Starting phenix.real_space_refine on Fri Feb 6 23:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nby_49238/02_2026/9nby_49238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nby_49238/02_2026/9nby_49238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nby_49238/02_2026/9nby_49238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nby_49238/02_2026/9nby_49238.map" model { file = "/net/cci-nas-00/data/ceres_data/9nby_49238/02_2026/9nby_49238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nby_49238/02_2026/9nby_49238.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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 163 5.16 5 C 17850 2.51 5 N 4686 2.21 5 O 5890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28589 Number of models: 1 Model: "" Number of chains: 80 Chain: "G" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "H" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1020 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "J" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "L" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1020 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "M" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "N" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "O" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "Q" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "R" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1020 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "S" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1007 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "T" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3594 Classifications: {'peptide': 454} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Chain: "F" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1133 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain breaks: 1 Chain: "A" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3540 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "B" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1048 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3518 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 2 Chain: "D" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1026 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: 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: "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: 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 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: "o" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 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: "1" 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: "2" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 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: "6" 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: "7" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "8" Number of atoms: 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: "9" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "AA" 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: "BA" 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: "CA" 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: "DA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "EA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "FA" Number of atoms: 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: "GA" 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: "HA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "IA" Number of atoms: 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: "JA" 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: "KA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "LA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "MA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 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 Time building chain proxies: 6.26, per 1000 atoms: 0.22 Number of scatterers: 28589 At special positions: 0 Unit cell: (163.37, 153.884, 167.586, 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 163 16.00 O 5890 8.00 N 4686 7.00 C 17850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 32 " - pdb=" SG CYS I 98 " distance=2.11 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.20 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 32 " - pdb=" SG CYS M 98 " distance=2.06 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.17 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 32 " - pdb=" SG CYS P 98 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.02 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.06 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.11 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.18 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.07 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.15 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.10 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.06 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.14 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.16 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.08 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN r 4 " - " MAN r 5 " " MAN u 4 " - " MAN u 5 " " MAN u 5 " - " MAN u 6 " " MANDA 4 " - " MANDA 5 " " MANDA 5 " - " MANDA 6 " ALPHA1-3 " MAN 2 4 " - " MAN 2 5 " " BMA 8 3 " - " MAN 8 4 " " BMA 9 3 " - " MAN 9 7 " " MAN 9 4 " - " MAN 9 5 " " BMA c 3 " - " MAN c 6 " " MAN c 4 " - " MAN c 5 " " BMA f 3 " - " MAN f 4 " " MAN f 7 " - " MAN f 8 " " MAN n 4 " - " MAN n 5 " " BMA r 3 " - " MAN r 4 " " BMA u 3 " - " MAN u 4 " " MAN u 7 " - " MAN u 8 " " BMADA 3 " - " MANDA 4 " " MANDA 7 " - " MANDA 8 " ALPHA1-6 " BMA 2 3 " - " MAN 2 4 " " MAN 2 4 " - " MAN 2 6 " " BMA 8 3 " - " MAN 8 5 " " BMA 9 3 " - " MAN 9 4 " " MAN 9 4 " - " MAN 9 6 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 7 " " MAN f 7 " - " MAN f 9 " " BMA n 3 " - " MAN n 4 " " MAN n 4 " - " MAN n 6 " " BMA r 3 " - " MAN r 6 " " BMA u 3 " - " MAN u 7 " " MAN u 7 " - " MAN u 9 " " BMADA 3 " - " MANDA 7 " " MANDA 7 " - " MANDA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG 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 u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " 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 z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGIA 1 " - " NAGIA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGKA 1 " - " NAGKA 2 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " BETA1-6 " NAG o 1 " - " FUC o 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG 0 1 " - " ASN A 241 " " NAG 1 1 " - " ASN A 295 " " NAG 2 1 " - " ASN A 276 " " NAG 3 1 " - " ASN A 160 " " NAG 4 1 " - " ASN C 88 " " NAG 5 1 " - " ASN C 160 " " NAG 6 1 " - " ASN C 197 " " NAG 7 1 " - " ASN C 241 " " NAG 8 1 " - " ASN C 262 " " NAG 9 1 " - " ASN C 276 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 356 " " NAG A 604 " - " ASN A 396 " " NAG B 701 " - " ASN B 625 " " NAG C 601 " - " ASN C 463 " " NAG C 602 " - " ASN C 339 " " NAG E 601 " - " ASN E 339 " " NAG E 602 " - " ASN E 411 " " NAG J 301 " - " ASN J 72 " " NAG U 1 " - " ASN N 72 " " NAG V 1 " - " ASN O 72 " " NAG W 1 " - " ASN E 88 " " NAG X 1 " - " ASN E 130 " " NAG Y 1 " - " ASN E 156 " " NAG Z 1 " - " ASN E 160 " " NAG a 1 " - " ASN E 197 " " NAG b 1 " - " ASN E 241 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 289 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 332 " " NAG g 1 " - " ASN E 356 " " NAG h 1 " - " ASN E 362 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 392 " " NAG k 1 " - " ASN E 396 " " NAG l 1 " - " ASN E 448 " " NAG m 1 " - " ASN E 301 " " NAG n 1 " - " ASN E 276 " " NAG o 1 " - " ASN F 625 " " NAG p 1 " - " ASN A 130 " " NAG q 1 " - " ASN A 156 " " NAG r 1 " - " ASN A 262 " " NAG s 1 " - " ASN A 289 " " NAG t 1 " - " ASN A 301 " " NAG u 1 " - " ASN A 332 " " NAG v 1 " - " ASN A 362 " " NAG w 1 " - " ASN A 386 " " NAG x 1 " - " ASN A 392 " " NAG y 1 " - " ASN A 448 " " NAG z 1 " - " ASN A 197 " " NAGAA 1 " - " ASN C 289 " " NAGBA 1 " - " ASN C 295 " " NAGCA 1 " - " ASN C 301 " " NAGDA 1 " - " ASN C 332 " " NAGEA 1 " - " ASN C 362 " " NAGFA 1 " - " ASN C 386 " " NAGGA 1 " - " ASN C 392 " " NAGHA 1 " - " ASN C 396 " " NAGIA 1 " - " ASN C 130 " " NAGJA 1 " - " ASN C 156 " " NAGKA 1 " - " ASN C 448 " " NAGLA 1 " - " ASN C 356 " " NAGMA 1 " - " ASN D 625 " Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6154 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 52 sheets defined 19.0% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.593A pdb=" N SER H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.933A pdb=" N PHE J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.670A pdb=" N ASP L 31 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 100D through 100H Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.673A pdb=" N CYS M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.968A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.581A pdb=" N PHE O 83 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.618A pdb=" N CYS P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.937A pdb=" N SER R 32 " --> pdb=" O ILE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'R' and resid 100D through 100H Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.501A pdb=" N TYR S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 64 Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'S' and resid 100E through 100I removed outlier: 3.561A pdb=" N PHE S 100I" --> pdb=" O SER S 100F" (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.629A pdb=" N GLU T 83 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.003A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 396 through 405 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.785A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 528 removed outlier: 3.727A pdb=" N PHE F 522 " --> pdb=" O PHE F 519 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY F 524 " --> pdb=" O GLY F 521 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 539 Processing helix chain 'F' and resid 545 through 553 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.576A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.082A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.881A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.590A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.623A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.212A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.844A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.540A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.567A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing sheet with id=AA1, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.394A pdb=" N ILE G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR G 86 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR G 103 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA G 84 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 19 through 23 removed outlier: 3.576A pdb=" N ALA G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 59 current: chain 'H' and resid 100J through 101 Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 46 through 52 removed outlier: 4.152A pdb=" N ALA I 56 " --> pdb=" O LYS I 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 56 through 59 current: chain 'I' and resid 102 through 103 Processing sheet with id=AA7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.553A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.736A pdb=" N ILE K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR K 86 " --> pdb=" O GLY K 101 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AB2, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 33 through 40 removed outlier: 6.881A pdb=" N TRP L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR L 50 " --> pdb=" O TRP L 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 58 through 59 current: chain 'L' and resid 100J through 101 Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 12 current: chain 'M' and resid 46 through 52 removed outlier: 4.127A pdb=" N ALA M 56 " --> pdb=" O LYS M 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 56 through 59 current: chain 'M' and resid 102 through 103 Processing sheet with id=AB7, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.560A pdb=" N TRP N 35 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.509A pdb=" N TRP O 35 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'P' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 10 through 12 current: chain 'P' and resid 46 through 52 removed outlier: 4.174A pdb=" N ALA P 56 " --> pdb=" O LYS P 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 56 through 59 current: chain 'P' and resid 102 through 103 Processing sheet with id=AC4, first strand: chain 'Q' and resid 11 through 13 removed outlier: 6.766A pdb=" N ILE Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR Q 86 " --> pdb=" O GLY Q 101 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR Q 103 " --> pdb=" O ALA Q 84 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA Q 84 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP Q 35 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 19 through 23 removed outlier: 3.640A pdb=" N ALA Q 71 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'R' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 11 through 12 current: chain 'R' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 58 through 59 current: chain 'R' and resid 100J through 101 Processing sheet with id=AC8, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'S' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 10 through 12 current: chain 'S' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 57 through 59 current: chain 'S' and resid 100K through 103 Processing sheet with id=AD1, first strand: chain 'T' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 9 through 13 current: chain 'T' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 45 through 48 current: chain 'T' and resid 95A through 98 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'T' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.283A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.603A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD8, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.990A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.726A pdb=" N ASN E 301 " --> pdb=" O ILE E 322A" (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE E 322A" --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 322A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AE1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.211A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.843A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AE4, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.777A pdb=" N ARG A 66 " --> pdb=" O THR A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AE6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AE7, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.951A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.951A pdb=" N ASN A 301 " --> pdb=" O ILE A 322A" (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE A 322A" --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AE9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.308A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.270A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.063A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AF4, first strand: chain 'C' and resid 170 through 177 removed outlier: 3.504A pdb=" N GLN C 170 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.933A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 298 removed outlier: 7.017A pdb=" N VAL C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 334 " --> pdb=" O VAL C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 329 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AF7, first strand: chain 'C' and resid 301 through 308 removed outlier: 6.873A pdb=" N ASN C 301 " --> pdb=" O ILE C 322A" (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE C 322A" --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) 814 hydrogen bonds defined for protein. 2034 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: 5.46 Time building geometry restraints manager: 3.70 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: 6041 1.33 - 1.45: 8088 1.45 - 1.58: 14828 1.58 - 1.71: 0 1.71 - 1.84: 225 Bond restraints: 29182 Sorted by residual: bond pdb=" NE ARG H 66 " pdb=" CZ ARG H 66 " ideal model delta sigma weight residual 1.326 1.359 -0.033 1.10e-02 8.26e+03 8.95e+00 bond pdb=" CB HIS S 35 " pdb=" CG HIS S 35 " ideal model delta sigma weight residual 1.497 1.457 0.040 1.40e-02 5.10e+03 8.34e+00 bond pdb=" NE ARG N 54 " pdb=" CZ ARG N 54 " ideal model delta sigma weight residual 1.326 1.357 -0.031 1.10e-02 8.26e+03 8.05e+00 bond pdb=" NE ARG G 94 " pdb=" CZ ARG G 94 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.64e+00 bond pdb=" CG ASP E 397 " pdb=" OD1 ASP E 397 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.12e+00 ... (remaining 29177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 34339 1.70 - 3.40: 4336 3.40 - 5.11: 729 5.11 - 6.81: 206 6.81 - 8.51: 34 Bond angle restraints: 39644 Sorted by residual: angle pdb=" C LYS M 52 " pdb=" N PRO M 52A" pdb=" CA PRO M 52A" ideal model delta sigma weight residual 119.56 128.07 -8.51 1.02e+00 9.61e-01 6.96e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 125.66 -6.00 7.30e-01 1.88e+00 6.75e+01 angle pdb=" C GLY N 68 " pdb=" N PRO N 69 " pdb=" CA PRO N 69 " ideal model delta sigma weight residual 119.56 127.87 -8.31 1.02e+00 9.61e-01 6.64e+01 angle pdb=" C LYS I 52 " pdb=" N PRO I 52A" pdb=" CA PRO I 52A" ideal model delta sigma weight residual 119.56 127.86 -8.30 1.02e+00 9.61e-01 6.63e+01 angle pdb=" C LYS P 52 " pdb=" N PRO P 52A" pdb=" CA PRO P 52A" ideal model delta sigma weight residual 119.56 127.85 -8.29 1.02e+00 9.61e-01 6.60e+01 ... (remaining 39639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 18879 21.32 - 42.64: 394 42.64 - 63.96: 122 63.96 - 85.28: 131 85.28 - 106.60: 65 Dihedral angle restraints: 19591 sinusoidal: 9986 harmonic: 9605 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual -86.00 -154.57 68.57 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS R 22 " pdb=" SG CYS R 22 " pdb=" SG CYS R 92 " pdb=" CB CYS R 92 " ideal model delta sinusoidal sigma weight residual 93.00 45.83 47.17 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -129.11 43.11 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 19588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 4829 0.228 - 0.455: 61 0.455 - 0.683: 2 0.683 - 0.910: 0 0.910 - 1.138: 1 Chirality restraints: 4893 Sorted by residual: chirality pdb=" C1 NAGLA 2 " pdb=" O4 NAGLA 1 " pdb=" C2 NAGLA 2 " pdb=" O5 NAGLA 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.26 -1.14 2.00e-02 2.50e+03 3.24e+03 chirality pdb=" C1 BMA 8 3 " pdb=" O4 NAG 8 2 " pdb=" C2 BMA 8 3 " pdb=" O5 BMA 8 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-02 2.50e+03 7.64e+02 chirality pdb=" C1 MAN u 8 " pdb=" O3 MAN u 7 " pdb=" C2 MAN u 8 " pdb=" O5 MAN u 8 " both_signs ideal model delta sigma weight residual False 2.40 1.88 0.52 2.00e-02 2.50e+03 6.79e+02 ... (remaining 4890 not shown) Planarity restraints: 4887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 72 " 0.060 2.00e-02 2.50e+03 6.17e-02 4.76e+01 pdb=" CG ASN J 72 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN J 72 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN J 72 " -0.095 2.00e-02 2.50e+03 pdb=" C1 NAG J 301 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 332 " -0.059 2.00e-02 2.50e+03 6.14e-02 4.71e+01 pdb=" CG ASN C 332 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 332 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 332 " 0.096 2.00e-02 2.50e+03 pdb=" C1 NAGDA 1 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 332 " -0.055 2.00e-02 2.50e+03 5.71e-02 4.07e+01 pdb=" CG ASN A 332 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 332 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 332 " 0.090 2.00e-02 2.50e+03 pdb=" C1 NAG u 1 " -0.068 2.00e-02 2.50e+03 ... (remaining 4884 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 12150 2.90 - 3.40: 23821 3.40 - 3.90: 48742 3.90 - 4.40: 53487 4.40 - 4.90: 90034 Nonbonded interactions: 228234 Sorted by model distance: nonbonded pdb=" O3 NAG w 1 " pdb=" O5 NAG w 2 " model vdw 2.405 3.040 nonbonded pdb=" O3 NAG 6 2 " pdb=" O5 BMA 6 3 " model vdw 2.407 3.040 nonbonded pdb=" O3 NAG o 2 " pdb=" O5 BMA o 3 " model vdw 2.420 3.040 nonbonded pdb=" O3 NAG h 1 " pdb=" O5 NAG h 2 " model vdw 2.445 3.040 nonbonded pdb=" N ASN K 51 " pdb=" OD1 ASN K 51 " model vdw 2.458 3.120 ... (remaining 228229 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 '1' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain 'AA' selection = chain 'BA' selection = chain 'CA' selection = chain 'EA' selection = chain 'FA' selection = chain 'GA' selection = chain 'HA' selection = chain 'IA' selection = chain 'JA' selection = chain 'KA' selection = chain 'LA' selection = chain 'MA' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = (chain '2' and (resid 1 or resid 4 through 6)) selection = (chain '9' and (resid 2 or resid 5 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 6)) selection = (chain 'n' and (resid 1 or resid 4 through 6)) selection = (chain 'r' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain '6' selection = chain '7' selection = chain 'W' selection = chain 'b' selection = chain 'e' selection = chain 'z' } ncs_group { reference = (chain 'A' and (resid 32 through 59 or resid 67 through 151 or resid 153 through \ 505)) selection = (chain 'C' and resid 32 through 505) selection = (chain 'E' and (resid 32 through 59 or resid 67 through 505)) } ncs_group { reference = (chain 'B' and (resid 518 through 546 or resid 568 through 664)) selection = (chain 'D' and (resid 518 through 546 or resid 568 through 664)) selection = (chain 'F' and (resid 518 through 546 or resid 568 through 664)) } ncs_group { reference = chain 'DA' selection = chain 'f' selection = chain 'u' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = chain 'L' selection = chain 'R' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'P' } ncs_group { reference = (chain 'J' and resid 3 through 107) selection = chain 'N' selection = chain 'O' } 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.350 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.164 29405 Z= 0.677 Angle : 1.437 18.359 40263 Z= 0.840 Chirality : 0.075 1.138 4893 Planarity : 0.005 0.036 4822 Dihedral : 13.601 106.600 13287 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.07 % Allowed : 0.79 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % 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: 2.88 (0.14), residues: 3298 helix: 0.18 (0.20), residues: 440 sheet: 1.68 (0.15), residues: 1031 loop : 2.86 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 66 TYR 0.044 0.005 TYR T 36 PHE 0.024 0.004 PHE K 98 TRP 0.031 0.005 TRP E 427 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.01193 (29182) covalent geometry : angle 1.25872 (39644) SS BOND : bond 0.05199 ( 50) SS BOND : angle 3.84739 ( 100) hydrogen bonds : bond 0.18628 ( 814) hydrogen bonds : angle 7.77962 ( 2034) link_ALPHA1-2 : bond 0.04696 ( 7) link_ALPHA1-2 : angle 6.57777 ( 21) link_ALPHA1-3 : bond 0.04741 ( 14) link_ALPHA1-3 : angle 5.09471 ( 42) link_ALPHA1-6 : bond 0.03740 ( 15) link_ALPHA1-6 : angle 4.19755 ( 45) link_BETA1-4 : bond 0.04713 ( 71) link_BETA1-4 : angle 7.47843 ( 213) link_BETA1-6 : bond 0.03724 ( 1) link_BETA1-6 : angle 2.88339 ( 3) link_NAG-ASN : bond 0.06860 ( 65) link_NAG-ASN : angle 4.61323 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 734 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 44 PRO cc_start: 0.7713 (Cg_exo) cc_final: 0.7383 (Cg_endo) REVERT: H 47 TRP cc_start: 0.7344 (t60) cc_final: 0.6171 (t60) REVERT: H 50 TYR cc_start: 0.6967 (p90) cc_final: 0.6294 (p90) REVERT: H 100 MET cc_start: 0.4545 (mpt) cc_final: 0.4316 (mpp) REVERT: I 31 ASP cc_start: 0.7760 (m-30) cc_final: 0.7297 (m-30) REVERT: L 92 CYS cc_start: 0.4350 (t) cc_final: 0.3230 (t) REVERT: L 100 THR cc_start: 0.7323 (m) cc_final: 0.6787 (t) REVERT: M 12 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7536 (mmmt) REVERT: P 48 MET cc_start: 0.8607 (mtp) cc_final: 0.8358 (mtm) REVERT: Q 31 ARG cc_start: 0.5231 (ptt180) cc_final: 0.4767 (mtm180) REVERT: Q 46 LEU cc_start: 0.5063 (tp) cc_final: 0.4793 (tp) REVERT: Q 67 SER cc_start: 0.7995 (p) cc_final: 0.7562 (t) REVERT: R 46 GLU cc_start: 0.5185 (tt0) cc_final: 0.4672 (mp0) REVERT: R 50 TYR cc_start: 0.4600 (m-80) cc_final: 0.3462 (m-10) REVERT: E 114 GLN cc_start: 0.8298 (tt0) cc_final: 0.8079 (tt0) REVERT: F 518 MET cc_start: 0.6858 (mpp) cc_final: 0.6425 (mtm) REVERT: A 315 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7525 (mtm180) REVERT: B 518 MET cc_start: 0.2787 (mmm) cc_final: 0.2330 (mtt) REVERT: C 336 THR cc_start: 0.8749 (m) cc_final: 0.8538 (p) outliers start: 2 outliers final: 0 residues processed: 735 average time/residue: 0.2075 time to fit residues: 229.9179 Evaluate side-chains 421 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 34 GLN P 102 HIS Q 50 ASN R 100HASN S 35 HIS E 249 HIS A 249 HIS B 540 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 67 ASN D 652 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.168789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133083 restraints weight = 40049.196| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.47 r_work: 0.3319 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29405 Z= 0.148 Angle : 0.727 13.594 40263 Z= 0.341 Chirality : 0.048 0.893 4893 Planarity : 0.004 0.046 4822 Dihedral : 10.315 79.540 7158 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.72 % Allowed : 6.77 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 2.48 (0.14), residues: 3298 helix: 1.98 (0.24), residues: 436 sheet: 1.33 (0.14), residues: 1105 loop : 2.03 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 71 TYR 0.027 0.001 TYR N 49 PHE 0.027 0.002 PHE N 62 TRP 0.033 0.002 TRP Q 35 HIS 0.010 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00327 (29182) covalent geometry : angle 0.66993 (39644) SS BOND : bond 0.00348 ( 50) SS BOND : angle 1.56946 ( 100) hydrogen bonds : bond 0.05054 ( 814) hydrogen bonds : angle 5.93169 ( 2034) link_ALPHA1-2 : bond 0.00562 ( 7) link_ALPHA1-2 : angle 2.02614 ( 21) link_ALPHA1-3 : bond 0.00970 ( 14) link_ALPHA1-3 : angle 2.06145 ( 42) link_ALPHA1-6 : bond 0.00520 ( 15) link_ALPHA1-6 : angle 1.52214 ( 45) link_BETA1-4 : bond 0.00503 ( 71) link_BETA1-4 : angle 2.44331 ( 213) link_BETA1-6 : bond 0.00360 ( 1) link_BETA1-6 : angle 1.23708 ( 3) link_NAG-ASN : bond 0.00829 ( 65) link_NAG-ASN : angle 2.85833 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 473 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 87 TYR cc_start: 0.7208 (m-80) cc_final: 0.6977 (m-10) REVERT: H 36 TRP cc_start: 0.5704 (m100) cc_final: 0.4626 (m100) REVERT: H 47 TRP cc_start: 0.7867 (t60) cc_final: 0.7222 (t60) REVERT: H 50 TYR cc_start: 0.7525 (p90) cc_final: 0.7173 (p90) REVERT: H 94 ARG cc_start: 0.6657 (tmm-80) cc_final: 0.6403 (ttp80) REVERT: H 100 MET cc_start: 0.5648 (mpt) cc_final: 0.5340 (mpp) REVERT: I 31 ASP cc_start: 0.8292 (m-30) cc_final: 0.7898 (m-30) REVERT: K 35 TRP cc_start: 0.7688 (m100) cc_final: 0.7477 (m100) REVERT: K 90 ILE cc_start: 0.7584 (mm) cc_final: 0.7265 (mt) REVERT: L 100 THR cc_start: 0.8146 (m) cc_final: 0.7930 (t) REVERT: M 12 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7365 (mmmt) REVERT: M 86 ASP cc_start: 0.7627 (m-30) cc_final: 0.6906 (m-30) REVERT: N 100 GLN cc_start: 0.7652 (pm20) cc_final: 0.7326 (pm20) REVERT: O 60 ASP cc_start: 0.7710 (t0) cc_final: 0.7487 (t0) REVERT: O 71 TYR cc_start: 0.9077 (m-80) cc_final: 0.8655 (m-80) REVERT: O 77 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.6810 (t0) REVERT: Q 31 ARG cc_start: 0.6634 (ptt180) cc_final: 0.6405 (ptm-80) REVERT: Q 48 ILE cc_start: 0.6426 (mm) cc_final: 0.5738 (tp) REVERT: Q 67 SER cc_start: 0.7996 (p) cc_final: 0.7588 (t) REVERT: R 46 GLU cc_start: 0.6391 (tt0) cc_final: 0.5338 (mp0) REVERT: R 69 LEU cc_start: 0.4595 (OUTLIER) cc_final: 0.4308 (mt) REVERT: R 99 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7072 (ttp-170) REVERT: F 543 ASN cc_start: 0.7764 (t0) cc_final: 0.7554 (t0) REVERT: F 589 ASP cc_start: 0.8446 (m-30) cc_final: 0.8146 (m-30) REVERT: A 117 LYS cc_start: 0.8296 (ttpp) cc_final: 0.8071 (pttp) REVERT: A 315 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7739 (mtm110) REVERT: C 191 TYR cc_start: 0.8636 (m-80) cc_final: 0.8400 (m-80) REVERT: D 636 ASP cc_start: 0.8357 (t0) cc_final: 0.8131 (t0) outliers start: 50 outliers final: 31 residues processed: 506 average time/residue: 0.2048 time to fit residues: 159.1887 Evaluate side-chains 421 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 387 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 625 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 254 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 235 optimal weight: 0.8980 chunk 240 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 316 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 102 HIS J 37 GLN L 97 HIS ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 HIS Q 50 ASN F 550 GLN C 302 ASN D 652 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.163472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127359 restraints weight = 40082.360| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.55 r_work: 0.3222 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29405 Z= 0.196 Angle : 0.687 12.833 40263 Z= 0.328 Chirality : 0.046 0.302 4893 Planarity : 0.004 0.048 4822 Dihedral : 8.971 82.927 7158 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 8.17 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.14), residues: 3298 helix: 1.88 (0.24), residues: 452 sheet: 1.02 (0.15), residues: 1098 loop : 1.56 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 504 TYR 0.022 0.001 TYR N 49 PHE 0.016 0.002 PHE O 98 TRP 0.033 0.002 TRP Q 35 HIS 0.007 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00458 (29182) covalent geometry : angle 0.63533 (39644) SS BOND : bond 0.00813 ( 50) SS BOND : angle 1.97742 ( 100) hydrogen bonds : bond 0.04552 ( 814) hydrogen bonds : angle 5.48985 ( 2034) link_ALPHA1-2 : bond 0.00287 ( 7) link_ALPHA1-2 : angle 1.88213 ( 21) link_ALPHA1-3 : bond 0.00877 ( 14) link_ALPHA1-3 : angle 1.97206 ( 42) link_ALPHA1-6 : bond 0.00458 ( 15) link_ALPHA1-6 : angle 1.64272 ( 45) link_BETA1-4 : bond 0.00498 ( 71) link_BETA1-4 : angle 2.20318 ( 213) link_BETA1-6 : bond 0.00271 ( 1) link_BETA1-6 : angle 1.33040 ( 3) link_NAG-ASN : bond 0.00519 ( 65) link_NAG-ASN : angle 2.50541 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 404 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.5919 (m100) cc_final: 0.4843 (m100) REVERT: H 47 TRP cc_start: 0.8018 (t60) cc_final: 0.7463 (t60) REVERT: J 37 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: K 90 ILE cc_start: 0.7589 (mm) cc_final: 0.7325 (mt) REVERT: L 7 SER cc_start: 0.7017 (m) cc_final: 0.6488 (t) REVERT: M 12 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7319 (mmmt) REVERT: M 86 ASP cc_start: 0.7797 (m-30) cc_final: 0.7094 (m-30) REVERT: N 100 GLN cc_start: 0.7837 (pm20) cc_final: 0.7468 (pm20) REVERT: O 60 ASP cc_start: 0.7853 (t0) cc_final: 0.7464 (t0) REVERT: O 77 ASN cc_start: 0.7501 (m-40) cc_final: 0.6792 (t0) REVERT: Q 67 SER cc_start: 0.8059 (p) cc_final: 0.7673 (t) REVERT: R 46 GLU cc_start: 0.6477 (tt0) cc_final: 0.5375 (mp0) REVERT: R 91 TYR cc_start: 0.4541 (m-80) cc_final: 0.4248 (m-10) REVERT: T 60 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7311 (tm-30) REVERT: F 543 ASN cc_start: 0.7804 (t0) cc_final: 0.7590 (t0) REVERT: F 589 ASP cc_start: 0.8479 (m-30) cc_final: 0.8110 (m-30) REVERT: A 190 ASN cc_start: 0.8219 (m-40) cc_final: 0.7870 (p0) REVERT: B 588 ARG cc_start: 0.8219 (tpt170) cc_final: 0.7915 (ttm110) REVERT: B 656 ASN cc_start: 0.8467 (m-40) cc_final: 0.8164 (m-40) REVERT: D 636 ASP cc_start: 0.8554 (t0) cc_final: 0.8295 (t0) outliers start: 78 outliers final: 44 residues processed: 457 average time/residue: 0.1970 time to fit residues: 138.6563 Evaluate side-chains 416 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 371 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 637 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 138 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 209 optimal weight: 0.5980 chunk 255 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 89 HIS ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN Q 50 ASN E 190 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.161921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125525 restraints weight = 39952.766| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.40 r_work: 0.3200 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29405 Z= 0.188 Angle : 0.652 10.246 40263 Z= 0.308 Chirality : 0.046 0.400 4893 Planarity : 0.004 0.048 4822 Dihedral : 8.162 82.928 7158 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.37 % Allowed : 9.31 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.14), residues: 3298 helix: 1.92 (0.24), residues: 454 sheet: 0.88 (0.15), residues: 1089 loop : 1.28 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 61 TYR 0.023 0.002 TYR N 49 PHE 0.015 0.002 PHE O 98 TRP 0.017 0.002 TRP I 50 HIS 0.007 0.001 HIS Q 89 Details of bonding type rmsd covalent geometry : bond 0.00450 (29182) covalent geometry : angle 0.60708 (39644) SS BOND : bond 0.00405 ( 50) SS BOND : angle 1.62335 ( 100) hydrogen bonds : bond 0.04205 ( 814) hydrogen bonds : angle 5.28709 ( 2034) link_ALPHA1-2 : bond 0.00430 ( 7) link_ALPHA1-2 : angle 1.81574 ( 21) link_ALPHA1-3 : bond 0.00793 ( 14) link_ALPHA1-3 : angle 1.93881 ( 42) link_ALPHA1-6 : bond 0.00555 ( 15) link_ALPHA1-6 : angle 1.64659 ( 45) link_BETA1-4 : bond 0.00454 ( 71) link_BETA1-4 : angle 2.00474 ( 213) link_BETA1-6 : bond 0.00284 ( 1) link_BETA1-6 : angle 1.37709 ( 3) link_NAG-ASN : bond 0.00420 ( 65) link_NAG-ASN : angle 2.30559 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 400 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.6023 (m100) cc_final: 0.5053 (m100) REVERT: H 47 TRP cc_start: 0.7916 (t60) cc_final: 0.7441 (t60) REVERT: I 18 MET cc_start: 0.8303 (ptt) cc_final: 0.8040 (ptt) REVERT: J 79 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6780 (mt-10) REVERT: K 35 TRP cc_start: 0.7745 (m100) cc_final: 0.7351 (m100) REVERT: K 50 ASN cc_start: 0.6526 (t0) cc_final: 0.6097 (t0) REVERT: K 90 ILE cc_start: 0.7583 (mm) cc_final: 0.7298 (mt) REVERT: L 7 SER cc_start: 0.7018 (m) cc_final: 0.6479 (t) REVERT: M 12 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7303 (mmmt) REVERT: M 86 ASP cc_start: 0.7745 (m-30) cc_final: 0.7033 (m-30) REVERT: N 79 GLU cc_start: 0.6929 (mp0) cc_final: 0.6594 (mp0) REVERT: N 100 GLN cc_start: 0.7892 (pm20) cc_final: 0.7537 (pm20) REVERT: O 60 ASP cc_start: 0.7951 (t0) cc_final: 0.7610 (t0) REVERT: O 77 ASN cc_start: 0.7555 (m-40) cc_final: 0.6785 (t0) REVERT: P 51 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9063 (tp) REVERT: Q 31 ARG cc_start: 0.6775 (ptm-80) cc_final: 0.6466 (ptm-80) REVERT: Q 67 SER cc_start: 0.8135 (p) cc_final: 0.7779 (t) REVERT: R 46 GLU cc_start: 0.6592 (tt0) cc_final: 0.5454 (mp0) REVERT: T 60 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7282 (tm-30) REVERT: F 543 ASN cc_start: 0.7797 (t0) cc_final: 0.7521 (t0) REVERT: F 589 ASP cc_start: 0.8501 (m-30) cc_final: 0.8131 (m-30) REVERT: B 588 ARG cc_start: 0.8193 (tpt170) cc_final: 0.7887 (ttm110) REVERT: B 654 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 656 ASN cc_start: 0.8404 (m-40) cc_final: 0.8149 (m-40) REVERT: D 636 ASP cc_start: 0.8565 (t0) cc_final: 0.8293 (t0) outliers start: 69 outliers final: 48 residues processed: 444 average time/residue: 0.1911 time to fit residues: 131.2499 Evaluate side-chains 419 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 370 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 637 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 3 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 182 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 324 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 100AASN J 37 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN Q 50 ASN S 43 GLN C 229 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.163481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118772 restraints weight = 40924.788| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.18 r_work: 0.3242 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 29405 Z= 0.288 Angle : 0.729 10.179 40263 Z= 0.345 Chirality : 0.048 0.242 4893 Planarity : 0.005 0.050 4822 Dihedral : 8.292 86.626 7158 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.26 % Allowed : 9.79 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.14), residues: 3298 helix: 1.63 (0.24), residues: 448 sheet: 0.67 (0.15), residues: 1068 loop : 0.92 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 503 TYR 0.021 0.002 TYR G 87 PHE 0.018 0.002 PHE E 159 TRP 0.022 0.002 TRP P 100B HIS 0.007 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00700 (29182) covalent geometry : angle 0.68423 (39644) SS BOND : bond 0.00610 ( 50) SS BOND : angle 1.84240 ( 100) hydrogen bonds : bond 0.04780 ( 814) hydrogen bonds : angle 5.35314 ( 2034) link_ALPHA1-2 : bond 0.00505 ( 7) link_ALPHA1-2 : angle 1.89156 ( 21) link_ALPHA1-3 : bond 0.00719 ( 14) link_ALPHA1-3 : angle 2.01958 ( 42) link_ALPHA1-6 : bond 0.00557 ( 15) link_ALPHA1-6 : angle 1.64967 ( 45) link_BETA1-4 : bond 0.00469 ( 71) link_BETA1-4 : angle 2.07049 ( 213) link_BETA1-6 : bond 0.00126 ( 1) link_BETA1-6 : angle 1.51646 ( 3) link_NAG-ASN : bond 0.00617 ( 65) link_NAG-ASN : angle 2.48549 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 383 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 MET cc_start: 0.6863 (mmp) cc_final: 0.6624 (mmm) REVERT: H 47 TRP cc_start: 0.8004 (t60) cc_final: 0.7649 (t60) REVERT: H 69 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5507 (tt) REVERT: I 18 MET cc_start: 0.8748 (ptt) cc_final: 0.8441 (ptt) REVERT: J 54 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8371 (ttm-80) REVERT: J 79 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6629 (mt-10) REVERT: K 50 ASN cc_start: 0.6391 (t0) cc_final: 0.5774 (t0) REVERT: K 90 ILE cc_start: 0.7563 (mm) cc_final: 0.7358 (mt) REVERT: L 7 SER cc_start: 0.7239 (m) cc_final: 0.6664 (t) REVERT: M 12 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7963 (mmmt) REVERT: M 72 ASP cc_start: 0.8128 (t0) cc_final: 0.7857 (t70) REVERT: M 86 ASP cc_start: 0.7772 (m-30) cc_final: 0.7024 (m-30) REVERT: N 79 GLU cc_start: 0.6974 (mp0) cc_final: 0.6597 (mp0) REVERT: N 100 GLN cc_start: 0.7976 (pm20) cc_final: 0.7553 (pm20) REVERT: O 60 ASP cc_start: 0.8244 (t0) cc_final: 0.7983 (t0) REVERT: O 77 ASN cc_start: 0.7354 (m-40) cc_final: 0.6510 (t0) REVERT: O 96 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8847 (pt0) REVERT: P 51 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9165 (tp) REVERT: Q 31 ARG cc_start: 0.6903 (ptm-80) cc_final: 0.6411 (ptm160) REVERT: Q 67 SER cc_start: 0.8222 (p) cc_final: 0.7839 (t) REVERT: R 46 GLU cc_start: 0.6522 (tt0) cc_final: 0.5398 (mp0) REVERT: R 50 TYR cc_start: 0.5151 (m-80) cc_final: 0.4722 (m-80) REVERT: T 60 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7161 (tm-30) REVERT: F 543 ASN cc_start: 0.8263 (t0) cc_final: 0.7824 (t0) REVERT: F 574 LYS cc_start: 0.8581 (mttm) cc_final: 0.8255 (mtpt) REVERT: F 589 ASP cc_start: 0.8894 (m-30) cc_final: 0.8524 (m-30) REVERT: B 588 ARG cc_start: 0.8323 (tpt170) cc_final: 0.7731 (ttm110) REVERT: B 626 MET cc_start: 0.8473 (mtp) cc_final: 0.8252 (mtm) REVERT: B 654 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7794 (mm-30) REVERT: C 108 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8519 (mm) REVERT: D 535 MET cc_start: 0.8759 (mpp) cc_final: 0.8542 (mtt) REVERT: D 636 ASP cc_start: 0.8777 (t0) cc_final: 0.8529 (t0) outliers start: 95 outliers final: 68 residues processed: 454 average time/residue: 0.2149 time to fit residues: 149.8918 Evaluate side-chains 430 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 358 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 43 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 637 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 274 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 204 optimal weight: 0.6980 chunk 285 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 279 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.162268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122142 restraints weight = 40681.194| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.33 r_work: 0.3191 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29405 Z= 0.234 Angle : 0.675 9.222 40263 Z= 0.320 Chirality : 0.046 0.245 4893 Planarity : 0.004 0.047 4822 Dihedral : 8.079 85.760 7158 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.16 % Allowed : 10.61 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 3298 helix: 1.68 (0.24), residues: 448 sheet: 0.61 (0.15), residues: 1067 loop : 0.81 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 419 TYR 0.022 0.002 TYR G 87 PHE 0.014 0.002 PHE E 159 TRP 0.022 0.002 TRP S 50 HIS 0.005 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00566 (29182) covalent geometry : angle 0.63285 (39644) SS BOND : bond 0.00479 ( 50) SS BOND : angle 1.67385 ( 100) hydrogen bonds : bond 0.04413 ( 814) hydrogen bonds : angle 5.27335 ( 2034) link_ALPHA1-2 : bond 0.00500 ( 7) link_ALPHA1-2 : angle 1.82338 ( 21) link_ALPHA1-3 : bond 0.00744 ( 14) link_ALPHA1-3 : angle 1.97030 ( 42) link_ALPHA1-6 : bond 0.00578 ( 15) link_ALPHA1-6 : angle 1.64966 ( 45) link_BETA1-4 : bond 0.00437 ( 71) link_BETA1-4 : angle 1.90538 ( 213) link_BETA1-6 : bond 0.00233 ( 1) link_BETA1-6 : angle 1.42805 ( 3) link_NAG-ASN : bond 0.00484 ( 65) link_NAG-ASN : angle 2.31379 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 372 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.6115 (m100) cc_final: 0.5328 (m100) REVERT: H 47 TRP cc_start: 0.8015 (t60) cc_final: 0.7754 (t60) REVERT: H 51 VAL cc_start: 0.7707 (p) cc_final: 0.7093 (t) REVERT: H 69 LEU cc_start: 0.5611 (OUTLIER) cc_final: 0.5300 (tt) REVERT: I 6 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: I 18 MET cc_start: 0.8549 (ptt) cc_final: 0.8238 (ptt) REVERT: J 54 ARG cc_start: 0.8549 (ttm110) cc_final: 0.8249 (ttm-80) REVERT: J 79 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6685 (mt-10) REVERT: K 50 ASN cc_start: 0.6457 (t0) cc_final: 0.5886 (t0) REVERT: L 7 SER cc_start: 0.7233 (m) cc_final: 0.6700 (t) REVERT: L 50 TYR cc_start: 0.6979 (m-80) cc_final: 0.6689 (m-80) REVERT: M 72 ASP cc_start: 0.8124 (t0) cc_final: 0.7898 (t0) REVERT: M 86 ASP cc_start: 0.7905 (m-30) cc_final: 0.7309 (m-30) REVERT: N 72 ASN cc_start: 0.6441 (m-40) cc_final: 0.6167 (m-40) REVERT: N 79 GLU cc_start: 0.6788 (mp0) cc_final: 0.6447 (mp0) REVERT: N 100 GLN cc_start: 0.7928 (pm20) cc_final: 0.7565 (pm20) REVERT: O 60 ASP cc_start: 0.8158 (t0) cc_final: 0.7871 (t0) REVERT: O 77 ASN cc_start: 0.7331 (m-40) cc_final: 0.6541 (t0) REVERT: O 96 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8723 (pt0) REVERT: Q 31 ARG cc_start: 0.6935 (ptm-80) cc_final: 0.6467 (ptm160) REVERT: Q 67 SER cc_start: 0.8214 (p) cc_final: 0.7836 (t) REVERT: R 46 GLU cc_start: 0.6593 (tt0) cc_final: 0.5429 (mp0) REVERT: R 69 LEU cc_start: 0.3447 (OUTLIER) cc_final: 0.3113 (tp) REVERT: T 37 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7817 (pp30) REVERT: T 60 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7204 (tm-30) REVERT: F 543 ASN cc_start: 0.8113 (t0) cc_final: 0.7723 (t0) REVERT: F 574 LYS cc_start: 0.8519 (mttm) cc_final: 0.8229 (mtpt) REVERT: F 589 ASP cc_start: 0.8658 (m-30) cc_final: 0.8262 (m-30) REVERT: F 624 ASN cc_start: 0.9278 (OUTLIER) cc_final: 0.8969 (m-40) REVERT: B 588 ARG cc_start: 0.8194 (tpt170) cc_final: 0.7667 (ttm110) REVERT: B 616 ASN cc_start: 0.7599 (p0) cc_final: 0.7228 (p0) REVERT: B 654 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7706 (mm-30) REVERT: C 442 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: D 535 MET cc_start: 0.8576 (mpp) cc_final: 0.8370 (mtt) REVERT: D 636 ASP cc_start: 0.8676 (t0) cc_final: 0.8406 (t0) outliers start: 92 outliers final: 63 residues processed: 441 average time/residue: 0.2135 time to fit residues: 145.2118 Evaluate side-chains 426 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 356 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 637 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 127 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.161975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121866 restraints weight = 40538.876| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.32 r_work: 0.3190 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29405 Z= 0.225 Angle : 0.666 9.442 40263 Z= 0.316 Chirality : 0.046 0.272 4893 Planarity : 0.004 0.047 4822 Dihedral : 7.924 85.518 7158 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.30 % Allowed : 10.54 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.15), residues: 3298 helix: 1.71 (0.24), residues: 448 sheet: 0.55 (0.15), residues: 1073 loop : 0.71 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 45 TYR 0.028 0.002 TYR T 36 PHE 0.013 0.002 PHE E 159 TRP 0.023 0.002 TRP S 50 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00544 (29182) covalent geometry : angle 0.62475 (39644) SS BOND : bond 0.00458 ( 50) SS BOND : angle 1.70635 ( 100) hydrogen bonds : bond 0.04333 ( 814) hydrogen bonds : angle 5.21543 ( 2034) link_ALPHA1-2 : bond 0.00496 ( 7) link_ALPHA1-2 : angle 1.78300 ( 21) link_ALPHA1-3 : bond 0.00742 ( 14) link_ALPHA1-3 : angle 1.96240 ( 42) link_ALPHA1-6 : bond 0.00612 ( 15) link_ALPHA1-6 : angle 1.62494 ( 45) link_BETA1-4 : bond 0.00425 ( 71) link_BETA1-4 : angle 1.84230 ( 213) link_BETA1-6 : bond 0.00226 ( 1) link_BETA1-6 : angle 1.43407 ( 3) link_NAG-ASN : bond 0.00481 ( 65) link_NAG-ASN : angle 2.26925 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 368 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.6079 (m100) cc_final: 0.5317 (m100) REVERT: H 47 TRP cc_start: 0.8077 (t60) cc_final: 0.7771 (t60) REVERT: H 51 VAL cc_start: 0.7762 (p) cc_final: 0.7100 (t) REVERT: H 69 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5470 (tt) REVERT: I 6 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: I 18 MET cc_start: 0.8581 (ptt) cc_final: 0.8276 (ptt) REVERT: K 50 ASN cc_start: 0.6723 (t0) cc_final: 0.6128 (t0) REVERT: L 7 SER cc_start: 0.7100 (m) cc_final: 0.6579 (t) REVERT: L 50 TYR cc_start: 0.7097 (m-80) cc_final: 0.6738 (m-80) REVERT: L 94 ARG cc_start: 0.7325 (tpt-90) cc_final: 0.7102 (tpt-90) REVERT: M 72 ASP cc_start: 0.8136 (t0) cc_final: 0.7868 (t0) REVERT: M 86 ASP cc_start: 0.7899 (m-30) cc_final: 0.7357 (m-30) REVERT: N 72 ASN cc_start: 0.6434 (m-40) cc_final: 0.6177 (m-40) REVERT: N 79 GLU cc_start: 0.6826 (mp0) cc_final: 0.6562 (mp0) REVERT: N 100 GLN cc_start: 0.7919 (pm20) cc_final: 0.7595 (pm20) REVERT: O 60 ASP cc_start: 0.8146 (t0) cc_final: 0.7847 (t0) REVERT: O 77 ASN cc_start: 0.7328 (m-40) cc_final: 0.6512 (t0) REVERT: O 96 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8692 (pt0) REVERT: P 51 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9060 (tp) REVERT: Q 31 ARG cc_start: 0.6925 (ptm-80) cc_final: 0.6472 (ptm160) REVERT: R 46 GLU cc_start: 0.6630 (tt0) cc_final: 0.5414 (mp0) REVERT: R 50 TYR cc_start: 0.5045 (m-80) cc_final: 0.4656 (m-80) REVERT: R 69 LEU cc_start: 0.3457 (OUTLIER) cc_final: 0.3164 (tp) REVERT: T 37 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7841 (pp30) REVERT: T 60 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7234 (tm-30) REVERT: F 543 ASN cc_start: 0.8132 (t0) cc_final: 0.7747 (t0) REVERT: F 589 ASP cc_start: 0.8624 (m-30) cc_final: 0.8224 (m-30) REVERT: F 624 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8959 (m-40) REVERT: B 588 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7703 (ttm110) REVERT: B 616 ASN cc_start: 0.7777 (p0) cc_final: 0.7366 (p0) REVERT: B 654 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7710 (mm-30) REVERT: C 371 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8849 (mp) REVERT: D 636 ASP cc_start: 0.8685 (t0) cc_final: 0.8427 (t0) outliers start: 96 outliers final: 72 residues processed: 436 average time/residue: 0.2088 time to fit residues: 141.0054 Evaluate side-chains 434 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 354 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 637 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 212 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 319 optimal weight: 0.6980 chunk 300 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 325 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.163791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123877 restraints weight = 40752.665| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 4.12 r_work: 0.3237 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29405 Z= 0.137 Angle : 0.603 9.373 40263 Z= 0.287 Chirality : 0.043 0.246 4893 Planarity : 0.004 0.046 4822 Dihedral : 7.522 83.122 7158 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.71 % Allowed : 11.33 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3298 helix: 2.10 (0.24), residues: 440 sheet: 0.63 (0.16), residues: 1063 loop : 0.74 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 61 TYR 0.030 0.001 TYR G 87 PHE 0.012 0.001 PHE S 100K TRP 0.023 0.001 TRP S 50 HIS 0.006 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00322 (29182) covalent geometry : angle 0.56561 (39644) SS BOND : bond 0.00356 ( 50) SS BOND : angle 1.53000 ( 100) hydrogen bonds : bond 0.03719 ( 814) hydrogen bonds : angle 5.07421 ( 2034) link_ALPHA1-2 : bond 0.00496 ( 7) link_ALPHA1-2 : angle 1.67071 ( 21) link_ALPHA1-3 : bond 0.00807 ( 14) link_ALPHA1-3 : angle 1.91733 ( 42) link_ALPHA1-6 : bond 0.00651 ( 15) link_ALPHA1-6 : angle 1.63357 ( 45) link_BETA1-4 : bond 0.00419 ( 71) link_BETA1-4 : angle 1.67896 ( 213) link_BETA1-6 : bond 0.00377 ( 1) link_BETA1-6 : angle 1.29540 ( 3) link_NAG-ASN : bond 0.00314 ( 65) link_NAG-ASN : angle 2.00387 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 379 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.6140 (m100) cc_final: 0.5381 (m100) REVERT: H 47 TRP cc_start: 0.8032 (t60) cc_final: 0.7804 (t60) REVERT: H 51 VAL cc_start: 0.7682 (p) cc_final: 0.7072 (t) REVERT: H 69 LEU cc_start: 0.5693 (OUTLIER) cc_final: 0.5409 (tt) REVERT: I 6 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: I 18 MET cc_start: 0.8562 (ptt) cc_final: 0.8271 (ptt) REVERT: J 28 TYR cc_start: 0.8393 (m-80) cc_final: 0.8160 (m-80) REVERT: K 50 ASN cc_start: 0.6620 (t0) cc_final: 0.6037 (t0) REVERT: L 7 SER cc_start: 0.7023 (m) cc_final: 0.6519 (t) REVERT: M 72 ASP cc_start: 0.8097 (t0) cc_final: 0.7804 (t0) REVERT: M 86 ASP cc_start: 0.7893 (m-30) cc_final: 0.7219 (m-30) REVERT: N 72 ASN cc_start: 0.6399 (m-40) cc_final: 0.6161 (m-40) REVERT: N 79 GLU cc_start: 0.6798 (mp0) cc_final: 0.6530 (mp0) REVERT: N 100 GLN cc_start: 0.7875 (pm20) cc_final: 0.7608 (pm20) REVERT: O 60 ASP cc_start: 0.8099 (t0) cc_final: 0.7768 (t0) REVERT: O 77 ASN cc_start: 0.7338 (m-40) cc_final: 0.6530 (t0) REVERT: O 96 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8635 (pt0) REVERT: P 21 SER cc_start: 0.8880 (p) cc_final: 0.8668 (m) REVERT: P 51 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9045 (tp) REVERT: Q 31 ARG cc_start: 0.6891 (ptm-80) cc_final: 0.6446 (ptp-170) REVERT: R 46 GLU cc_start: 0.6619 (tt0) cc_final: 0.5324 (mp0) REVERT: R 69 LEU cc_start: 0.3419 (OUTLIER) cc_final: 0.3119 (tp) REVERT: T 37 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7773 (pp30) REVERT: T 60 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7337 (tm-30) REVERT: E 205 CYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6544 (m) REVERT: F 543 ASN cc_start: 0.8123 (t0) cc_final: 0.7732 (t0) REVERT: F 589 ASP cc_start: 0.8594 (m-30) cc_final: 0.8183 (m-30) REVERT: B 588 ARG cc_start: 0.8211 (tpt170) cc_final: 0.7660 (ttm110) REVERT: B 616 ASN cc_start: 0.7747 (p0) cc_final: 0.7337 (p0) REVERT: B 654 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7728 (mm-30) REVERT: D 636 ASP cc_start: 0.8657 (t0) cc_final: 0.8399 (t0) outliers start: 79 outliers final: 58 residues processed: 432 average time/residue: 0.2083 time to fit residues: 139.7045 Evaluate side-chains 432 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 367 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 637 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 86 optimal weight: 10.0000 chunk 115 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 318 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 273 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 34 GLN K 89 HIS ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.161771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121521 restraints weight = 40700.684| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.23 r_work: 0.3195 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29405 Z= 0.216 Angle : 0.658 9.616 40263 Z= 0.311 Chirality : 0.045 0.244 4893 Planarity : 0.004 0.046 4822 Dihedral : 7.621 84.657 7158 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.75 % Allowed : 11.37 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.15), residues: 3298 helix: 1.88 (0.24), residues: 448 sheet: 0.59 (0.16), residues: 1057 loop : 0.65 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 61 TYR 0.032 0.002 TYR G 87 PHE 0.022 0.002 PHE S 100K TRP 0.024 0.002 TRP R 47 HIS 0.008 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00527 (29182) covalent geometry : angle 0.62031 (39644) SS BOND : bond 0.00445 ( 50) SS BOND : angle 1.64972 ( 100) hydrogen bonds : bond 0.04199 ( 814) hydrogen bonds : angle 5.13644 ( 2034) link_ALPHA1-2 : bond 0.00478 ( 7) link_ALPHA1-2 : angle 1.74486 ( 21) link_ALPHA1-3 : bond 0.00718 ( 14) link_ALPHA1-3 : angle 1.95177 ( 42) link_ALPHA1-6 : bond 0.00656 ( 15) link_ALPHA1-6 : angle 1.59368 ( 45) link_BETA1-4 : bond 0.00429 ( 71) link_BETA1-4 : angle 1.77957 ( 213) link_BETA1-6 : bond 0.00174 ( 1) link_BETA1-6 : angle 1.45719 ( 3) link_NAG-ASN : bond 0.00446 ( 65) link_NAG-ASN : angle 2.15166 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 358 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.6160 (m100) cc_final: 0.5389 (m100) REVERT: H 47 TRP cc_start: 0.8042 (t60) cc_final: 0.7815 (t60) REVERT: H 51 VAL cc_start: 0.7712 (p) cc_final: 0.7141 (t) REVERT: H 69 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5567 (tt) REVERT: I 6 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: I 18 MET cc_start: 0.8606 (ptt) cc_final: 0.8289 (ptt) REVERT: K 50 ASN cc_start: 0.6658 (t0) cc_final: 0.6024 (t0) REVERT: L 7 SER cc_start: 0.7190 (m) cc_final: 0.6680 (t) REVERT: M 72 ASP cc_start: 0.8157 (t0) cc_final: 0.7842 (t0) REVERT: M 86 ASP cc_start: 0.7945 (m-30) cc_final: 0.7366 (m-30) REVERT: N 72 ASN cc_start: 0.6436 (m-40) cc_final: 0.6210 (m-40) REVERT: N 100 GLN cc_start: 0.7911 (pm20) cc_final: 0.7619 (pm20) REVERT: O 60 ASP cc_start: 0.8132 (t0) cc_final: 0.7835 (t0) REVERT: O 77 ASN cc_start: 0.7322 (m-40) cc_final: 0.6483 (t0) REVERT: O 96 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8709 (pt0) REVERT: P 51 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9062 (tp) REVERT: Q 31 ARG cc_start: 0.6884 (ptm-80) cc_final: 0.6439 (ptp-170) REVERT: R 69 LEU cc_start: 0.3340 (OUTLIER) cc_final: 0.3037 (tp) REVERT: T 60 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7343 (tm-30) REVERT: F 543 ASN cc_start: 0.8200 (t0) cc_final: 0.7785 (t0) REVERT: F 589 ASP cc_start: 0.8643 (m-30) cc_final: 0.8236 (m-30) REVERT: B 588 ARG cc_start: 0.8259 (tpt170) cc_final: 0.7688 (ttm110) REVERT: B 616 ASN cc_start: 0.7928 (p0) cc_final: 0.7515 (p0) REVERT: B 654 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7793 (mm-30) REVERT: D 636 ASP cc_start: 0.8687 (t0) cc_final: 0.8427 (t0) outliers start: 80 outliers final: 68 residues processed: 415 average time/residue: 0.2120 time to fit residues: 136.5593 Evaluate side-chains 424 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 351 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 637 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 23 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 300 optimal weight: 0.8980 chunk 311 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.162895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122862 restraints weight = 40401.684| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 4.27 r_work: 0.3220 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29405 Z= 0.167 Angle : 0.621 9.976 40263 Z= 0.293 Chirality : 0.044 0.248 4893 Planarity : 0.004 0.050 4822 Dihedral : 7.413 83.172 7158 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.58 % Allowed : 11.47 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 3298 helix: 2.09 (0.24), residues: 440 sheet: 0.63 (0.16), residues: 1057 loop : 0.61 (0.15), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 61 TYR 0.035 0.001 TYR G 87 PHE 0.018 0.002 PHE S 100K TRP 0.042 0.002 TRP Q 35 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00402 (29182) covalent geometry : angle 0.58501 (39644) SS BOND : bond 0.00353 ( 50) SS BOND : angle 1.51319 ( 100) hydrogen bonds : bond 0.03844 ( 814) hydrogen bonds : angle 5.05644 ( 2034) link_ALPHA1-2 : bond 0.00463 ( 7) link_ALPHA1-2 : angle 1.66328 ( 21) link_ALPHA1-3 : bond 0.00750 ( 14) link_ALPHA1-3 : angle 1.90304 ( 42) link_ALPHA1-6 : bond 0.00676 ( 15) link_ALPHA1-6 : angle 1.59395 ( 45) link_BETA1-4 : bond 0.00421 ( 71) link_BETA1-4 : angle 1.67022 ( 213) link_BETA1-6 : bond 0.00306 ( 1) link_BETA1-6 : angle 1.33449 ( 3) link_NAG-ASN : bond 0.00361 ( 65) link_NAG-ASN : angle 2.01299 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 364 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.6226 (m100) cc_final: 0.5474 (m100) REVERT: H 47 TRP cc_start: 0.8063 (t60) cc_final: 0.7783 (t60) REVERT: H 51 VAL cc_start: 0.7708 (p) cc_final: 0.7138 (t) REVERT: H 69 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5606 (tt) REVERT: I 6 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: I 18 MET cc_start: 0.8568 (ptt) cc_final: 0.8275 (ptt) REVERT: J 28 TYR cc_start: 0.8432 (m-80) cc_final: 0.8191 (m-80) REVERT: K 50 ASN cc_start: 0.6635 (t0) cc_final: 0.5981 (t0) REVERT: K 95 LYS cc_start: 0.6963 (mtmm) cc_final: 0.6725 (ptpp) REVERT: L 7 SER cc_start: 0.7177 (m) cc_final: 0.6667 (t) REVERT: M 72 ASP cc_start: 0.8147 (t0) cc_final: 0.7828 (t0) REVERT: M 86 ASP cc_start: 0.7907 (m-30) cc_final: 0.7382 (m-30) REVERT: N 72 ASN cc_start: 0.6400 (m-40) cc_final: 0.6194 (m-40) REVERT: N 79 GLU cc_start: 0.6714 (mp0) cc_final: 0.5968 (mp0) REVERT: N 100 GLN cc_start: 0.7902 (pm20) cc_final: 0.7615 (pm20) REVERT: O 60 ASP cc_start: 0.8105 (t0) cc_final: 0.7814 (t0) REVERT: O 77 ASN cc_start: 0.7329 (m-40) cc_final: 0.6523 (t0) REVERT: O 96 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8627 (pt0) REVERT: P 3 GLN cc_start: 0.8088 (mt0) cc_final: 0.7768 (mp-120) REVERT: P 51 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9034 (tp) REVERT: P 96 LYS cc_start: 0.8473 (ttmt) cc_final: 0.7349 (tttp) REVERT: Q 31 ARG cc_start: 0.6872 (ptm-80) cc_final: 0.6504 (ptm160) REVERT: R 69 LEU cc_start: 0.3345 (OUTLIER) cc_final: 0.3017 (tp) REVERT: F 543 ASN cc_start: 0.8171 (t0) cc_final: 0.7759 (t0) REVERT: F 589 ASP cc_start: 0.8594 (m-30) cc_final: 0.8172 (m-30) REVERT: B 588 ARG cc_start: 0.8240 (tpt170) cc_final: 0.7659 (ttm110) REVERT: B 616 ASN cc_start: 0.7927 (p0) cc_final: 0.7529 (p0) REVERT: B 654 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7736 (mm-30) REVERT: D 636 ASP cc_start: 0.8644 (t0) cc_final: 0.8382 (t0) outliers start: 75 outliers final: 67 residues processed: 413 average time/residue: 0.2067 time to fit residues: 132.1370 Evaluate side-chains 424 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 352 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain T residue 36 TYR Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 637 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 96 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 292 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 323 optimal weight: 3.9990 chunk 275 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.164475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125082 restraints weight = 40542.780| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.81 r_work: 0.3239 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29405 Z= 0.123 Angle : 0.594 10.523 40263 Z= 0.281 Chirality : 0.043 0.247 4893 Planarity : 0.004 0.047 4822 Dihedral : 7.102 81.329 7158 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.40 % Allowed : 11.98 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 3298 helix: 2.26 (0.24), residues: 439 sheet: 0.67 (0.16), residues: 1074 loop : 0.63 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 61 TYR 0.020 0.001 TYR T 36 PHE 0.021 0.001 PHE S 100K TRP 0.031 0.001 TRP R 47 HIS 0.005 0.001 HIS P 102 Details of bonding type rmsd covalent geometry : bond 0.00285 (29182) covalent geometry : angle 0.55906 (39644) SS BOND : bond 0.00322 ( 50) SS BOND : angle 1.49147 ( 100) hydrogen bonds : bond 0.03473 ( 814) hydrogen bonds : angle 4.93428 ( 2034) link_ALPHA1-2 : bond 0.00474 ( 7) link_ALPHA1-2 : angle 1.58282 ( 21) link_ALPHA1-3 : bond 0.00802 ( 14) link_ALPHA1-3 : angle 1.86723 ( 42) link_ALPHA1-6 : bond 0.00709 ( 15) link_ALPHA1-6 : angle 1.59173 ( 45) link_BETA1-4 : bond 0.00418 ( 71) link_BETA1-4 : angle 1.58719 ( 213) link_BETA1-6 : bond 0.00380 ( 1) link_BETA1-6 : angle 1.25622 ( 3) link_NAG-ASN : bond 0.00360 ( 65) link_NAG-ASN : angle 1.94209 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7534.91 seconds wall clock time: 129 minutes 56.11 seconds (7796.11 seconds total)