 1 " - " ASN B 171 " " NAG s 1 " - " ASN B 220 " " NAG t 1 " - " ASN B 242 " " NAG u 1 " - " ASN B 462 " " NAG v 1 " - " ASN B 516 " " NAG w 1 " - " ASN B 536 " " NAG x 1 " - " ASN B 566 " " NAG y 1 " - " ASN B 579 " " NAG z 1 " - " ASN B 585 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5560 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 39 sheets defined 27.7% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 518 through 522 removed outlier: 4.115A pdb=" N GLY C 521 " --> pdb=" O THR C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 612 Processing helix chain 'C' and resid 614 through 622 removed outlier: 3.612A pdb=" N GLU C 619 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 620 " --> pdb=" O ARG C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 650 removed outlier: 4.034A pdb=" N CYS C 628 " --> pdb=" O TYR C 624 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C 629 " --> pdb=" O THR C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 659 through 660 No H-bonds generated for 'chain 'C' and resid 659 through 660' Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 739 through 754 removed outlier: 3.952A pdb=" N ILE C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 763 removed outlier: 3.503A pdb=" N ALA C 763 " --> pdb=" O THR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 779 removed outlier: 3.756A pdb=" N VAL C 778 " --> pdb=" O ARG C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 809 removed outlier: 4.207A pdb=" N ILE C 791 " --> pdb=" O GLU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 817 removed outlier: 5.082A pdb=" N GLN C 816 " --> pdb=" O ALA C 813 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 817 " --> pdb=" O ILE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 837 removed outlier: 3.718A pdb=" N VAL C 824 " --> pdb=" O ALA C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 848 Processing helix chain 'C' and resid 849 through 851 No H-bonds generated for 'chain 'C' and resid 849 through 851' Processing helix chain 'C' and resid 859 through 865 Processing helix chain 'C' and resid 868 through 915 removed outlier: 4.285A pdb=" N GLN C 874 " --> pdb=" O PRO C 870 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 875 " --> pdb=" O GLN C 871 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 878 " --> pdb=" O GLN C 874 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 879 " --> pdb=" O GLN C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1004 No H-bonds generated for 'chain 'C' and resid 1002 through 1004' Processing helix chain 'C' and resid 1020 through 1027 removed outlier: 4.343A pdb=" N GLN C1025 " --> pdb=" O SER C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1042 removed outlier: 3.545A pdb=" N GLN C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 518 through 522 removed outlier: 3.715A pdb=" N GLY A 521 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 626 through 650 removed outlier: 3.633A pdb=" N ILE A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 662 through 666 removed outlier: 3.784A pdb=" N GLY A 666 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 673 removed outlier: 4.515A pdb=" N SER A 672 " --> pdb=" O ASN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 696 Processing helix chain 'A' and resid 700 through 704 removed outlier: 4.459A pdb=" N LEU A 703 " --> pdb=" O THR A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 716 removed outlier: 3.897A pdb=" N CYS A 713 " --> pdb=" O ASP A 709 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 714 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 739 through 754 removed outlier: 3.855A pdb=" N ILE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 removed outlier: 4.014A pdb=" N ALA A 763 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 779 removed outlier: 3.615A pdb=" N ALA A 770 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 809 removed outlier: 4.305A pdb=" N ILE A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 818 through 848 removed outlier: 3.737A pdb=" N VAL A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 838 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 839 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 842 " --> pdb=" O GLN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 868 through 915 removed outlier: 4.467A pdb=" N ARG A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1004 No H-bonds generated for 'chain 'A' and resid 1002 through 1004' Processing helix chain 'A' and resid 1022 through 1027 removed outlier: 4.274A pdb=" N GLN A1025 " --> pdb=" O SER A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1039 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.552A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.800A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.703A pdb=" N SER B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 518 through 522 removed outlier: 4.054A pdb=" N GLY B 521 " --> pdb=" O THR B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 614 through 622 removed outlier: 3.664A pdb=" N GLU B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 650 removed outlier: 3.619A pdb=" N MET B 649 " --> pdb=" O ASP B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 658 removed outlier: 3.656A pdb=" N THR B 658 " --> pdb=" O LYS B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 660 No H-bonds generated for 'chain 'B' and resid 659 through 660' Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 709 through 716 removed outlier: 3.631A pdb=" N THR B 714 " --> pdb=" O TYR B 710 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 716 " --> pdb=" O LYS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 739 through 754 removed outlier: 3.953A pdb=" N ILE B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 766 through 777 Processing helix chain 'B' and resid 788 through 809 removed outlier: 3.612A pdb=" N LEU B 792 " --> pdb=" O ASN B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 817 Processing helix chain 'B' and resid 818 through 848 removed outlier: 4.137A pdb=" N VAL B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 838 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLY B 839 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU B 842 " --> pdb=" O GLN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 851 No H-bonds generated for 'chain 'B' and resid 849 through 851' Processing helix chain 'B' and resid 859 through 867 Processing helix chain 'B' and resid 868 through 915 removed outlier: 4.055A pdb=" N GLN B 874 " --> pdb=" O PRO B 870 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 875 " --> pdb=" O GLN B 871 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 878 " --> pdb=" O GLN B 874 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 879 " --> pdb=" O GLN B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1004 No H-bonds generated for 'chain 'B' and resid 1002 through 1004' Processing helix chain 'B' and resid 1023 through 1027 Processing helix chain 'B' and resid 1035 through 1040 removed outlier: 3.547A pdb=" N GLU B1040 " --> pdb=" O LYS B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1043 No H-bonds generated for 'chain 'B' and resid 1041 through 1043' Processing sheet with id=AA1, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.613A pdb=" N THR B 472 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR B 471 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 479 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 68 through 83 removed outlier: 5.345A pdb=" N VAL C 70 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL C 243 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG C 72 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 241 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE C 74 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C 239 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA C 237 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C 233 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 82 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 231 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE C 201 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 68 through 83 removed outlier: 5.345A pdb=" N VAL C 70 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL C 243 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG C 72 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 241 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE C 74 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C 239 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA C 237 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C 233 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 82 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 231 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN C 250 " --> pdb=" O ASN C 242 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N SER C 244 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.949A pdb=" N ALA C 216 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY C 130 " --> pdb=" O CYS C 145 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N CYS C 145 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY C 184 " --> pdb=" O CYS C 168 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 170 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N PHE C 182 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR C 172 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER C 180 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE C 174 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.739A pdb=" N TYR C 504 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL C 508 " --> pdb=" O TYR C 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 437 through 438 removed outlier: 5.392A pdb=" N LEU C 479 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 546 through 548 removed outlier: 3.721A pdb=" N LEU C 546 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.001A pdb=" N ARG C 565 " --> pdb=" O PHE A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 579 through 596 removed outlier: 6.851A pdb=" N ASN C 579 " --> pdb=" O GLU C 959 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU C 959 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER C 581 " --> pdb=" O ASP C 957 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP C 957 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR C 955 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASN C 585 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 933 " --> pdb=" O THR C 948 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU C 950 " --> pdb=" O HIS C 931 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS C 931 " --> pdb=" O LEU C 950 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 579 through 596 removed outlier: 6.851A pdb=" N ASN C 579 " --> pdb=" O GLU C 959 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU C 959 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER C 581 " --> pdb=" O ASP C 957 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP C 957 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR C 955 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASN C 585 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 959 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 981 " --> pdb=" O TRP C 961 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 602 through 604 Processing sheet with id=AB3, first strand: chain 'C' and resid 651 through 652 Processing sheet with id=AB4, first strand: chain 'C' and resid 1006 through 1009 removed outlier: 3.764A pdb=" N GLY C 971 " --> pdb=" O ILE C1009 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 69 through 83 removed outlier: 6.411A pdb=" N SER A 235 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU A 79 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 233 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N CYS A 81 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 231 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TRP A 83 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N CYS A 229 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 228 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASN A 122 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 230 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG A 191 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE A 201 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 69 through 83 removed outlier: 6.411A pdb=" N SER A 235 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU A 79 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 233 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N CYS A 81 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 231 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TRP A 83 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N CYS A 229 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASP A 238 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR A 253 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 240 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 251 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A 242 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.644A pdb=" N ALA A 216 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 140 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N CYS A 168 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 183 " --> pdb=" O CYS A 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 273 through 277 removed outlier: 3.581A pdb=" N GLY A 510 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR A 504 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 437 through 438 removed outlier: 5.430A pdb=" N LEU A 479 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR A 471 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 323 through 327 removed outlier: 4.077A pdb=" N VAL A 323 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 308 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 398 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER A 412 " --> pdb=" O MET A 396 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N MET A 396 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 414 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS A 394 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 338 through 339 removed outlier: 5.475A pdb=" N LYS A 379 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLY A 420 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER A 418 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 383 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 416 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE A 385 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR A 414 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 546 through 548 removed outlier: 3.867A pdb=" N LEU A 546 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 579 through 596 removed outlier: 6.642A pdb=" N ASN A 579 " --> pdb=" O GLU A 959 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU A 959 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 581 " --> pdb=" O ASP A 957 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP A 957 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A 955 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN A 585 " --> pdb=" O THR A 953 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 933 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 950 " --> pdb=" O HIS A 931 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N HIS A 931 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 579 through 596 removed outlier: 6.642A pdb=" N ASN A 579 " --> pdb=" O GLU A 959 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU A 959 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 581 " --> pdb=" O ASP A 957 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP A 957 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A 955 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN A 585 " --> pdb=" O THR A 953 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 959 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 981 " --> pdb=" O TRP A 961 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 987 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AC7, first strand: chain 'A' and resid 1006 through 1009 removed outlier: 3.674A pdb=" N GLY A 971 " --> pdb=" O ILE A1009 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.979A pdb=" N GLY H 10 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.979A pdb=" N GLY H 10 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.702A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 69 through 84 removed outlier: 6.362A pdb=" N SER B 235 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 79 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 233 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS B 81 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL B 231 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TRP B 83 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N CYS B 229 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN B 120 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 231 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 118 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU B 233 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 116 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N TYR B 119 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 11.393A pdb=" N SER B 196 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N ILE B 121 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N VAL B 194 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 11.176A pdb=" N PHE B 123 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N GLU B 192 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU B 125 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE B 201 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 69 through 84 removed outlier: 6.362A pdb=" N SER B 235 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 79 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 233 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS B 81 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL B 231 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TRP B 83 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N CYS B 229 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP B 238 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR B 253 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 240 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE B 251 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN B 242 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.579A pdb=" N ALA B 216 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 142 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 170 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE B 182 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 273 through 277 Processing sheet with id=AD8, first strand: chain 'B' and resid 546 through 548 removed outlier: 3.563A pdb=" N LEU B 546 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 579 through 596 removed outlier: 6.943A pdb=" N ASN B 579 " --> pdb=" O GLU B 959 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU B 959 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER B 581 " --> pdb=" O ASP B 957 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP B 957 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR B 955 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN B 585 " --> pdb=" O THR B 953 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 933 " --> pdb=" O THR B 948 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 950 " --> pdb=" O HIS B 931 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N HIS B 931 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 579 through 596 removed outlier: 6.943A pdb=" N ASN B 579 " --> pdb=" O GLU B 959 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU B 959 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER B 581 " --> pdb=" O ASP B 957 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP B 957 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR B 955 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN B 585 " --> pdb=" O THR B 953 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU B 959 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 981 " --> pdb=" O TRP B 961 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 602 through 604 Processing sheet with id=AE3, first strand: chain 'B' and resid 1006 through 1009 removed outlier: 3.748A pdb=" N GLY B 971 " --> pdb=" O ILE B1009 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2673 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: 5.12 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4710 1.33 - 1.46: 8036 1.46 - 1.59: 12717 1.59 - 1.72: 0 1.72 - 1.84: 146 Bond restraints: 25609 Sorted by residual: bond pdb=" CA ALA B 155 " pdb=" C ALA B 155 " ideal model delta sigma weight residual 1.521 1.480 0.041 1.26e-02 6.30e+03 1.08e+01 bond pdb=" C HIS B 156 " pdb=" O HIS B 156 " ideal model delta sigma weight residual 1.235 1.198 0.037 1.21e-02 6.83e+03 9.47e+00 bond pdb=" N ASP B 154 " pdb=" CA ASP B 154 " ideal model delta sigma weight residual 1.457 1.421 0.036 1.23e-02 6.61e+03 8.71e+00 bond pdb=" N VAL C 39 " pdb=" CA VAL C 39 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.89e+00 bond pdb=" C SER B 159 " pdb=" N GLY B 160 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.46e-02 4.69e+03 7.83e+00 ... (remaining 25604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 33653 2.57 - 5.14: 1106 5.14 - 7.72: 108 7.72 - 10.29: 18 10.29 - 12.86: 4 Bond angle restraints: 34889 Sorted by residual: angle pdb=" N GLU B 37 " pdb=" CA GLU B 37 " pdb=" C GLU B 37 " ideal model delta sigma weight residual 113.23 104.98 8.25 1.24e+00 6.50e-01 4.43e+01 angle pdb=" N HIS A 35 " pdb=" CA HIS A 35 " pdb=" C HIS A 35 " ideal model delta sigma weight residual 113.21 106.06 7.15 1.15e+00 7.56e-01 3.87e+01 angle pdb=" N ASN A 928 " pdb=" CA ASN A 928 " pdb=" CB ASN A 928 " ideal model delta sigma weight residual 110.44 118.35 -7.91 1.43e+00 4.89e-01 3.06e+01 angle pdb=" CB ASN B 242 " pdb=" CG ASN B 242 " pdb=" ND2 ASN B 242 " ideal model delta sigma weight residual 116.40 124.63 -8.23 1.50e+00 4.44e-01 3.01e+01 angle pdb=" CA ASN B 242 " pdb=" CB ASN B 242 " pdb=" CG ASN B 242 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.00e+00 1.00e+00 3.00e+01 ... (remaining 34884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 15925 21.85 - 43.69: 969 43.69 - 65.54: 352 65.54 - 87.39: 141 87.39 - 109.23: 7 Dihedral angle restraints: 17394 sinusoidal: 8709 harmonic: 8685 Sorted by residual: dihedral pdb=" CB CYS C 81 " pdb=" SG CYS C 81 " pdb=" SG CYS C 105 " pdb=" CB CYS C 105 " ideal model delta sinusoidal sigma weight residual -86.00 -4.71 -81.29 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS B 541 " pdb=" SG CYS B 541 " pdb=" SG CYS B 554 " pdb=" CB CYS B 554 " ideal model delta sinusoidal sigma weight residual -86.00 -156.67 70.67 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CB CYS B 444 " pdb=" SG CYS B 444 " pdb=" SG CYS B 495 " pdb=" CB CYS B 495 " ideal model delta sinusoidal sigma weight residual -86.00 -129.36 43.36 1 1.00e+01 1.00e-02 2.62e+01 ... (remaining 17391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 4539 0.218 - 0.435: 38 0.435 - 0.653: 6 0.653 - 0.870: 1 0.870 - 1.088: 2 Chirality restraints: 4586 Sorted by residual: chirality pdb=" C1 NAG C1203 " pdb=" ND2 ASN C 176 " pdb=" C2 NAG C1203 " pdb=" O5 NAG C1203 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 111 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" C1 NAG C1204 " pdb=" ND2 ASN C 486 " pdb=" C2 NAG C1204 " pdb=" O5 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 4583 not shown) Planarity restraints: 4295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 579 " -0.444 2.00e-02 2.50e+03 4.52e-01 2.56e+03 pdb=" CG ASN B 579 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN B 579 " 0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN B 579 " 0.733 2.00e-02 2.50e+03 pdb=" C1 NAG y 1 " -0.511 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 516 " 0.061 2.00e-02 2.50e+03 5.54e-02 3.83e+01 pdb=" CG ASN A 516 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 516 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 516 " -0.058 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1018 " 0.060 2.00e-02 2.50e+03 5.38e-02 3.62e+01 pdb=" CG ASN C1018 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C1018 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C1018 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.058 2.00e-02 2.50e+03 ... (remaining 4292 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 2 2.15 - 2.84: 8082 2.84 - 3.52: 32996 3.52 - 4.21: 57690 4.21 - 4.90: 97649 Nonbonded interactions: 196419 Sorted by model distance: nonbonded pdb=" ND2 ASN B 579 " pdb=" N2 NAG y 1 " model vdw 1.459 2.560 nonbonded pdb=" ND2 ASN B 579 " pdb=" C7 NAG y 1 " model vdw 1.903 3.350 nonbonded pdb=" O ASN A 540 " pdb=" OD1 ASN A 540 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASN B1018 " pdb=" O5 NAG 3 1 " model vdw 2.343 3.040 nonbonded pdb=" O VAL C 221 " pdb=" O THR C 222 " model vdw 2.381 3.040 ... (remaining 196414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain 'S' selection = chain 'U' selection = chain 'Y' selection = chain 'j' selection = chain 'l' selection = chain 't' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'D' selection = chain 'T' selection = chain 'V' selection = chain 'k' selection = chain 'o' } ncs_group { reference = chain '4' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain 'A' and (resid 32 through 294 or resid 435 through 1205)) selection = chain 'B' selection = (chain 'C' and (resid 32 through 294 or resid 435 through 1205)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'W' selection = chain 'b' selection = chain 'c' selection = chain 'm' selection = chain 'r' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.230 Find NCS groups from input model: 0.630 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.007 0.534 25819 Z= 0.417 Angle : 1.224 50.324 35478 Z= 0.580 Chirality : 0.069 1.088 4586 Planarity : 0.006 0.101 4225 Dihedral : 16.546 109.232 11720 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.14 % Favored : 95.66 % Rotamer: Outliers : 1.01 % Allowed : 16.17 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: -0.82 (0.14), residues: 2973 helix: -0.20 (0.18), residues: 639 sheet: -0.14 (0.19), residues: 610 loop : -0.79 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 459 TYR 0.033 0.006 TYR B 504 PHE 0.040 0.002 PHE C 532 TRP 0.022 0.002 TRP A 961 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00474 (25609) covalent geometry : angle 1.01527 (34889) SS BOND : bond 0.00573 ( 38) SS BOND : angle 1.75987 ( 76) hydrogen bonds : bond 0.23159 ( 936) hydrogen bonds : angle 8.06971 ( 2673) Misc. bond : bond 0.47741 ( 1) link_ALPHA1-3 : bond 0.00978 ( 12) link_ALPHA1-3 : angle 2.50029 ( 36) link_ALPHA1-6 : bond 0.00982 ( 13) link_ALPHA1-6 : angle 1.88681 ( 39) link_BETA1-4 : bond 0.01474 ( 76) link_BETA1-4 : angle 4.14068 ( 228) link_NAG-ASN : bond 0.06849 ( 70) link_NAG-ASN : angle 7.77974 ( 210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 373 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7880 (mtp180) REVERT: C 166 PHE cc_start: 0.4641 (m-80) cc_final: 0.4363 (m-80) REVERT: C 632 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8263 (mt-10) REVERT: C 741 GLU cc_start: 0.8680 (tt0) cc_final: 0.8477 (tp30) REVERT: C 814 ILE cc_start: 0.0418 (OUTLIER) cc_final: -0.0742 (mt) REVERT: C 822 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 959 GLU cc_start: 0.8031 (tt0) cc_final: 0.7524 (tm-30) REVERT: A 35 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7648 (t70) REVERT: A 100 THR cc_start: 0.8511 (m) cc_final: 0.8128 (p) REVERT: A 128 ARG cc_start: 0.7209 (mpt-90) cc_final: 0.6988 (mpt-90) REVERT: A 616 ARG cc_start: 0.8696 (tpt170) cc_final: 0.8481 (tpt-90) REVERT: A 626 SER cc_start: 0.8017 (m) cc_final: 0.7659 (t) REVERT: A 674 ILE cc_start: 0.9083 (pt) cc_final: 0.8808 (mt) REVERT: A 784 VAL cc_start: 0.8847 (p) cc_final: 0.8640 (m) REVERT: A 798 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8416 (tppt) REVERT: A 811 ASN cc_start: 0.7227 (OUTLIER) cc_final: 0.6160 (t0) REVERT: A 822 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7836 (tm-30) REVERT: H 31 SER cc_start: 0.9031 (m) cc_final: 0.8656 (t) REVERT: H 82 MET cc_start: 0.8792 (mtp) cc_final: 0.8543 (mtm) REVERT: L 50 ASP cc_start: 0.8549 (t70) cc_final: 0.8235 (t0) REVERT: L 53 ASN cc_start: 0.8590 (m-40) cc_final: 0.8321 (m-40) REVERT: L 92 ASP cc_start: 0.8345 (t70) cc_final: 0.8102 (t0) REVERT: B 35 HIS cc_start: 0.6927 (m90) cc_final: 0.6641 (m90) REVERT: B 106 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8264 (mtpp) REVERT: B 132 ILE cc_start: 0.8967 (mt) cc_final: 0.8723 (mt) REVERT: B 189 THR cc_start: 0.8958 (p) cc_final: 0.8601 (t) REVERT: B 495 CYS cc_start: 0.7911 (t) cc_final: 0.7685 (m) REVERT: B 530 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8204 (mptp) REVERT: B 697 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6772 (tmmt) REVERT: B 707 ASP cc_start: 0.8209 (p0) cc_final: 0.7857 (p0) REVERT: B 788 ASN cc_start: 0.7596 (t0) cc_final: 0.7081 (t0) REVERT: B 800 MET cc_start: 0.8967 (mmt) cc_final: 0.8734 (mmt) REVERT: B 822 GLN cc_start: 0.8425 (tp-100) cc_final: 0.7667 (tm130) REVERT: B 851 GLN cc_start: 0.8703 (mp10) cc_final: 0.8461 (mt0) outliers start: 26 outliers final: 10 residues processed: 392 average time/residue: 0.6501 time to fit residues: 292.6988 Evaluate side-chains 347 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 332 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 182 PHE Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 506 GLN C 874 GLN A 38 ASN A 840 ASN A 851 GLN L 6 GLN B 120 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.108351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089881 restraints weight = 47534.331| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.60 r_work: 0.3087 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25819 Z= 0.167 Angle : 0.810 16.816 35478 Z= 0.374 Chirality : 0.051 0.405 4586 Planarity : 0.004 0.050 4225 Dihedral : 12.095 107.753 6757 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 3.51 % Allowed : 14.30 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 2973 helix: 1.15 (0.20), residues: 665 sheet: 0.01 (0.19), residues: 624 loop : -0.75 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 128 TYR 0.019 0.002 TYR C 109 PHE 0.019 0.002 PHE C 201 TRP 0.011 0.001 TRP C 83 HIS 0.008 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00364 (25609) covalent geometry : angle 0.72641 (34889) SS BOND : bond 0.00446 ( 38) SS BOND : angle 1.20207 ( 76) hydrogen bonds : bond 0.05699 ( 936) hydrogen bonds : angle 5.44351 ( 2673) Misc. bond : bond 0.02812 ( 1) link_ALPHA1-3 : bond 0.01171 ( 12) link_ALPHA1-3 : angle 2.40652 ( 36) link_ALPHA1-6 : bond 0.00774 ( 13) link_ALPHA1-6 : angle 1.59795 ( 39) link_BETA1-4 : bond 0.00873 ( 76) link_BETA1-4 : angle 2.99780 ( 228) link_NAG-ASN : bond 0.00883 ( 70) link_NAG-ASN : angle 3.37671 ( 210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 349 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 PHE cc_start: 0.8648 (t80) cc_final: 0.8445 (t80) REVERT: C 197 ARG cc_start: 0.8410 (tmm-80) cc_final: 0.8049 (ttp80) REVERT: C 260 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8337 (mtp85) REVERT: C 512 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8197 (mtp) REVERT: C 803 ILE cc_start: 0.8639 (mt) cc_final: 0.8438 (mp) REVERT: A 38 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7437 (t0) REVERT: A 100 THR cc_start: 0.8568 (m) cc_final: 0.8107 (p) REVERT: A 145 CYS cc_start: 0.5378 (t) cc_final: 0.5059 (t) REVERT: A 415 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.8838 (m) REVERT: A 674 ILE cc_start: 0.9091 (pt) cc_final: 0.8710 (mp) REVERT: A 798 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8239 (tppt) REVERT: A 811 ASN cc_start: 0.7361 (OUTLIER) cc_final: 0.6399 (t0) REVERT: L 18 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8289 (tmt90) REVERT: L 70 ASP cc_start: 0.8003 (m-30) cc_final: 0.7797 (m-30) REVERT: B 120 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8060 (t0) REVERT: B 132 ILE cc_start: 0.8960 (mt) cc_final: 0.8715 (mt) REVERT: B 154 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7676 (p0) REVERT: B 189 THR cc_start: 0.8900 (p) cc_final: 0.8533 (t) REVERT: B 495 CYS cc_start: 0.7978 (t) cc_final: 0.7661 (m) REVERT: B 633 ASP cc_start: 0.8333 (m-30) cc_final: 0.8128 (m-30) REVERT: B 697 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6938 (tmmt) REVERT: B 707 ASP cc_start: 0.8266 (p0) cc_final: 0.7873 (p0) REVERT: B 788 ASN cc_start: 0.7713 (t0) cc_final: 0.7086 (t0) REVERT: B 850 ARG cc_start: 0.8714 (mtm-85) cc_final: 0.8464 (mtm180) REVERT: B 851 GLN cc_start: 0.8598 (mp10) cc_final: 0.8321 (mt0) REVERT: B 902 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8400 (ttm-80) outliers start: 90 outliers final: 40 residues processed: 412 average time/residue: 0.5905 time to fit residues: 282.4523 Evaluate side-chains 365 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 317 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 207 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 524 ASN C 822 GLN C 874 GLN A 38 ASN A 120 ASN A 840 ASN A 851 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.107488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.088853 restraints weight = 47429.530| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.59 r_work: 0.3071 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25819 Z= 0.179 Angle : 0.765 16.995 35478 Z= 0.353 Chirality : 0.050 0.422 4586 Planarity : 0.004 0.047 4225 Dihedral : 10.735 105.175 6742 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 3.62 % Allowed : 15.31 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: -0.06 (0.15), residues: 2973 helix: 1.59 (0.20), residues: 662 sheet: 0.16 (0.20), residues: 602 loop : -0.77 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 128 TYR 0.018 0.001 TYR C 746 PHE 0.026 0.002 PHE C 108 TRP 0.010 0.001 TRP C 83 HIS 0.008 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00409 (25609) covalent geometry : angle 0.69048 (34889) SS BOND : bond 0.00416 ( 38) SS BOND : angle 1.16676 ( 76) hydrogen bonds : bond 0.05438 ( 936) hydrogen bonds : angle 5.12045 ( 2673) Misc. bond : bond 0.00688 ( 1) link_ALPHA1-3 : bond 0.01149 ( 12) link_ALPHA1-3 : angle 2.47381 ( 36) link_ALPHA1-6 : bond 0.00717 ( 13) link_ALPHA1-6 : angle 1.63971 ( 39) link_BETA1-4 : bond 0.00836 ( 76) link_BETA1-4 : angle 2.86522 ( 228) link_NAG-ASN : bond 0.00721 ( 70) link_NAG-ASN : angle 2.96251 ( 210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 329 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 ARG cc_start: 0.8370 (tmm-80) cc_final: 0.8004 (ttp80) REVERT: C 260 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8433 (mtp85) REVERT: C 267 SER cc_start: 0.9031 (m) cc_final: 0.8614 (p) REVERT: C 512 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8197 (mtp) REVERT: C 527 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: C 790 ARG cc_start: 0.8073 (ttp-170) cc_final: 0.7777 (ttp80) REVERT: C 803 ILE cc_start: 0.8620 (mt) cc_final: 0.8413 (mp) REVERT: C 814 ILE cc_start: 0.0570 (OUTLIER) cc_final: -0.0482 (mt) REVERT: C 1030 GLU cc_start: 0.8646 (tp30) cc_final: 0.8415 (mm-30) REVERT: A 100 THR cc_start: 0.8506 (m) cc_final: 0.7903 (p) REVERT: A 512 MET cc_start: 0.8884 (mtm) cc_final: 0.8626 (mtt) REVERT: A 515 GLU cc_start: 0.8450 (pm20) cc_final: 0.8098 (pm20) REVERT: A 616 ARG cc_start: 0.8069 (tpt170) cc_final: 0.7802 (tpt-90) REVERT: A 674 ILE cc_start: 0.9109 (pt) cc_final: 0.8738 (mp) REVERT: A 798 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8192 (tppt) REVERT: A 811 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6368 (t0) REVERT: A 1010 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7984 (mt-10) REVERT: L 50 ASP cc_start: 0.8345 (t0) cc_final: 0.8111 (t0) REVERT: L 70 ASP cc_start: 0.8070 (m-30) cc_final: 0.7863 (m-30) REVERT: B 154 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7686 (p0) REVERT: B 189 THR cc_start: 0.8907 (p) cc_final: 0.8538 (t) REVERT: B 495 CYS cc_start: 0.8031 (t) cc_final: 0.7690 (m) REVERT: B 633 ASP cc_start: 0.8330 (m-30) cc_final: 0.8072 (m-30) REVERT: B 697 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6775 (tmmt) REVERT: B 707 ASP cc_start: 0.8340 (p0) cc_final: 0.8039 (p0) REVERT: B 741 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: B 788 ASN cc_start: 0.7666 (t0) cc_final: 0.7021 (t0) REVERT: B 850 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8525 (mtm180) REVERT: B 851 GLN cc_start: 0.8577 (mp10) cc_final: 0.8314 (mt0) outliers start: 93 outliers final: 51 residues processed: 393 average time/residue: 0.6083 time to fit residues: 277.7475 Evaluate side-chains 370 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 312 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain B residue 828 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 137 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 822 GLN C 874 GLN ** C1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 786 GLN A 840 ASN A 851 GLN L 34 ASN L 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.107041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088590 restraints weight = 47024.793| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.59 r_work: 0.3061 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25819 Z= 0.178 Angle : 0.741 16.399 35478 Z= 0.343 Chirality : 0.049 0.387 4586 Planarity : 0.004 0.045 4225 Dihedral : 9.770 104.030 6741 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.90 % Rotamer: Outliers : 4.13 % Allowed : 15.78 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 0.01 (0.15), residues: 2973 helix: 1.72 (0.20), residues: 664 sheet: 0.20 (0.20), residues: 600 loop : -0.76 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 128 TYR 0.017 0.001 TYR C 548 PHE 0.026 0.002 PHE C 108 TRP 0.010 0.001 TRP C 83 HIS 0.009 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00407 (25609) covalent geometry : angle 0.67091 (34889) SS BOND : bond 0.00612 ( 38) SS BOND : angle 1.20848 ( 76) hydrogen bonds : bond 0.05034 ( 936) hydrogen bonds : angle 4.92758 ( 2673) Misc. bond : bond 0.00517 ( 1) link_ALPHA1-3 : bond 0.01138 ( 12) link_ALPHA1-3 : angle 2.48025 ( 36) link_ALPHA1-6 : bond 0.00753 ( 13) link_ALPHA1-6 : angle 1.66702 ( 39) link_BETA1-4 : bond 0.00813 ( 76) link_BETA1-4 : angle 2.68934 ( 228) link_NAG-ASN : bond 0.00702 ( 70) link_NAG-ASN : angle 2.83199 ( 210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 335 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 260 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8396 (mtp85) REVERT: C 267 SER cc_start: 0.9060 (m) cc_final: 0.8648 (p) REVERT: C 527 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: C 803 ILE cc_start: 0.8650 (mt) cc_final: 0.8439 (mp) REVERT: C 814 ILE cc_start: 0.0732 (OUTLIER) cc_final: -0.0333 (mt) REVERT: C 1030 GLU cc_start: 0.8687 (tp30) cc_final: 0.8442 (mm-30) REVERT: A 100 THR cc_start: 0.8488 (m) cc_final: 0.7833 (p) REVERT: A 106 LYS cc_start: 0.7957 (mmmm) cc_final: 0.7459 (mtpt) REVERT: A 218 ASN cc_start: 0.8675 (t0) cc_final: 0.7924 (t0) REVERT: A 297 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8034 (mtmm) REVERT: A 512 MET cc_start: 0.8883 (mtm) cc_final: 0.8661 (mtt) REVERT: A 515 GLU cc_start: 0.8449 (pm20) cc_final: 0.8120 (pm20) REVERT: A 674 ILE cc_start: 0.9113 (pt) cc_final: 0.8755 (mp) REVERT: A 798 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8182 (tppt) REVERT: A 811 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.6483 (t0) REVERT: A 822 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7568 (tm-30) REVERT: A 1010 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8031 (mt-10) REVERT: H 19 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7995 (mmm160) REVERT: H 70 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8750 (p) REVERT: L 50 ASP cc_start: 0.8361 (t0) cc_final: 0.8098 (t0) REVERT: L 70 ASP cc_start: 0.8119 (m-30) cc_final: 0.7907 (m-30) REVERT: B 154 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7827 (p0) REVERT: B 189 THR cc_start: 0.8914 (p) cc_final: 0.8528 (t) REVERT: B 495 CYS cc_start: 0.8039 (t) cc_final: 0.7679 (m) REVERT: B 633 ASP cc_start: 0.8343 (m-30) cc_final: 0.8086 (m-30) REVERT: B 697 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6719 (tmmt) REVERT: B 707 ASP cc_start: 0.8396 (p0) cc_final: 0.8099 (p0) REVERT: B 788 ASN cc_start: 0.7696 (t0) cc_final: 0.7020 (t0) REVERT: B 850 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8524 (mtm180) REVERT: B 851 GLN cc_start: 0.8591 (mp10) cc_final: 0.8331 (mt0) outliers start: 106 outliers final: 61 residues processed: 408 average time/residue: 0.5972 time to fit residues: 284.0171 Evaluate side-chains 381 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 312 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 856 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 231 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 80 ASN C 874 GLN ** C1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 786 GLN A 851 GLN L 53 ASN B 838 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.087608 restraints weight = 47043.649| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.73 r_work: 0.3042 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25819 Z= 0.178 Angle : 0.725 16.566 35478 Z= 0.338 Chirality : 0.048 0.384 4586 Planarity : 0.004 0.045 4225 Dihedral : 9.374 104.801 6741 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.47 % Favored : 95.36 % Rotamer: Outliers : 4.29 % Allowed : 16.32 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 0.03 (0.15), residues: 2973 helix: 1.83 (0.20), residues: 662 sheet: 0.20 (0.20), residues: 600 loop : -0.78 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.017 0.001 TYR C 548 PHE 0.029 0.002 PHE C 108 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00410 (25609) covalent geometry : angle 0.65810 (34889) SS BOND : bond 0.00400 ( 38) SS BOND : angle 1.32059 ( 76) hydrogen bonds : bond 0.04936 ( 936) hydrogen bonds : angle 4.84086 ( 2673) Misc. bond : bond 0.00359 ( 1) link_ALPHA1-3 : bond 0.01105 ( 12) link_ALPHA1-3 : angle 2.47540 ( 36) link_ALPHA1-6 : bond 0.00746 ( 13) link_ALPHA1-6 : angle 1.63667 ( 39) link_BETA1-4 : bond 0.00807 ( 76) link_BETA1-4 : angle 2.58283 ( 228) link_NAG-ASN : bond 0.00682 ( 70) link_NAG-ASN : angle 2.74266 ( 210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 331 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: C 182 PHE cc_start: 0.6130 (p90) cc_final: 0.5900 (t80) REVERT: C 260 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8393 (mtp85) REVERT: C 267 SER cc_start: 0.9110 (m) cc_final: 0.8703 (p) REVERT: C 527 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: C 803 ILE cc_start: 0.8664 (mt) cc_final: 0.8454 (mp) REVERT: C 814 ILE cc_start: 0.0749 (OUTLIER) cc_final: -0.0299 (mt) REVERT: C 1030 GLU cc_start: 0.8739 (tp30) cc_final: 0.8490 (mm-30) REVERT: A 38 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7795 (t0) REVERT: A 39 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 106 LYS cc_start: 0.7656 (mmmm) cc_final: 0.7308 (mttt) REVERT: A 145 CYS cc_start: 0.5625 (t) cc_final: 0.5349 (t) REVERT: A 218 ASN cc_start: 0.8687 (t0) cc_final: 0.7922 (t0) REVERT: A 297 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8058 (mtmm) REVERT: A 512 MET cc_start: 0.8920 (mtm) cc_final: 0.8695 (mtt) REVERT: A 515 GLU cc_start: 0.8453 (pm20) cc_final: 0.8117 (pm20) REVERT: A 674 ILE cc_start: 0.9120 (pt) cc_final: 0.8759 (mp) REVERT: A 795 SER cc_start: 0.8613 (t) cc_final: 0.8314 (p) REVERT: A 798 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8183 (tppt) REVERT: A 811 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.6450 (t0) REVERT: A 1010 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8100 (mt-10) REVERT: H 70 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8770 (p) REVERT: L 50 ASP cc_start: 0.8402 (t0) cc_final: 0.8131 (t0) REVERT: L 70 ASP cc_start: 0.8200 (m-30) cc_final: 0.7982 (m-30) REVERT: B 189 THR cc_start: 0.8911 (p) cc_final: 0.8529 (t) REVERT: B 464 THR cc_start: 0.8699 (p) cc_final: 0.8347 (t) REVERT: B 495 CYS cc_start: 0.8087 (t) cc_final: 0.7733 (m) REVERT: B 633 ASP cc_start: 0.8364 (m-30) cc_final: 0.8138 (m-30) REVERT: B 697 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.7044 (tmmt) REVERT: B 707 ASP cc_start: 0.8380 (p0) cc_final: 0.8135 (p0) REVERT: B 742 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7705 (ttt180) REVERT: B 788 ASN cc_start: 0.7736 (t0) cc_final: 0.7031 (t0) REVERT: B 850 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8538 (mtm180) REVERT: B 851 GLN cc_start: 0.8608 (mp10) cc_final: 0.8347 (mt0) outliers start: 110 outliers final: 67 residues processed: 408 average time/residue: 0.5690 time to fit residues: 271.9251 Evaluate side-chains 390 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 313 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 847 SER Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 742 ARG Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 856 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 227 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 524 ASN C 874 GLN ** C1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 309 HIS A 786 GLN A 851 GLN L 34 ASN L 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.087364 restraints weight = 47127.527| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.69 r_work: 0.3032 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25819 Z= 0.214 Angle : 0.749 16.624 35478 Z= 0.351 Chirality : 0.049 0.397 4586 Planarity : 0.004 0.047 4225 Dihedral : 9.255 104.778 6739 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.54 % Favored : 95.29 % Rotamer: Outliers : 4.21 % Allowed : 17.22 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: -0.00 (0.15), residues: 2973 helix: 1.77 (0.20), residues: 664 sheet: 0.20 (0.20), residues: 590 loop : -0.80 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 61 TYR 0.020 0.002 TYR C 144 PHE 0.032 0.002 PHE C 108 TRP 0.014 0.002 TRP C 83 HIS 0.005 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00502 (25609) covalent geometry : angle 0.68205 (34889) SS BOND : bond 0.00411 ( 38) SS BOND : angle 1.47579 ( 76) hydrogen bonds : bond 0.05122 ( 936) hydrogen bonds : angle 4.84027 ( 2673) Misc. bond : bond 0.00318 ( 1) link_ALPHA1-3 : bond 0.01076 ( 12) link_ALPHA1-3 : angle 2.45524 ( 36) link_ALPHA1-6 : bond 0.00739 ( 13) link_ALPHA1-6 : angle 1.58215 ( 39) link_BETA1-4 : bond 0.00812 ( 76) link_BETA1-4 : angle 2.58515 ( 228) link_NAG-ASN : bond 0.00705 ( 70) link_NAG-ASN : angle 2.82635 ( 210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 321 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: C 182 PHE cc_start: 0.6060 (p90) cc_final: 0.5832 (t80) REVERT: C 197 ARG cc_start: 0.8448 (tmm-80) cc_final: 0.8121 (ttm-80) REVERT: C 260 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8455 (mtp85) REVERT: C 267 SER cc_start: 0.9145 (m) cc_final: 0.8762 (p) REVERT: C 527 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: C 803 ILE cc_start: 0.8652 (mt) cc_final: 0.8438 (mp) REVERT: C 814 ILE cc_start: 0.0215 (OUTLIER) cc_final: -0.0578 (mt) REVERT: C 1030 GLU cc_start: 0.8704 (tp30) cc_final: 0.8441 (mm-30) REVERT: A 38 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7671 (t0) REVERT: A 39 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 100 THR cc_start: 0.8391 (m) cc_final: 0.7710 (p) REVERT: A 218 ASN cc_start: 0.8726 (t0) cc_final: 0.8021 (t0) REVERT: A 230 THR cc_start: 0.9024 (p) cc_final: 0.8787 (t) REVERT: A 297 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8149 (mtmm) REVERT: A 512 MET cc_start: 0.8944 (mtm) cc_final: 0.8710 (mtt) REVERT: A 648 GLU cc_start: 0.8618 (tp30) cc_final: 0.8236 (tp30) REVERT: A 674 ILE cc_start: 0.9106 (pt) cc_final: 0.8816 (mt) REVERT: A 795 SER cc_start: 0.8696 (t) cc_final: 0.8413 (p) REVERT: A 798 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8209 (tppt) REVERT: A 811 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.6535 (t0) REVERT: A 1010 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8035 (mt-10) REVERT: L 50 ASP cc_start: 0.8358 (t0) cc_final: 0.8088 (t0) REVERT: L 70 ASP cc_start: 0.8238 (m-30) cc_final: 0.8011 (m-30) REVERT: B 189 THR cc_start: 0.8900 (p) cc_final: 0.8511 (t) REVERT: B 464 THR cc_start: 0.8697 (p) cc_final: 0.8364 (t) REVERT: B 495 CYS cc_start: 0.8195 (t) cc_final: 0.7906 (m) REVERT: B 633 ASP cc_start: 0.8438 (m-30) cc_final: 0.8178 (m-30) REVERT: B 697 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.7098 (tmmt) REVERT: B 707 ASP cc_start: 0.8436 (p0) cc_final: 0.8211 (p0) REVERT: B 788 ASN cc_start: 0.7813 (t0) cc_final: 0.7093 (t0) REVERT: B 850 ARG cc_start: 0.8801 (mtm-85) cc_final: 0.8568 (mtm180) REVERT: B 878 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.6814 (mtm180) outliers start: 108 outliers final: 70 residues processed: 398 average time/residue: 0.5838 time to fit residues: 270.3422 Evaluate side-chains 390 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 311 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 847 SER Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 ARG Chi-restraints excluded: chain B residue 969 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 262 optimal weight: 0.9980 chunk 191 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 254 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 220 optimal weight: 0.0970 chunk 116 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 729 ASN C 874 GLN ** C1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 309 HIS A 786 GLN ** A 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN L 53 ASN B 477 ASN B 786 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.107582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087793 restraints weight = 46729.214| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.75 r_work: 0.3045 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 25819 Z= 0.163 Angle : 0.739 16.621 35478 Z= 0.347 Chirality : 0.048 0.397 4586 Planarity : 0.004 0.051 4225 Dihedral : 9.039 104.226 6739 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.24 % Favored : 95.59 % Rotamer: Outliers : 3.74 % Allowed : 18.11 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 0.09 (0.15), residues: 2973 helix: 1.85 (0.20), residues: 662 sheet: 0.32 (0.20), residues: 584 loop : -0.76 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 61 TYR 0.020 0.001 TYR A 109 PHE 0.032 0.002 PHE C 108 TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00370 (25609) covalent geometry : angle 0.67259 (34889) SS BOND : bond 0.00389 ( 38) SS BOND : angle 1.83623 ( 76) hydrogen bonds : bond 0.04752 ( 936) hydrogen bonds : angle 4.76475 ( 2673) Misc. bond : bond 0.00269 ( 1) link_ALPHA1-3 : bond 0.01073 ( 12) link_ALPHA1-3 : angle 2.37783 ( 36) link_ALPHA1-6 : bond 0.00767 ( 13) link_ALPHA1-6 : angle 1.48524 ( 39) link_BETA1-4 : bond 0.00807 ( 76) link_BETA1-4 : angle 2.50642 ( 228) link_NAG-ASN : bond 0.00666 ( 70) link_NAG-ASN : angle 2.76826 ( 210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 324 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: C 197 ARG cc_start: 0.8458 (tmm-80) cc_final: 0.8113 (ttm-80) REVERT: C 260 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8409 (mtp85) REVERT: C 267 SER cc_start: 0.9157 (m) cc_final: 0.8768 (p) REVERT: C 527 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: C 732 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8272 (ptp) REVERT: C 803 ILE cc_start: 0.8598 (mt) cc_final: 0.8384 (mp) REVERT: C 814 ILE cc_start: 0.0066 (OUTLIER) cc_final: -0.0706 (mt) REVERT: C 843 ASN cc_start: 0.8396 (m-40) cc_final: 0.8078 (m110) REVERT: C 1030 GLU cc_start: 0.8719 (tp30) cc_final: 0.8445 (mm-30) REVERT: A 38 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7597 (t0) REVERT: A 39 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.7841 (p) REVERT: A 100 THR cc_start: 0.8384 (m) cc_final: 0.7669 (p) REVERT: A 218 ASN cc_start: 0.8724 (t0) cc_final: 0.7908 (t0) REVERT: A 297 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8081 (mtmm) REVERT: A 512 MET cc_start: 0.8950 (mtm) cc_final: 0.8718 (mtt) REVERT: A 616 ARG cc_start: 0.8114 (tpt170) cc_final: 0.7851 (tpt170) REVERT: A 648 GLU cc_start: 0.8618 (tp30) cc_final: 0.8122 (tp30) REVERT: A 674 ILE cc_start: 0.9093 (pt) cc_final: 0.8734 (mp) REVERT: A 791 ILE cc_start: 0.8489 (tp) cc_final: 0.8174 (tt) REVERT: A 798 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8148 (tppt) REVERT: A 1010 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8109 (mt-10) REVERT: H 19 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8169 (mmm160) REVERT: L 50 ASP cc_start: 0.8382 (t0) cc_final: 0.8116 (t0) REVERT: L 70 ASP cc_start: 0.8265 (m-30) cc_final: 0.8040 (m-30) REVERT: B 189 THR cc_start: 0.8883 (p) cc_final: 0.8491 (t) REVERT: B 464 THR cc_start: 0.8698 (p) cc_final: 0.8379 (t) REVERT: B 495 CYS cc_start: 0.8210 (t) cc_final: 0.7927 (m) REVERT: B 633 ASP cc_start: 0.8365 (m-30) cc_final: 0.7944 (m-30) REVERT: B 637 ASN cc_start: 0.8740 (m-40) cc_final: 0.8462 (m-40) REVERT: B 697 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7189 (tmmt) REVERT: B 707 ASP cc_start: 0.8461 (p0) cc_final: 0.8249 (p0) REVERT: B 788 ASN cc_start: 0.7920 (t0) cc_final: 0.7175 (t0) REVERT: B 850 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8550 (mtm180) REVERT: B 878 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6744 (mtm180) outliers start: 96 outliers final: 64 residues processed: 391 average time/residue: 0.5910 time to fit residues: 269.0097 Evaluate side-chains 383 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 309 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 847 SER Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 ARG Chi-restraints excluded: chain B residue 969 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 54 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 203 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 874 GLN ** C1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 309 HIS A 786 GLN A 851 GLN L 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.107771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088618 restraints weight = 46860.238| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.69 r_work: 0.3040 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25819 Z= 0.160 Angle : 0.726 16.638 35478 Z= 0.342 Chirality : 0.048 0.394 4586 Planarity : 0.004 0.054 4225 Dihedral : 8.847 103.775 6737 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.41 % Favored : 95.43 % Rotamer: Outliers : 3.78 % Allowed : 18.27 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 0.14 (0.15), residues: 2973 helix: 1.90 (0.20), residues: 659 sheet: 0.37 (0.20), residues: 585 loop : -0.73 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 61 TYR 0.021 0.001 TYR A 109 PHE 0.033 0.001 PHE C 108 TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00365 (25609) covalent geometry : angle 0.66188 (34889) SS BOND : bond 0.00406 ( 38) SS BOND : angle 1.58284 ( 76) hydrogen bonds : bond 0.04635 ( 936) hydrogen bonds : angle 4.73882 ( 2673) Misc. bond : bond 0.00251 ( 1) link_ALPHA1-3 : bond 0.01046 ( 12) link_ALPHA1-3 : angle 2.32561 ( 36) link_ALPHA1-6 : bond 0.00750 ( 13) link_ALPHA1-6 : angle 1.46727 ( 39) link_BETA1-4 : bond 0.00802 ( 76) link_BETA1-4 : angle 2.46574 ( 228) link_NAG-ASN : bond 0.00649 ( 70) link_NAG-ASN : angle 2.72900 ( 210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 324 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: C 182 PHE cc_start: 0.6535 (t80) cc_final: 0.6333 (t80) REVERT: C 197 ARG cc_start: 0.8478 (tmm-80) cc_final: 0.8120 (ttm-80) REVERT: C 260 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8394 (mtp85) REVERT: C 267 SER cc_start: 0.9166 (m) cc_final: 0.8776 (p) REVERT: C 527 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: C 649 MET cc_start: 0.8875 (ttm) cc_final: 0.8660 (ttt) REVERT: C 732 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8301 (ptp) REVERT: C 765 ILE cc_start: 0.8860 (pt) cc_final: 0.8615 (OUTLIER) REVERT: C 803 ILE cc_start: 0.8608 (mt) cc_final: 0.8389 (mp) REVERT: C 814 ILE cc_start: 0.0024 (OUTLIER) cc_final: -0.0741 (mt) REVERT: C 843 ASN cc_start: 0.8380 (m-40) cc_final: 0.8086 (m110) REVERT: C 871 GLN cc_start: 0.8153 (mp-120) cc_final: 0.7775 (mp10) REVERT: C 1030 GLU cc_start: 0.8738 (tp30) cc_final: 0.8458 (mm-30) REVERT: A 38 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7624 (t0) REVERT: A 39 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7705 (p) REVERT: A 100 THR cc_start: 0.8370 (m) cc_final: 0.7655 (p) REVERT: A 218 ASN cc_start: 0.8724 (t0) cc_final: 0.7918 (t0) REVERT: A 297 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8069 (mtmm) REVERT: A 315 LYS cc_start: 0.7346 (tttt) cc_final: 0.7120 (ttpt) REVERT: A 512 MET cc_start: 0.8959 (mtm) cc_final: 0.8728 (mtt) REVERT: A 515 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8115 (pm20) REVERT: A 616 ARG cc_start: 0.8133 (tpt170) cc_final: 0.7856 (tpt170) REVERT: A 632 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: A 648 GLU cc_start: 0.8629 (tp30) cc_final: 0.8130 (tp30) REVERT: A 674 ILE cc_start: 0.9085 (pt) cc_final: 0.8749 (mp) REVERT: A 798 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8128 (tppt) REVERT: A 811 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.6675 (t0) REVERT: A 1010 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8113 (mt-10) REVERT: L 50 ASP cc_start: 0.8378 (t0) cc_final: 0.7686 (t0) REVERT: L 53 ASN cc_start: 0.8667 (m-40) cc_final: 0.8441 (m110) REVERT: L 70 ASP cc_start: 0.8281 (m-30) cc_final: 0.8051 (m-30) REVERT: B 189 THR cc_start: 0.8881 (p) cc_final: 0.8480 (t) REVERT: B 464 THR cc_start: 0.8737 (p) cc_final: 0.8435 (t) REVERT: B 495 CYS cc_start: 0.8225 (t) cc_final: 0.7938 (m) REVERT: B 633 ASP cc_start: 0.8379 (m-30) cc_final: 0.7939 (m-30) REVERT: B 637 ASN cc_start: 0.8752 (m-40) cc_final: 0.8436 (m-40) REVERT: B 697 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7184 (tmmt) REVERT: B 788 ASN cc_start: 0.7877 (t0) cc_final: 0.7108 (t0) REVERT: B 850 ARG cc_start: 0.8785 (mtm-85) cc_final: 0.8525 (mtm180) REVERT: B 878 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.6727 (mtm180) outliers start: 97 outliers final: 66 residues processed: 395 average time/residue: 0.6440 time to fit residues: 295.7490 Evaluate side-chains 393 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 316 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 847 SER Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 ARG Chi-restraints excluded: chain B residue 969 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 74 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 293 optimal weight: 0.0370 chunk 294 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 906 GLN ** C1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 309 HIS A 786 GLN A 851 GLN L 34 ASN L 90 GLN B 838 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.107985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088855 restraints weight = 46762.830| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.68 r_work: 0.3052 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25819 Z= 0.153 Angle : 0.718 16.708 35478 Z= 0.338 Chirality : 0.047 0.390 4586 Planarity : 0.004 0.059 4225 Dihedral : 8.736 103.552 6737 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 3.66 % Allowed : 18.74 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 0.17 (0.15), residues: 2973 helix: 1.93 (0.20), residues: 659 sheet: 0.40 (0.20), residues: 585 loop : -0.72 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 61 TYR 0.020 0.001 TYR A 109 PHE 0.033 0.002 PHE C 108 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00347 (25609) covalent geometry : angle 0.65662 (34889) SS BOND : bond 0.00392 ( 38) SS BOND : angle 1.24803 ( 76) hydrogen bonds : bond 0.04519 ( 936) hydrogen bonds : angle 4.71387 ( 2673) Misc. bond : bond 0.00237 ( 1) link_ALPHA1-3 : bond 0.01031 ( 12) link_ALPHA1-3 : angle 2.28313 ( 36) link_ALPHA1-6 : bond 0.00744 ( 13) link_ALPHA1-6 : angle 1.45487 ( 39) link_BETA1-4 : bond 0.00796 ( 76) link_BETA1-4 : angle 2.42634 ( 228) link_NAG-ASN : bond 0.00632 ( 70) link_NAG-ASN : angle 2.69976 ( 210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 323 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: C 178 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8058 (t) REVERT: C 182 PHE cc_start: 0.6692 (t80) cc_final: 0.6465 (t80) REVERT: C 197 ARG cc_start: 0.8474 (tmm-80) cc_final: 0.8109 (ttm-80) REVERT: C 260 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.8372 (mtp85) REVERT: C 267 SER cc_start: 0.9165 (m) cc_final: 0.8774 (p) REVERT: C 527 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: C 648 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8271 (tp30) REVERT: C 649 MET cc_start: 0.8901 (ttm) cc_final: 0.8686 (ttt) REVERT: C 765 ILE cc_start: 0.8839 (pt) cc_final: 0.8591 (OUTLIER) REVERT: C 803 ILE cc_start: 0.8594 (mt) cc_final: 0.8373 (mp) REVERT: C 814 ILE cc_start: 0.0036 (OUTLIER) cc_final: -0.0724 (mt) REVERT: C 843 ASN cc_start: 0.8369 (m-40) cc_final: 0.8069 (m110) REVERT: C 871 GLN cc_start: 0.8136 (mp-120) cc_final: 0.7813 (mp10) REVERT: C 1030 GLU cc_start: 0.8715 (tp30) cc_final: 0.8435 (mm-30) REVERT: A 39 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7550 (p) REVERT: A 100 THR cc_start: 0.8352 (m) cc_final: 0.7635 (p) REVERT: A 108 PHE cc_start: 0.9098 (t80) cc_final: 0.8864 (t80) REVERT: A 218 ASN cc_start: 0.8715 (t0) cc_final: 0.7914 (t0) REVERT: A 297 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8029 (mtmm) REVERT: A 421 ASP cc_start: 0.8082 (p0) cc_final: 0.7754 (p0) REVERT: A 512 MET cc_start: 0.8934 (mtm) cc_final: 0.8702 (mtt) REVERT: A 515 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: A 616 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7838 (tpt170) REVERT: A 642 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8315 (tt0) REVERT: A 648 GLU cc_start: 0.8611 (tp30) cc_final: 0.8114 (tp30) REVERT: A 674 ILE cc_start: 0.9080 (pt) cc_final: 0.8763 (mp) REVERT: A 722 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8463 (tm) REVERT: A 798 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8110 (tppt) REVERT: A 811 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6611 (t0) REVERT: A 1010 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8140 (mt-10) REVERT: L 50 ASP cc_start: 0.8160 (t0) cc_final: 0.7863 (t0) REVERT: L 70 ASP cc_start: 0.8286 (m-30) cc_final: 0.8071 (m-30) REVERT: B 37 GLU cc_start: 0.8171 (pm20) cc_final: 0.7949 (pm20) REVERT: B 189 THR cc_start: 0.8877 (p) cc_final: 0.8492 (t) REVERT: B 464 THR cc_start: 0.8729 (p) cc_final: 0.8434 (t) REVERT: B 495 CYS cc_start: 0.8199 (t) cc_final: 0.7913 (m) REVERT: B 633 ASP cc_start: 0.8355 (m-30) cc_final: 0.7913 (m-30) REVERT: B 637 ASN cc_start: 0.8736 (m-40) cc_final: 0.8409 (m-40) REVERT: B 697 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7223 (tmmt) REVERT: B 788 ASN cc_start: 0.7857 (t0) cc_final: 0.7043 (t0) REVERT: B 850 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8522 (mtm180) REVERT: B 878 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6707 (mtm180) outliers start: 94 outliers final: 64 residues processed: 392 average time/residue: 0.6266 time to fit residues: 285.8386 Evaluate side-chains 391 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 317 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 847 SER Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 ARG Chi-restraints excluded: chain B residue 969 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 906 GLN ** C1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 309 HIS A 851 GLN L 27 GLN L 34 ASN L 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086415 restraints weight = 47023.483| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.81 r_work: 0.3010 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25819 Z= 0.240 Angle : 0.777 16.736 35478 Z= 0.367 Chirality : 0.050 0.416 4586 Planarity : 0.004 0.059 4225 Dihedral : 8.992 104.205 6737 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.84 % Favored : 94.99 % Rotamer: Outliers : 3.47 % Allowed : 18.78 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: -0.01 (0.15), residues: 2973 helix: 1.72 (0.20), residues: 667 sheet: 0.23 (0.20), residues: 599 loop : -0.81 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 61 TYR 0.021 0.002 TYR A 317 PHE 0.034 0.002 PHE C 108 TRP 0.015 0.002 TRP C 83 HIS 0.006 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00566 (25609) covalent geometry : angle 0.71416 (34889) SS BOND : bond 0.00496 ( 38) SS BOND : angle 1.62470 ( 76) hydrogen bonds : bond 0.05219 ( 936) hydrogen bonds : angle 4.84921 ( 2673) Misc. bond : bond 0.00259 ( 1) link_ALPHA1-3 : bond 0.00950 ( 12) link_ALPHA1-3 : angle 2.32294 ( 36) link_ALPHA1-6 : bond 0.00699 ( 13) link_ALPHA1-6 : angle 1.51469 ( 39) link_BETA1-4 : bond 0.00802 ( 76) link_BETA1-4 : angle 2.53068 ( 228) link_NAG-ASN : bond 0.00694 ( 70) link_NAG-ASN : angle 2.82447 ( 210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 322 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 ARG cc_start: 0.8514 (tmm-80) cc_final: 0.8132 (ttm-80) REVERT: C 260 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8410 (mtp85) REVERT: C 267 SER cc_start: 0.9168 (m) cc_final: 0.8799 (p) REVERT: C 527 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: C 648 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8300 (tp30) REVERT: C 649 MET cc_start: 0.8946 (ttm) cc_final: 0.8734 (ttt) REVERT: C 803 ILE cc_start: 0.8612 (mt) cc_final: 0.8386 (mp) REVERT: C 814 ILE cc_start: 0.0300 (OUTLIER) cc_final: -0.0464 (mt) REVERT: C 843 ASN cc_start: 0.8487 (m-40) cc_final: 0.8177 (m110) REVERT: C 871 GLN cc_start: 0.8158 (mp-120) cc_final: 0.7947 (mp10) REVERT: C 1030 GLU cc_start: 0.8751 (tp30) cc_final: 0.8472 (mm-30) REVERT: A 39 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.7955 (p) REVERT: A 100 THR cc_start: 0.8400 (m) cc_final: 0.7780 (p) REVERT: A 218 ASN cc_start: 0.8754 (t0) cc_final: 0.7970 (t0) REVERT: A 297 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8190 (mtmm) REVERT: A 512 MET cc_start: 0.8962 (mtm) cc_final: 0.8738 (mtt) REVERT: A 515 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: A 616 ARG cc_start: 0.8190 (tpt170) cc_final: 0.7906 (tpt170) REVERT: A 642 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8332 (tt0) REVERT: A 648 GLU cc_start: 0.8665 (tp30) cc_final: 0.8194 (tp30) REVERT: A 674 ILE cc_start: 0.9099 (pt) cc_final: 0.8802 (mt) REVERT: A 786 GLN cc_start: 0.7470 (tt0) cc_final: 0.7220 (tt0) REVERT: A 798 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8149 (tppt) REVERT: A 811 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.6631 (t0) REVERT: A 1010 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8167 (mt-10) REVERT: L 50 ASP cc_start: 0.8292 (t0) cc_final: 0.7995 (t0) REVERT: L 70 ASP cc_start: 0.8411 (m-30) cc_final: 0.8177 (m-30) REVERT: L 107 LYS cc_start: 0.6278 (OUTLIER) cc_final: 0.4334 (tppt) REVERT: B 37 GLU cc_start: 0.8205 (pm20) cc_final: 0.7961 (pm20) REVERT: B 125 GLU cc_start: 0.7535 (tp30) cc_final: 0.6954 (mp0) REVERT: B 189 THR cc_start: 0.8902 (p) cc_final: 0.8510 (t) REVERT: B 464 THR cc_start: 0.8759 (p) cc_final: 0.8465 (t) REVERT: B 495 CYS cc_start: 0.8247 (t) cc_final: 0.8026 (t) REVERT: B 633 ASP cc_start: 0.8474 (m-30) cc_final: 0.8054 (m-30) REVERT: B 637 ASN cc_start: 0.8765 (m-40) cc_final: 0.8473 (m-40) REVERT: B 788 ASN cc_start: 0.7841 (t0) cc_final: 0.7139 (t0) REVERT: B 850 ARG cc_start: 0.8809 (mtm-85) cc_final: 0.8537 (mtm180) REVERT: B 878 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.6788 (mtm180) outliers start: 89 outliers final: 66 residues processed: 387 average time/residue: 0.5978 time to fit residues: 269.5515 Evaluate side-chains 386 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 312 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 732 MET Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 847 SER Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 ARG Chi-restraints excluded: chain B residue 969 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 151 optimal weight: 0.0770 chunk 230 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 277 optimal weight: 0.6980 chunk 17 optimal weight: 0.0170 chunk 84 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** C1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 309 HIS A 851 GLN L 90 GLN B 120 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.108385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.088657 restraints weight = 46642.067| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.74 r_work: 0.3058 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25819 Z= 0.135 Angle : 0.705 16.793 35478 Z= 0.333 Chirality : 0.047 0.380 4586 Planarity : 0.004 0.059 4225 Dihedral : 8.609 103.400 6733 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 3.00 % Allowed : 19.40 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 0.20 (0.15), residues: 2973 helix: 2.01 (0.20), residues: 658 sheet: 0.40 (0.20), residues: 601 loop : -0.73 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 61 TYR 0.021 0.001 TYR A 109 PHE 0.036 0.001 PHE C 108 TRP 0.015 0.001 TRP H 47 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00295 (25609) covalent geometry : angle 0.64600 (34889) SS BOND : bond 0.00331 ( 38) SS BOND : angle 1.22389 ( 76) hydrogen bonds : bond 0.04328 ( 936) hydrogen bonds : angle 4.70480 ( 2673) Misc. bond : bond 0.00210 ( 1) link_ALPHA1-3 : bond 0.01009 ( 12) link_ALPHA1-3 : angle 2.17793 ( 36) link_ALPHA1-6 : bond 0.00741 ( 13) link_ALPHA1-6 : angle 1.41497 ( 39) link_BETA1-4 : bond 0.00808 ( 76) link_BETA1-4 : angle 2.38271 ( 228) link_NAG-ASN : bond 0.00595 ( 70) link_NAG-ASN : angle 2.61645 ( 210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9764.67 seconds wall clock time: 167 minutes 6.45 seconds (10026.45 seconds total)