Starting phenix.real_space_refine on Mon Oct 13 10:19:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cdi_7460/10_2025/6cdi_7460_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cdi_7460/10_2025/6cdi_7460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cdi_7460/10_2025/6cdi_7460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cdi_7460/10_2025/6cdi_7460.map" model { file = "/net/cci-nas-00/data/ceres_data/6cdi_7460/10_2025/6cdi_7460_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cdi_7460/10_2025/6cdi_7460_neut.cif" } resolution = 3.6 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= 0.012 sd= 0.121 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 168 5.16 5 C 20523 2.51 5 N 5316 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32763 Number of models: 1 Model: "" Number of chains: 81 Chain: "c" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "d" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "h" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "l" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "2" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "7" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "3" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "4" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" 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: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" 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: "i" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 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: "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: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "v" Number of atoms: 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "1" Number of atoms: 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: "9" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "AA" Number of atoms: 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: "BA" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "CA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "DA" 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: "EA" 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: "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: 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: "IA" 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: "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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" 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: "d" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" 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: "2" 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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 Time building chain proxies: 9.52, per 1000 atoms: 0.29 Number of scatterers: 32763 At special positions: 0 Unit cell: (157.29, 160.5, 154.08, 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 168 16.00 O 6756 8.00 N 5316 7.00 C 20523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.02 Simple disulfide: pdb=" SG CYS d 54 " - pdb=" SG CYS d 74 " distance=2.03 Simple disulfide: pdb=" SG CYS d 119 " - pdb=" SG CYS d 205 " distance=2.03 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.02 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.02 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 433 " distance=2.04 Simple disulfide: pdb=" SG CYS d 218 " - pdb=" SG CYS d 247 " distance=2.03 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " distance=2.03 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.02 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.03 Simple disulfide: pdb=" SG CYS d 385 " - pdb=" SG CYS d 418 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.04 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=2.02 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 N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM30180 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31880 O5 NAG 0 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31030 O5 NAG b 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30230 O5 NAG F 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31930 O5 NAG 1 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31080 O5 NAG e 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30780 O5 NAG W 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32480 O5 NAGJA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31630 O5 NAG v 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30513 O5 NAG O 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32213 O5 NAGDA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31363 O5 NAG k 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32719 O5 NAG A 702 .*. O " rejected from bonding due to valence issues. Atom "HETATM32747 O5 NAG D 702 .*. O " rejected from bonding due to valence issues. Atom "HETATM32691 O5 NAG c 702 .*. O " rejected from bonding due to valence issues. Atom "HETATM30369 O5 NAG J 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32069 O5 NAGBA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31219 O5 NAG i 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30808 O5 NAG X 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31658 O5 NAG w 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32508 O5 NAGKA 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN P 4 " - " MAN P 5 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN o 4 " - " MAN o 5 " " MAN w 4 " - " MAN w 5 " " MAN w 5 " - " MAN w 6 " " MANBA 4 " - " MANBA 5 " " MANBA 5 " - " MANBA 6 " " MANEA 4 " - " MANEA 5 " " MANKA 4 " - " MANKA 5 " " MANKA 5 " - " MANKA 6 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 9 3 " - " MAN 9 4 " " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " MAN X 7 " - " MAN X 8 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 8 " " BMA o 3 " - " MAN o 4 " " BMA u 3 " - " MAN u 4 " " BMA w 3 " - " MAN w 4 " " MAN w 7 " - " MAN w 8 " " BMA y 3 " - " MAN y 4 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " " MANBA 7 " - " MANBA 8 " " BMAEA 3 " - " MANEA 4 " " BMAIA 3 " - " MANIA 4 " " BMAKA 3 " - " MANKA 4 " " MANKA 7 " - " MANKA 8 " " BMAMA 3 " - " MANMA 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 7 " " BMA K 3 " - " MAN K 4 " " BMA P 3 " - " MAN P 6 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 7 " " MAN X 7 " - " MAN X 9 " " BMA g 3 " - " MAN g 5 " " BMA i 3 " - " MAN i 7 " " BMA j 3 " - " MAN j 4 " " BMA o 3 " - " MAN o 6 " " BMA u 3 " - " MAN u 5 " " BMA w 3 " - " MAN w 7 " " MAN w 7 " - " MAN w 9 " " BMAAA 3 " - " MANAA 5 " " BMABA 3 " - " MANBA 7 " " BMACA 3 " - " MANCA 4 " " BMAEA 3 " - " MANEA 6 " " BMAIA 3 " - " MANIA 5 " " BMAKA 3 " - " MANKA 7 " " MANKA 7 " - " MANKA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGKA 1 " - " NAGKA 2 " " NAGKA 2 " - " BMAKA 3 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGMA 2 " - " BMAMA 3 " NAG-ASN " NAG 0 1 " - " ASN C 88 " " NAG 1 1 " - " ASN C 133 " " NAG 2 644 " - " ASN 2 355 " " NAG 9 1 " - " ASN C 137 " " NAG A 702 " - " ASN A 637 " " NAG B 1 " - " ASN c 611 " " NAG C 644 " - " ASN C 355 " " NAG D 702 " - " ASN D 637 " " NAG E 1 " - " ASN d 88 " " NAG F 1 " - " ASN d 133 " " NAG G 1 " - " ASN d 137 " " NAG I 1 " - " ASN d 156 " " NAG J 1 " - " ASN d 160 " " NAG K 1 " - " ASN d 197 " " NAG O 1 " - " ASN d 234 " " NAG P 1 " - " ASN d 262 " " NAG S 1 " - " ASN d 295 " " NAG T 1 " - " ASN d 301 " " NAG U 1 " - " ASN d 363 " " NAG V 1 " - " ASN d 386 " " NAG W 1 " - " ASN d 392 " " NAG X 1 " - " ASN d 332 " " NAG Y 1 " - " ASN d 448 " " NAG Z 1 " - " ASN d 276 " " NAG a 1 " - " ASN A 611 " " NAG b 1 " - " ASN 2 88 " " NAG c 702 " - " ASN c 637 " " NAG d 644 " - " ASN d 355 " " NAG e 1 " - " ASN 2 133 " " NAG f 1 " - " ASN 2 137 " " NAG g 1 " - " ASN 2 156 " " NAG i 1 " - " ASN 2 160 " " NAG j 1 " - " ASN 2 197 " " NAG k 1 " - " ASN 2 234 " " NAG o 1 " - " ASN 2 262 " " NAG p 1 " - " ASN 2 295 " " NAG s 1 " - " ASN 2 301 " " NAG t 1 " - " ASN 2 363 " " NAG u 1 " - " ASN 2 386 " " NAG v 1 " - " ASN 2 392 " " NAG w 1 " - " ASN 2 332 " " NAG x 1 " - " ASN 2 448 " " NAG y 1 " - " ASN 2 276 " " NAG z 1 " - " ASN D 611 " " NAGAA 1 " - " ASN C 156 " " NAGBA 1 " - " ASN C 160 " " NAGCA 1 " - " ASN C 197 " " NAGDA 1 " - " ASN C 234 " " NAGEA 1 " - " ASN C 262 " " NAGFA 1 " - " ASN C 295 " " NAGGA 1 " - " ASN C 301 " " NAGHA 1 " - " ASN C 363 " " NAGIA 1 " - " ASN C 386 " " NAGJA 1 " - " ASN C 392 " " NAGKA 1 " - " ASN C 332 " " NAGLA 1 " - " ASN C 448 " " NAGMA 1 " - " ASN C 276 " Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 99 sheets defined 13.0% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'c' and resid 514 through 520 removed outlier: 3.833A pdb=" N VAL c 518 " --> pdb=" O GLY c 514 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 537 through 543 Processing helix chain 'c' and resid 570 through 595 removed outlier: 3.639A pdb=" N LYS c 574 " --> pdb=" O VAL c 570 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 623 removed outlier: 3.584A pdb=" N ILE c 622 " --> pdb=" O ASN c 618 " (cutoff:3.500A) Processing helix chain 'c' and resid 627 through 636 removed outlier: 3.890A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 640 through 664 removed outlier: 3.653A pdb=" N GLY c 644 " --> pdb=" O GLN c 640 " (cutoff:3.500A) Processing helix chain 'd' and resid 57 through 63 removed outlier: 3.506A pdb=" N TYR d 61 " --> pdb=" O ASP d 57 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR d 63 " --> pdb=" O LYS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 115 removed outlier: 3.659A pdb=" N ILE d 109 " --> pdb=" O HIS d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 126 removed outlier: 3.661A pdb=" N CYS d 126 " --> pdb=" O THR d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 198 Processing helix chain 'd' and resid 335 through 350 Processing helix chain 'd' and resid 368 through 373 Processing helix chain 'd' and resid 475 through 481 removed outlier: 3.542A pdb=" N SER d 481 " --> pdb=" O ASP d 477 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.809A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'r' and resid 78 through 82 removed outlier: 3.597A pdb=" N PHE r 82 " --> pdb=" O ARG r 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 64 removed outlier: 3.583A pdb=" N GLN q 64 " --> pdb=" O ARG q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 61 through 64' Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.763A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 520 removed outlier: 3.833A pdb=" N VAL A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.641A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.584A pdb=" N ILE A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.889A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 664 removed outlier: 3.654A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain '2' and resid 57 through 63 removed outlier: 3.506A pdb=" N TYR 2 61 " --> pdb=" O ASP 2 57 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR 2 63 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 115 removed outlier: 3.659A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 126 removed outlier: 3.662A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 Processing helix chain '2' and resid 475 through 481 removed outlier: 3.543A pdb=" N SER 2 481 " --> pdb=" O ASP 2 477 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 87 removed outlier: 3.808A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '7' and resid 78 through 82 removed outlier: 3.596A pdb=" N PHE 7 82 " --> pdb=" O ARG 7 79 " (cutoff:3.500A) Processing helix chain '8' and resid 61 through 64 removed outlier: 3.583A pdb=" N GLN 8 64 " --> pdb=" O ARG 8 61 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 61 through 64' Processing helix chain '8' and resid 83 through 87 removed outlier: 3.764A pdb=" N THR 8 87 " --> pdb=" O PRO 8 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 520 removed outlier: 3.833A pdb=" N VAL D 518 " --> pdb=" O GLY D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.640A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 removed outlier: 3.584A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.889A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 664 removed outlier: 3.653A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.505A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.659A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.661A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.542A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.808A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 82 removed outlier: 3.597A pdb=" N PHE R 82 " --> pdb=" O ARG R 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.583A pdb=" N GLN Q 64 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.764A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 603 through 609 removed outlier: 3.513A pdb=" N VAL d 38 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR c 606 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL d 36 " --> pdb=" O THR c 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 45 through 47 removed outlier: 3.879A pdb=" N ILE d 225 " --> pdb=" O VAL d 245 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR d 244 " --> pdb=" O ILE d 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'd' and resid 91 through 94 removed outlier: 3.892A pdb=" N GLU d 91 " --> pdb=" O CYS d 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'd' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.471A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 271 through 273 removed outlier: 7.478A pdb=" N GLN d 293 " --> pdb=" O SER d 334 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER d 334 " --> pdb=" O GLN d 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'd' and resid 271 through 273 removed outlier: 11.176A pdb=" N VAL d 286 " --> pdb=" O THR d 455 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N THR d 455 " --> pdb=" O VAL d 286 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N PHE d 288 " --> pdb=" O ILE d 453 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N ILE d 453 " --> pdb=" O PHE d 288 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N THR d 290 " --> pdb=" O GLY d 451 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY d 451 " --> pdb=" O THR d 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 302 through 308 removed outlier: 5.530A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 359 through 361 removed outlier: 3.529A pdb=" N ILE d 359 " --> pdb=" O TRP d 395 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER d 393 " --> pdb=" O PHE d 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 374 through 377 removed outlier: 3.833A pdb=" N HIS d 374 " --> pdb=" O CYS d 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'n' and resid 9 through 12 removed outlier: 5.977A pdb=" N GLN n 37 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU n 46 " --> pdb=" O GLN n 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 19 through 23 removed outlier: 3.696A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'm' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'm' and resid 46 through 51 removed outlier: 6.476A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR m 90 " --> pdb=" O THR m 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'm' and resid 95 through 96 Processing sheet with id=AC1, first strand: chain 'm' and resid 99 through 100A Processing sheet with id=AC2, first strand: chain 'r' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.811A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE q 34 " --> pdb=" O TRP q 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP q 50 " --> pdb=" O ILE q 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP q 36 " --> pdb=" O ILE q 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.811A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 10 through 11 removed outlier: 3.703A pdb=" N GLU h 10 " --> pdb=" O THR h 108 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY h 49 " --> pdb=" O TRP h 36 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS h 38 " --> pdb=" O TRP h 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP h 47 " --> pdb=" O LYS h 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR h 40 " --> pdb=" O LEU h 45 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU h 45 " --> pdb=" O THR h 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'h' and resid 17 through 18 Processing sheet with id=AD2, first strand: chain 'h' and resid 22 through 23 removed outlier: 3.604A pdb=" N CYS h 22 " --> pdb=" O ALA h 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA h 78 " --> pdb=" O CYS h 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 5 through 7 Processing sheet with id=AD4, first strand: chain 'l' and resid 10 through 12 removed outlier: 3.952A pdb=" N GLY l 84 " --> pdb=" O LEU l 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'l' and resid 35 through 36 removed outlier: 6.443A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'l' and resid 89 through 90 removed outlier: 4.117A pdb=" N THR l 97 " --> pdb=" O GLN l 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.723A pdb=" N THR A 606 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL 2 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL A 608 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '2' and resid 45 through 47 removed outlier: 3.880A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR 2 244 " --> pdb=" O ILE 2 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '2' and resid 55 through 56 Processing sheet with id=AE1, first strand: chain '2' and resid 91 through 94 removed outlier: 3.891A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AE3, first strand: chain '2' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain '2' and resid 202 through 203 removed outlier: 6.471A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '2' and resid 271 through 273 removed outlier: 7.478A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '2' and resid 271 through 273 removed outlier: 11.176A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '2' and resid 302 through 308 removed outlier: 5.529A pdb=" N THR 2 303 " --> pdb=" O GLY 2 321 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '2' and resid 359 through 361 removed outlier: 3.529A pdb=" N ILE 2 359 " --> pdb=" O TRP 2 395 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER 2 393 " --> pdb=" O PHE 2 361 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '2' and resid 374 through 377 removed outlier: 3.834A pdb=" N HIS 2 374 " --> pdb=" O CYS 2 385 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '6' and resid 9 through 12 removed outlier: 5.977A pdb=" N GLN 6 37 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU 6 46 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '6' and resid 19 through 23 removed outlier: 3.696A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '5' and resid 6 through 7 Processing sheet with id=AF4, first strand: chain '5' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain '5' and resid 46 through 51 removed outlier: 6.475A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR 5 90 " --> pdb=" O THR 5 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR 5 105 " --> pdb=" O TYR 5 90 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '5' and resid 95 through 96 Processing sheet with id=AF7, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AF8, first strand: chain '7' and resid 4 through 6 Processing sheet with id=AF9, first strand: chain '7' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU 7 11 " --> pdb=" O GLU 7 100 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP 7 34 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '7' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU 7 11 " --> pdb=" O GLU 7 100 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AG3, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain '8' and resid 10 through 11 removed outlier: 6.812A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE 8 34 " --> pdb=" O TRP 8 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP 8 50 " --> pdb=" O ILE 8 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP 8 36 " --> pdb=" O ILE 8 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '8' and resid 10 through 11 removed outlier: 6.812A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '3' and resid 10 through 11 removed outlier: 3.704A pdb=" N GLU 3 10 " --> pdb=" O THR 3 108 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY 3 49 " --> pdb=" O TRP 3 36 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS 3 38 " --> pdb=" O TRP 3 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP 3 47 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR 3 40 " --> pdb=" O LEU 3 45 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU 3 45 " --> pdb=" O THR 3 40 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '3' and resid 17 through 18 Processing sheet with id=AG8, first strand: chain '3' and resid 22 through 23 removed outlier: 3.604A pdb=" N CYS 3 22 " --> pdb=" O ALA 3 78 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA 3 78 " --> pdb=" O CYS 3 22 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '4' and resid 5 through 7 Processing sheet with id=AH1, first strand: chain '4' and resid 10 through 12 removed outlier: 3.952A pdb=" N GLY 4 84 " --> pdb=" O LEU 4 104 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '4' and resid 35 through 36 removed outlier: 6.442A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '4' and resid 89 through 90 removed outlier: 4.118A pdb=" N THR 4 97 " --> pdb=" O GLN 4 90 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 603 through 609 removed outlier: 3.513A pdb=" N VAL C 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.879A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 244 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AH7, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.891A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AH9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AI1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.471A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.478A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.176A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 302 through 308 removed outlier: 5.529A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 359 through 361 removed outlier: 3.529A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 374 through 377 removed outlier: 3.833A pdb=" N HIS C 374 " --> pdb=" O CYS C 385 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 9 through 12 removed outlier: 5.977A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.696A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'M' and resid 6 through 7 Processing sheet with id=AJ1, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AJ2, first strand: chain 'M' and resid 46 through 51 removed outlier: 6.475A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR M 90 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR M 105 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'M' and resid 95 through 96 Processing sheet with id=AJ4, first strand: chain 'M' and resid 99 through 100A Processing sheet with id=AJ5, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AJ6, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP R 34 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AJ9, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AK1, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.812A pdb=" N VAL Q 10 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.812A pdb=" N VAL Q 10 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.703A pdb=" N GLU H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AK5, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.604A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AK7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.952A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'L' and resid 35 through 36 removed outlier: 6.442A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'L' and resid 89 through 90 removed outlier: 4.117A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.19 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9900 1.34 - 1.46: 8773 1.46 - 1.58: 14558 1.58 - 1.70: 9 1.70 - 1.82: 222 Bond restraints: 33462 Sorted by residual: bond pdb=" C1 MAN J 4 " pdb=" O5 MAN J 4 " ideal model delta sigma weight residual 1.399 1.502 -0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C1 MANBA 4 " pdb=" O5 MANBA 4 " ideal model delta sigma weight residual 1.399 1.501 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C1 MAN i 4 " pdb=" O5 MAN i 4 " ideal model delta sigma weight residual 1.399 1.501 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C1 MAN J 4 " pdb=" C2 MAN J 4 " ideal model delta sigma weight residual 1.526 1.620 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C1 MANBA 4 " pdb=" C2 MANBA 4 " ideal model delta sigma weight residual 1.526 1.620 -0.094 2.00e-02 2.50e+03 2.19e+01 ... (remaining 33457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 42713 1.99 - 3.98: 2138 3.98 - 5.98: 427 5.98 - 7.97: 136 7.97 - 9.96: 36 Bond angle restraints: 45450 Sorted by residual: angle pdb=" N VAL c 570 " pdb=" CA VAL c 570 " pdb=" C VAL c 570 " ideal model delta sigma weight residual 112.96 106.66 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" N VAL A 570 " pdb=" CA VAL A 570 " pdb=" C VAL A 570 " ideal model delta sigma weight residual 112.96 106.66 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" N VAL D 570 " pdb=" CA VAL D 570 " pdb=" C VAL D 570 " ideal model delta sigma weight residual 112.96 106.67 6.29 1.00e+00 1.00e+00 3.96e+01 angle pdb=" N ILE d 138 " pdb=" CA ILE d 138 " pdb=" C ILE d 138 " ideal model delta sigma weight residual 108.11 116.56 -8.45 1.40e+00 5.10e-01 3.64e+01 angle pdb=" N ILE C 138 " pdb=" CA ILE C 138 " pdb=" C ILE C 138 " ideal model delta sigma weight residual 108.11 116.56 -8.45 1.40e+00 5.10e-01 3.64e+01 ... (remaining 45445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 21282 22.61 - 45.21: 711 45.21 - 67.82: 169 67.82 - 90.42: 203 90.42 - 113.03: 123 Dihedral angle restraints: 22488 sinusoidal: 11484 harmonic: 11004 Sorted by residual: dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual -86.00 -173.23 87.23 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CB CYS d 201 " pdb=" SG CYS d 201 " pdb=" SG CYS d 433 " pdb=" CB CYS d 433 " ideal model delta sinusoidal sigma weight residual -86.00 -173.21 87.21 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS 2 201 " pdb=" SG CYS 2 201 " pdb=" SG CYS 2 433 " pdb=" CB CYS 2 433 " ideal model delta sinusoidal sigma weight residual -86.00 -173.21 87.21 1 1.00e+01 1.00e-02 9.13e+01 ... (remaining 22485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.306: 5619 0.306 - 0.613: 24 0.613 - 0.919: 3 0.919 - 1.226: 12 1.226 - 1.532: 6 Chirality restraints: 5664 Sorted by residual: chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN 2 88 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.87e+01 chirality pdb=" C1 NAG 0 1 " pdb=" ND2 ASN C 88 " pdb=" C2 NAG 0 1 " pdb=" O5 NAG 0 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.86e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN d 88 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.85e+01 ... (remaining 5661 not shown) Planarity restraints: 5520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN d 88 " -0.181 2.00e-02 2.50e+03 4.19e-01 2.20e+03 pdb=" CG ASN d 88 " 0.139 2.00e-02 2.50e+03 pdb=" OD1 ASN d 88 " -0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN d 88 " 0.708 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.559 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 88 " 0.181 2.00e-02 2.50e+03 4.19e-01 2.19e+03 pdb=" CG ASN 2 88 " -0.139 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 88 " 0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 88 " -0.708 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.559 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 88 " -0.181 2.00e-02 2.50e+03 4.19e-01 2.19e+03 pdb=" CG ASN C 88 " 0.139 2.00e-02 2.50e+03 pdb=" OD1 ASN C 88 " -0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN C 88 " 0.708 2.00e-02 2.50e+03 pdb=" C1 NAG 0 1 " -0.558 2.00e-02 2.50e+03 ... (remaining 5517 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 19 2.15 - 2.84: 10453 2.84 - 3.52: 40948 3.52 - 4.21: 74820 4.21 - 4.90: 126169 Nonbonded interactions: 252409 Sorted by model distance: nonbonded pdb=" OG SER n 12 " pdb=" CG1 ILE n 105 " model vdw 1.461 3.440 nonbonded pdb=" OG SER N 12 " pdb=" CG1 ILE N 105 " model vdw 1.461 3.440 nonbonded pdb=" OG SER 6 12 " pdb=" CG1 ILE 6 105 " model vdw 1.462 3.440 nonbonded pdb=" O VAL N 13 " pdb=" O ALA N 14 " model vdw 1.491 3.040 nonbonded pdb=" O VAL 6 13 " pdb=" O ALA 6 14 " model vdw 1.492 3.040 ... (remaining 252404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain '0' selection = chain '9' selection = chain 'CA' selection = chain 'E' selection = chain 'G' selection = chain 'K' selection = chain 'MA' selection = chain 'Z' selection = chain 'b' selection = chain 'f' selection = chain 'j' selection = chain 'y' } ncs_group { reference = chain '1' selection = chain 'F' selection = chain 'FA' selection = chain 'GA' selection = chain 'JA' selection = chain 'LA' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'e' selection = chain 'p' selection = chain 's' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'd' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '8' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'c' } ncs_group { reference = chain 'AA' selection = chain 'I' selection = chain 'IA' selection = chain 'V' selection = chain 'g' selection = chain 'u' } ncs_group { reference = chain 'B' selection = chain 'DA' selection = chain 'HA' selection = chain 'O' selection = chain 'U' selection = chain 'a' selection = chain 'k' selection = chain 't' selection = chain 'z' } ncs_group { reference = (chain 'BA' and (resid 1 or resid 4 through 8)) selection = (chain 'J' and (resid 1 or resid 4 through 8)) selection = (chain 'KA' and (resid 2 or resid 5 through 9)) selection = (chain 'X' and (resid 2 or resid 5 through 9)) selection = (chain 'i' and (resid 1 or resid 4 through 8)) selection = (chain 'w' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'EA' selection = chain 'P' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 36.260 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.009 0.312 33723 Z= 0.423 Angle : 1.850 53.966 46182 Z= 0.735 Chirality : 0.101 1.532 5664 Planarity : 0.006 0.068 5463 Dihedral : 16.867 113.026 15297 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 0.45 % Allowed : 2.98 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.12), residues: 3777 helix: -2.51 (0.20), residues: 378 sheet: -1.78 (0.14), residues: 1203 loop : -2.36 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 429 TYR 0.024 0.003 TYR 2 217 PHE 0.028 0.003 PHE d 93 TRP 0.037 0.003 TRP q 103 HIS 0.016 0.003 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00776 (33462) covalent geometry : angle 1.06234 (45450) SS BOND : bond 0.00517 ( 51) SS BOND : angle 7.23415 ( 102) hydrogen bonds : bond 0.17728 ( 900) hydrogen bonds : angle 7.58210 ( 2448) link_ALPHA1-2 : bond 0.00566 ( 15) link_ALPHA1-2 : angle 2.23059 ( 45) link_ALPHA1-3 : bond 0.00822 ( 30) link_ALPHA1-3 : angle 2.22267 ( 90) link_ALPHA1-6 : bond 0.00550 ( 21) link_ALPHA1-6 : angle 1.46681 ( 63) link_BETA1-4 : bond 0.00949 ( 87) link_BETA1-4 : angle 4.09555 ( 261) link_NAG-ASN : bond 0.10329 ( 57) link_NAG-ASN : angle 23.73462 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 831 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 595 ILE cc_start: 0.9225 (pt) cc_final: 0.8956 (mt) REVERT: c 632 ASP cc_start: 0.8393 (t0) cc_final: 0.8160 (t0) REVERT: c 659 ASP cc_start: 0.7990 (t0) cc_final: 0.7734 (t70) REVERT: m 48 ILE cc_start: 0.9103 (mt) cc_final: 0.8689 (mt) REVERT: m 72 ASP cc_start: 0.8017 (t0) cc_final: 0.6823 (t0) REVERT: m 100 MET cc_start: 0.9224 (mpp) cc_final: 0.8851 (mmm) REVERT: r 32 MET cc_start: 0.8908 (tpp) cc_final: 0.8612 (tpp) REVERT: r 33 THR cc_start: 0.9618 (m) cc_final: 0.9186 (p) REVERT: h 46 ASP cc_start: 0.7682 (m-30) cc_final: 0.7126 (m-30) REVERT: h 60 ASN cc_start: 0.7594 (m-40) cc_final: 0.7062 (p0) REVERT: h 80 MET cc_start: 0.6385 (mmt) cc_final: 0.5659 (tpp) REVERT: h 82 LEU cc_start: 0.8089 (mt) cc_final: 0.7717 (mp) REVERT: h 100 TYR cc_start: 0.8103 (p90) cc_final: 0.7818 (p90) REVERT: l 9 LEU cc_start: 0.8472 (mt) cc_final: 0.8254 (tt) REVERT: l 85 VAL cc_start: 0.7530 (t) cc_final: 0.7202 (t) REVERT: A 659 ASP cc_start: 0.8364 (t0) cc_final: 0.7985 (t70) REVERT: 6 26 GLU cc_start: 0.7517 (tt0) cc_final: 0.7170 (tt0) REVERT: 5 46 GLU cc_start: 0.8525 (tt0) cc_final: 0.8237 (tm-30) REVERT: 5 48 ILE cc_start: 0.9155 (mt) cc_final: 0.8869 (mt) REVERT: 5 72 ASP cc_start: 0.7525 (t0) cc_final: 0.6274 (t0) REVERT: 8 63 LEU cc_start: 0.9202 (mp) cc_final: 0.8994 (mt) REVERT: 3 46 ASP cc_start: 0.7536 (m-30) cc_final: 0.5716 (m-30) REVERT: 3 60 ASN cc_start: 0.7530 (m-40) cc_final: 0.6912 (p0) REVERT: 3 80 MET cc_start: 0.6803 (mmt) cc_final: 0.6515 (mmm) REVERT: 3 82 LEU cc_start: 0.7947 (mt) cc_final: 0.7716 (mt) REVERT: 4 11 LEU cc_start: 0.7970 (mt) cc_final: 0.7741 (tp) REVERT: 4 85 VAL cc_start: 0.7941 (t) cc_final: 0.7617 (t) REVERT: D 625 ASN cc_start: 0.7791 (t0) cc_final: 0.7480 (t0) REVERT: D 659 ASP cc_start: 0.8243 (t0) cc_final: 0.7842 (t70) REVERT: N 26 GLU cc_start: 0.7922 (tt0) cc_final: 0.7577 (tt0) REVERT: M 46 GLU cc_start: 0.8647 (tt0) cc_final: 0.8432 (tm-30) REVERT: M 48 ILE cc_start: 0.9255 (mt) cc_final: 0.8979 (mt) REVERT: M 72 ASP cc_start: 0.7941 (t0) cc_final: 0.6823 (t0) REVERT: R 32 MET cc_start: 0.8943 (tpp) cc_final: 0.8365 (tpp) REVERT: Q 76 ASP cc_start: 0.8008 (m-30) cc_final: 0.7722 (m-30) REVERT: Q 87 THR cc_start: 0.9200 (m) cc_final: 0.8959 (p) REVERT: H 80 MET cc_start: 0.6729 (mmt) cc_final: 0.5887 (tpp) REVERT: H 82 LEU cc_start: 0.7982 (mt) cc_final: 0.7499 (mp) REVERT: L 2 VAL cc_start: 0.7581 (t) cc_final: 0.6820 (p) REVERT: L 9 LEU cc_start: 0.8631 (mt) cc_final: 0.8238 (tt) outliers start: 15 outliers final: 7 residues processed: 844 average time/residue: 0.2622 time to fit residues: 328.3887 Evaluate side-chains 452 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 445 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 197 ASN Chi-restraints excluded: chain d residue 448 ASN Chi-restraints excluded: chain 2 residue 197 ASN Chi-restraints excluded: chain 2 residue 448 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 448 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.0470 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 591 GLN d 249 HIS d 302 ASN d 315 GLN d 374 HIS d 478 ASN n 42 GLN r 41 GLN q 6 GLN q 101 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN A 625 ASN ** 2 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 302 ASN 2 315 GLN 2 374 HIS 2 478 ASN 8 6 GLN 8 101 GLN 3 39 GLN D 591 GLN C 249 HIS C 302 ASN C 315 GLN C 374 HIS Q 6 GLN Q 101 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.084031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.060217 restraints weight = 106726.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062103 restraints weight = 58996.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063259 restraints weight = 42714.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063938 restraints weight = 35743.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.064211 restraints weight = 32312.406| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33723 Z= 0.152 Angle : 0.853 15.360 46182 Z= 0.382 Chirality : 0.049 0.229 5664 Planarity : 0.005 0.060 5463 Dihedral : 15.725 102.693 8383 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.80 % Allowed : 10.48 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.13), residues: 3777 helix: -1.22 (0.24), residues: 414 sheet: -1.20 (0.15), residues: 1164 loop : -1.96 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 53 TYR 0.026 0.001 TYR n 87 PHE 0.017 0.002 PHE n 9 TRP 0.018 0.001 TRP 6 96 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00318 (33462) covalent geometry : angle 0.75850 (45450) SS BOND : bond 0.00268 ( 51) SS BOND : angle 1.05772 ( 102) hydrogen bonds : bond 0.03952 ( 900) hydrogen bonds : angle 5.72466 ( 2448) link_ALPHA1-2 : bond 0.00620 ( 15) link_ALPHA1-2 : angle 1.93448 ( 45) link_ALPHA1-3 : bond 0.01502 ( 30) link_ALPHA1-3 : angle 2.55786 ( 90) link_ALPHA1-6 : bond 0.00595 ( 21) link_ALPHA1-6 : angle 1.82878 ( 63) link_BETA1-4 : bond 0.00776 ( 87) link_BETA1-4 : angle 3.01712 ( 261) link_NAG-ASN : bond 0.00627 ( 57) link_NAG-ASN : angle 4.82112 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 524 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 595 ILE cc_start: 0.9309 (pt) cc_final: 0.8947 (mt) REVERT: c 632 ASP cc_start: 0.8489 (t0) cc_final: 0.8260 (t0) REVERT: c 648 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7891 (tp30) REVERT: d 123 THR cc_start: 0.9202 (m) cc_final: 0.8997 (p) REVERT: d 139 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5763 (p) REVERT: d 475 MET cc_start: 0.8544 (tpt) cc_final: 0.8086 (mmt) REVERT: n 26 GLU cc_start: 0.8529 (tt0) cc_final: 0.8297 (tt0) REVERT: n 87 TYR cc_start: 0.7982 (m-10) cc_final: 0.7489 (m-80) REVERT: r 4 LEU cc_start: 0.9129 (mt) cc_final: 0.8880 (mm) REVERT: r 33 THR cc_start: 0.9602 (m) cc_final: 0.9164 (p) REVERT: h 33 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7792 (mm-30) REVERT: h 48 ILE cc_start: 0.8874 (mm) cc_final: 0.8598 (mp) REVERT: h 60 ASN cc_start: 0.7289 (m-40) cc_final: 0.7050 (p0) REVERT: h 80 MET cc_start: 0.6212 (mmt) cc_final: 0.6006 (tpp) REVERT: l 9 LEU cc_start: 0.8396 (mt) cc_final: 0.8144 (tt) REVERT: l 30 ASP cc_start: 0.7854 (p0) cc_final: 0.7626 (p0) REVERT: A 659 ASP cc_start: 0.8201 (t0) cc_final: 0.7999 (t70) REVERT: 2 125 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9266 (tt) REVERT: 2 139 THR cc_start: 0.5968 (OUTLIER) cc_final: 0.5764 (p) REVERT: 6 26 GLU cc_start: 0.7752 (tt0) cc_final: 0.7469 (tt0) REVERT: 6 79 GLU cc_start: 0.7529 (pt0) cc_final: 0.7236 (pt0) REVERT: 3 43 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7192 (ptt-90) REVERT: 3 60 ASN cc_start: 0.7249 (m-40) cc_final: 0.6969 (p0) REVERT: 4 11 LEU cc_start: 0.7906 (mt) cc_final: 0.7688 (tp) REVERT: 4 85 VAL cc_start: 0.7504 (t) cc_final: 0.6873 (t) REVERT: D 659 ASP cc_start: 0.7980 (t0) cc_final: 0.7753 (t70) REVERT: M 46 GLU cc_start: 0.8805 (tt0) cc_final: 0.8579 (tm-30) REVERT: R 32 MET cc_start: 0.8888 (tpp) cc_final: 0.8558 (tpp) REVERT: Q 61 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7748 (ttm-80) REVERT: Q 87 THR cc_start: 0.9133 (m) cc_final: 0.8907 (p) REVERT: H 80 MET cc_start: 0.6674 (mmt) cc_final: 0.6293 (mmm) REVERT: H 82 LEU cc_start: 0.7597 (mt) cc_final: 0.7391 (mp) REVERT: L 9 LEU cc_start: 0.8628 (mt) cc_final: 0.8303 (tp) REVERT: L 11 LEU cc_start: 0.7741 (mt) cc_final: 0.7532 (tp) REVERT: L 82 ASP cc_start: 0.6512 (m-30) cc_final: 0.6131 (m-30) REVERT: L 106 ILE cc_start: 0.8232 (mp) cc_final: 0.7922 (mm) outliers start: 93 outliers final: 51 residues processed: 582 average time/residue: 0.2374 time to fit residues: 212.2760 Evaluate side-chains 481 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 427 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 110 SER Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 69 TRP Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 434 MET Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 4 residue 4 MET Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 58 optimal weight: 9.9990 chunk 311 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.0570 chunk 210 optimal weight: 0.1980 overall best weight: 2.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN 2 249 HIS 5 23 ASN ** 5 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN M 23 ASN ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.081061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.057010 restraints weight = 107488.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058810 restraints weight = 59955.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059927 restraints weight = 43839.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060573 restraints weight = 36923.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.060838 restraints weight = 33531.821| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 33723 Z= 0.225 Angle : 0.814 12.692 46182 Z= 0.372 Chirality : 0.048 0.256 5664 Planarity : 0.005 0.074 5463 Dihedral : 13.487 111.496 8370 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.61 % Allowed : 10.99 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.13), residues: 3777 helix: -0.31 (0.26), residues: 414 sheet: -1.10 (0.14), residues: 1191 loop : -1.69 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG M 30 TYR 0.021 0.002 TYR L 87 PHE 0.023 0.002 PHE 2 288 TRP 0.020 0.002 TRP h 47 HIS 0.005 0.001 HIS m 52 Details of bonding type rmsd covalent geometry : bond 0.00500 (33462) covalent geometry : angle 0.74908 (45450) SS BOND : bond 0.00291 ( 51) SS BOND : angle 1.12803 ( 102) hydrogen bonds : bond 0.03740 ( 900) hydrogen bonds : angle 5.24893 ( 2448) link_ALPHA1-2 : bond 0.00673 ( 15) link_ALPHA1-2 : angle 1.90283 ( 45) link_ALPHA1-3 : bond 0.01373 ( 30) link_ALPHA1-3 : angle 2.24283 ( 90) link_ALPHA1-6 : bond 0.00651 ( 21) link_ALPHA1-6 : angle 1.75114 ( 63) link_BETA1-4 : bond 0.00600 ( 87) link_BETA1-4 : angle 2.83808 ( 261) link_NAG-ASN : bond 0.00545 ( 57) link_NAG-ASN : angle 3.45314 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 452 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 595 ILE cc_start: 0.9357 (pt) cc_final: 0.9076 (mt) REVERT: c 657 GLU cc_start: 0.8492 (tp30) cc_final: 0.8156 (mm-30) REVERT: r 4 LEU cc_start: 0.9111 (mt) cc_final: 0.8836 (mm) REVERT: r 33 THR cc_start: 0.9600 (m) cc_final: 0.9188 (p) REVERT: h 60 ASN cc_start: 0.7398 (m-40) cc_final: 0.7197 (p0) REVERT: l 9 LEU cc_start: 0.8411 (mt) cc_final: 0.8161 (tt) REVERT: l 30 ASP cc_start: 0.8006 (p0) cc_final: 0.7776 (p0) REVERT: l 34 GLU cc_start: 0.7078 (mp0) cc_final: 0.6864 (mp0) REVERT: 2 125 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9329 (tt) REVERT: 6 17 GLN cc_start: 0.8587 (mp10) cc_final: 0.8323 (mp10) REVERT: 6 25 GLU cc_start: 0.7116 (pp20) cc_final: 0.6344 (pp20) REVERT: 7 24 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8772 (ttmm) REVERT: 8 76 ASP cc_start: 0.9062 (p0) cc_final: 0.8707 (p0) REVERT: 3 33 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7836 (mm-30) REVERT: 3 80 MET cc_start: 0.7168 (mmm) cc_final: 0.5939 (mmm) REVERT: D 648 GLU cc_start: 0.8371 (tp30) cc_final: 0.8117 (tp30) REVERT: D 659 ASP cc_start: 0.8058 (t0) cc_final: 0.7794 (t70) REVERT: C 478 ASN cc_start: 0.8779 (m110) cc_final: 0.8573 (m-40) REVERT: M 46 GLU cc_start: 0.8821 (tt0) cc_final: 0.8572 (tm-30) REVERT: R 32 MET cc_start: 0.8969 (tpp) cc_final: 0.8580 (tpp) REVERT: Q 87 THR cc_start: 0.9183 (m) cc_final: 0.8959 (p) REVERT: H 48 ILE cc_start: 0.8799 (mm) cc_final: 0.8400 (mp) REVERT: H 80 MET cc_start: 0.6626 (mmt) cc_final: 0.6353 (mmm) REVERT: H 82 LEU cc_start: 0.7588 (mt) cc_final: 0.7387 (mp) REVERT: L 9 LEU cc_start: 0.8595 (mt) cc_final: 0.8257 (tp) REVERT: L 50 LYS cc_start: 0.7669 (tppt) cc_final: 0.7304 (ttpt) outliers start: 120 outliers final: 81 residues processed: 531 average time/residue: 0.2298 time to fit residues: 187.5430 Evaluate side-chains 476 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 394 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 538 THR Chi-restraints excluded: chain c residue 583 VAL Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 637 ASN Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 110 SER Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain h residue 27 TYR Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 434 MET Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 2 VAL Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 149 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 139 optimal weight: 0.0170 chunk 237 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 23 ASN ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 41 GLN ** h 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS R 41 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.081814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.058062 restraints weight = 105949.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.059860 restraints weight = 58921.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.060998 restraints weight = 43020.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061600 restraints weight = 36111.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.062010 restraints weight = 32878.931| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33723 Z= 0.143 Angle : 0.749 9.924 46182 Z= 0.339 Chirality : 0.047 0.235 5664 Planarity : 0.004 0.061 5463 Dihedral : 12.183 110.849 8370 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.25 % Allowed : 12.50 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.13), residues: 3777 helix: 0.13 (0.26), residues: 417 sheet: -0.89 (0.14), residues: 1266 loop : -1.55 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 4 53 TYR 0.022 0.001 TYR L 87 PHE 0.020 0.002 PHE 8 100D TRP 0.023 0.001 TRP N 96 HIS 0.005 0.001 HIS m 52 Details of bonding type rmsd covalent geometry : bond 0.00310 (33462) covalent geometry : angle 0.68794 (45450) SS BOND : bond 0.00428 ( 51) SS BOND : angle 1.15913 ( 102) hydrogen bonds : bond 0.03339 ( 900) hydrogen bonds : angle 4.99824 ( 2448) link_ALPHA1-2 : bond 0.00577 ( 15) link_ALPHA1-2 : angle 1.86926 ( 45) link_ALPHA1-3 : bond 0.01506 ( 30) link_ALPHA1-3 : angle 2.22157 ( 90) link_ALPHA1-6 : bond 0.00773 ( 21) link_ALPHA1-6 : angle 1.76332 ( 63) link_BETA1-4 : bond 0.00573 ( 87) link_BETA1-4 : angle 2.71769 ( 261) link_NAG-ASN : bond 0.00357 ( 57) link_NAG-ASN : angle 2.98942 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 437 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 595 ILE cc_start: 0.9344 (pt) cc_final: 0.9056 (mt) REVERT: d 123 THR cc_start: 0.9359 (m) cc_final: 0.9134 (p) REVERT: r 4 LEU cc_start: 0.9070 (mt) cc_final: 0.8766 (mm) REVERT: r 33 THR cc_start: 0.9556 (m) cc_final: 0.9147 (p) REVERT: h 48 ILE cc_start: 0.8861 (mm) cc_final: 0.8413 (mp) REVERT: h 80 MET cc_start: 0.7310 (mmm) cc_final: 0.6111 (mmm) REVERT: l 9 LEU cc_start: 0.8402 (mt) cc_final: 0.8160 (tt) REVERT: l 30 ASP cc_start: 0.7895 (p0) cc_final: 0.7668 (p0) REVERT: l 34 GLU cc_start: 0.7143 (mp0) cc_final: 0.6912 (mp0) REVERT: l 105 GLU cc_start: 0.4045 (OUTLIER) cc_final: 0.3679 (tt0) REVERT: A 633 LYS cc_start: 0.9051 (pptt) cc_final: 0.8849 (pptt) REVERT: 2 125 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9392 (tt) REVERT: 7 24 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8778 (ttmm) REVERT: 7 33 THR cc_start: 0.9669 (m) cc_final: 0.9236 (p) REVERT: 3 33 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7832 (mm-30) REVERT: 3 43 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6885 (ptt-90) REVERT: 3 80 MET cc_start: 0.7163 (mmm) cc_final: 0.5854 (mmm) REVERT: 4 34 GLU cc_start: 0.6984 (mp0) cc_final: 0.6660 (mp0) REVERT: 4 36 TYR cc_start: 0.7146 (m-10) cc_final: 0.6749 (m-10) REVERT: D 648 GLU cc_start: 0.8393 (tp30) cc_final: 0.8108 (tp30) REVERT: D 659 ASP cc_start: 0.7940 (t0) cc_final: 0.7691 (t70) REVERT: N 87 TYR cc_start: 0.8552 (m-80) cc_final: 0.8099 (m-80) REVERT: M 46 GLU cc_start: 0.8815 (tt0) cc_final: 0.8586 (tm-30) REVERT: R 32 MET cc_start: 0.8889 (tpp) cc_final: 0.8530 (tpp) REVERT: R 49 ASP cc_start: 0.8069 (t0) cc_final: 0.7665 (t0) REVERT: Q 87 THR cc_start: 0.9155 (m) cc_final: 0.8943 (p) REVERT: H 29 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7196 (t80) REVERT: H 48 ILE cc_start: 0.8740 (mm) cc_final: 0.8365 (mp) REVERT: H 80 MET cc_start: 0.6513 (mmt) cc_final: 0.6257 (mmm) REVERT: H 82 LEU cc_start: 0.7621 (mt) cc_final: 0.7414 (mp) REVERT: L 9 LEU cc_start: 0.8616 (mt) cc_final: 0.8267 (tp) REVERT: L 37 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8632 (pp) REVERT: L 90 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8258 (pp30) outliers start: 108 outliers final: 70 residues processed: 508 average time/residue: 0.2386 time to fit residues: 187.5445 Evaluate side-chains 465 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 390 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 110 SER Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 6 residue 13 VAL Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 13 LEU Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 3 residue 27 TYR Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 305 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 356 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 373 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 41 GLN ** h 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 352 HIS ** 5 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 41 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.081524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.057772 restraints weight = 106001.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059558 restraints weight = 59052.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060663 restraints weight = 43004.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.061300 restraints weight = 36189.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061658 restraints weight = 32843.430| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33723 Z= 0.152 Angle : 0.737 13.693 46182 Z= 0.334 Chirality : 0.046 0.245 5664 Planarity : 0.004 0.062 5463 Dihedral : 11.243 110.561 8370 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.40 % Allowed : 13.19 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.13), residues: 3777 helix: 0.38 (0.27), residues: 417 sheet: -0.74 (0.14), residues: 1266 loop : -1.42 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 4 53 TYR 0.020 0.001 TYR 4 87 PHE 0.019 0.002 PHE 3 98 TRP 0.012 0.001 TRP q 50 HIS 0.004 0.001 HIS m 52 Details of bonding type rmsd covalent geometry : bond 0.00336 (33462) covalent geometry : angle 0.67980 (45450) SS BOND : bond 0.00245 ( 51) SS BOND : angle 1.40425 ( 102) hydrogen bonds : bond 0.03225 ( 900) hydrogen bonds : angle 4.83294 ( 2448) link_ALPHA1-2 : bond 0.00538 ( 15) link_ALPHA1-2 : angle 1.83164 ( 45) link_ALPHA1-3 : bond 0.01507 ( 30) link_ALPHA1-3 : angle 2.20835 ( 90) link_ALPHA1-6 : bond 0.00847 ( 21) link_ALPHA1-6 : angle 1.70875 ( 63) link_BETA1-4 : bond 0.00569 ( 87) link_BETA1-4 : angle 2.62286 ( 261) link_NAG-ASN : bond 0.00353 ( 57) link_NAG-ASN : angle 2.75208 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 413 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 595 ILE cc_start: 0.9356 (pt) cc_final: 0.9092 (mt) REVERT: d 123 THR cc_start: 0.9382 (m) cc_final: 0.9168 (p) REVERT: d 125 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9219 (tt) REVERT: d 139 THR cc_start: 0.6510 (OUTLIER) cc_final: 0.6232 (p) REVERT: n 87 TYR cc_start: 0.7920 (m-80) cc_final: 0.7089 (m-80) REVERT: r 33 THR cc_start: 0.9560 (m) cc_final: 0.9149 (p) REVERT: h 48 ILE cc_start: 0.8829 (mm) cc_final: 0.8418 (mp) REVERT: h 80 MET cc_start: 0.7369 (mmm) cc_final: 0.6263 (mmm) REVERT: l 9 LEU cc_start: 0.8504 (mt) cc_final: 0.8272 (tt) REVERT: l 30 ASP cc_start: 0.7960 (p0) cc_final: 0.7734 (p0) REVERT: l 34 GLU cc_start: 0.7225 (mp0) cc_final: 0.7000 (mp0) REVERT: l 105 GLU cc_start: 0.3890 (OUTLIER) cc_final: 0.3548 (tt0) REVERT: 2 125 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9420 (tt) REVERT: 2 139 THR cc_start: 0.6327 (OUTLIER) cc_final: 0.6112 (p) REVERT: 7 24 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8833 (ttmm) REVERT: 7 33 THR cc_start: 0.9676 (m) cc_final: 0.9242 (p) REVERT: 3 33 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7758 (mm-30) REVERT: 3 43 ARG cc_start: 0.7146 (mtm-85) cc_final: 0.6921 (mtm-85) REVERT: 3 80 MET cc_start: 0.7097 (mmm) cc_final: 0.6155 (mmm) REVERT: 4 37 LEU cc_start: 0.8486 (pp) cc_final: 0.8285 (tt) REVERT: D 648 GLU cc_start: 0.8387 (tp30) cc_final: 0.8080 (tp30) REVERT: D 659 ASP cc_start: 0.8040 (t0) cc_final: 0.7809 (t70) REVERT: N 87 TYR cc_start: 0.8545 (m-80) cc_final: 0.8014 (m-80) REVERT: M 46 GLU cc_start: 0.8817 (tt0) cc_final: 0.8584 (tm-30) REVERT: R 32 MET cc_start: 0.8860 (tpp) cc_final: 0.8553 (tpp) REVERT: R 49 ASP cc_start: 0.8086 (t0) cc_final: 0.7652 (t0) REVERT: H 29 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7217 (t80) REVERT: H 48 ILE cc_start: 0.8760 (mm) cc_final: 0.8409 (mp) REVERT: H 82 LEU cc_start: 0.7617 (mt) cc_final: 0.7375 (mp) REVERT: L 4 MET cc_start: 0.7306 (mmm) cc_final: 0.7060 (mmm) REVERT: L 9 LEU cc_start: 0.8616 (mt) cc_final: 0.8281 (tp) REVERT: L 90 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8288 (pp30) outliers start: 113 outliers final: 79 residues processed: 491 average time/residue: 0.2357 time to fit residues: 177.7189 Evaluate side-chains 464 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 378 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 538 THR Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 626 MET Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 110 SER Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain q residue 63 LEU Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 13 LEU Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 332 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 chunk 303 optimal weight: 6.9990 chunk 225 optimal weight: 0.3980 chunk 190 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 246 GLN ** 5 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 64 GLN ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN R 41 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.080681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056758 restraints weight = 106132.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058518 restraints weight = 59520.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059621 restraints weight = 43592.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060246 restraints weight = 36697.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.060589 restraints weight = 33382.591| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33723 Z= 0.184 Angle : 0.747 10.943 46182 Z= 0.341 Chirality : 0.046 0.244 5664 Planarity : 0.004 0.060 5463 Dihedral : 10.656 111.261 8370 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.70 % Allowed : 13.37 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -1.29 (0.14), residues: 3777 helix: 0.60 (0.27), residues: 417 sheet: -0.59 (0.14), residues: 1263 loop : -1.33 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 4 53 TYR 0.018 0.001 TYR n 87 PHE 0.021 0.002 PHE H 98 TRP 0.013 0.001 TRP Q 50 HIS 0.003 0.001 HIS m 52 Details of bonding type rmsd covalent geometry : bond 0.00413 (33462) covalent geometry : angle 0.69166 (45450) SS BOND : bond 0.00338 ( 51) SS BOND : angle 1.69612 ( 102) hydrogen bonds : bond 0.03283 ( 900) hydrogen bonds : angle 4.75491 ( 2448) link_ALPHA1-2 : bond 0.00516 ( 15) link_ALPHA1-2 : angle 1.86387 ( 45) link_ALPHA1-3 : bond 0.01485 ( 30) link_ALPHA1-3 : angle 2.27098 ( 90) link_ALPHA1-6 : bond 0.00908 ( 21) link_ALPHA1-6 : angle 1.69543 ( 63) link_BETA1-4 : bond 0.00532 ( 87) link_BETA1-4 : angle 2.57111 ( 261) link_NAG-ASN : bond 0.00391 ( 57) link_NAG-ASN : angle 2.69008 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 403 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 543 ASN cc_start: 0.8673 (t0) cc_final: 0.8467 (t0) REVERT: c 595 ILE cc_start: 0.9346 (pt) cc_final: 0.9130 (mt) REVERT: d 103 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8149 (pp30) REVERT: d 125 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9238 (tt) REVERT: d 139 THR cc_start: 0.6439 (OUTLIER) cc_final: 0.6101 (p) REVERT: n 87 TYR cc_start: 0.8214 (m-80) cc_final: 0.7174 (m-80) REVERT: r 33 THR cc_start: 0.9614 (m) cc_final: 0.9170 (p) REVERT: h 46 ASP cc_start: 0.7951 (m-30) cc_final: 0.7299 (m-30) REVERT: h 48 ILE cc_start: 0.8868 (mm) cc_final: 0.8469 (mp) REVERT: h 80 MET cc_start: 0.7436 (mmm) cc_final: 0.6383 (mmm) REVERT: l 9 LEU cc_start: 0.8530 (mt) cc_final: 0.8282 (tt) REVERT: l 30 ASP cc_start: 0.8059 (p0) cc_final: 0.7841 (p0) REVERT: l 37 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8628 (pp) REVERT: l 105 GLU cc_start: 0.4183 (OUTLIER) cc_final: 0.3811 (tt0) REVERT: 2 139 THR cc_start: 0.6366 (OUTLIER) cc_final: 0.6110 (p) REVERT: 5 16 GLU cc_start: 0.8092 (tt0) cc_final: 0.7006 (tm-30) REVERT: 7 24 LYS cc_start: 0.9178 (ttmm) cc_final: 0.8840 (ttmm) REVERT: 8 1 GLN cc_start: 0.8805 (pm20) cc_final: 0.8445 (pp30) REVERT: 3 33 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7775 (mm-30) REVERT: 3 80 MET cc_start: 0.7069 (mmm) cc_final: 0.6112 (mmm) REVERT: 4 37 LEU cc_start: 0.8567 (pp) cc_final: 0.8330 (tt) REVERT: D 530 MET cc_start: 0.8013 (ptm) cc_final: 0.7566 (ptm) REVERT: D 648 GLU cc_start: 0.8418 (tp30) cc_final: 0.8107 (tp30) REVERT: D 659 ASP cc_start: 0.8019 (t0) cc_final: 0.7810 (t70) REVERT: N 87 TYR cc_start: 0.8620 (m-80) cc_final: 0.8016 (m-80) REVERT: M 46 GLU cc_start: 0.8805 (tt0) cc_final: 0.8499 (tm-30) REVERT: R 32 MET cc_start: 0.8898 (tpp) cc_final: 0.8566 (tpp) REVERT: R 49 ASP cc_start: 0.8108 (t0) cc_final: 0.7723 (t0) REVERT: H 29 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7304 (t80) REVERT: H 48 ILE cc_start: 0.8742 (mm) cc_final: 0.8421 (mp) REVERT: H 80 MET cc_start: 0.7092 (mmm) cc_final: 0.5779 (mmm) REVERT: H 82 LEU cc_start: 0.7638 (mt) cc_final: 0.7381 (mp) REVERT: L 9 LEU cc_start: 0.8653 (mt) cc_final: 0.8333 (tp) REVERT: L 90 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8355 (pp30) outliers start: 123 outliers final: 78 residues processed: 494 average time/residue: 0.2312 time to fit residues: 177.4922 Evaluate side-chains 457 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 371 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 538 THR Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 103 GLN Chi-restraints excluded: chain d residue 110 SER Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain q residue 63 LEU Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 13 LEU Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 370 optimal weight: 0.1980 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 160 optimal weight: 0.4980 chunk 355 optimal weight: 8.9990 chunk 263 optimal weight: 0.0370 chunk 340 optimal weight: 3.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 41 GLN h 1 GLN ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 203 GLN ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 41 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.081316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.057464 restraints weight = 106593.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.059261 restraints weight = 59270.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.060376 restraints weight = 43200.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.061023 restraints weight = 36252.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.061344 restraints weight = 32925.637| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33723 Z= 0.140 Angle : 0.733 11.011 46182 Z= 0.334 Chirality : 0.046 0.249 5664 Planarity : 0.004 0.061 5463 Dihedral : 10.165 109.168 8370 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.34 % Allowed : 14.06 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -1.15 (0.14), residues: 3777 helix: 0.75 (0.27), residues: 417 sheet: -0.48 (0.15), residues: 1254 loop : -1.25 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 4 53 TYR 0.019 0.001 TYR c 638 PHE 0.020 0.001 PHE H 98 TRP 0.012 0.001 TRP Q 50 HIS 0.004 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00311 (33462) covalent geometry : angle 0.67980 (45450) SS BOND : bond 0.00247 ( 51) SS BOND : angle 1.74629 ( 102) hydrogen bonds : bond 0.03119 ( 900) hydrogen bonds : angle 4.60697 ( 2448) link_ALPHA1-2 : bond 0.00477 ( 15) link_ALPHA1-2 : angle 1.82891 ( 45) link_ALPHA1-3 : bond 0.01525 ( 30) link_ALPHA1-3 : angle 2.14799 ( 90) link_ALPHA1-6 : bond 0.00957 ( 21) link_ALPHA1-6 : angle 1.68151 ( 63) link_BETA1-4 : bond 0.00546 ( 87) link_BETA1-4 : angle 2.51710 ( 261) link_NAG-ASN : bond 0.00311 ( 57) link_NAG-ASN : angle 2.53799 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 396 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 543 ASN cc_start: 0.8678 (t0) cc_final: 0.8414 (t0) REVERT: d 125 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9114 (tt) REVERT: d 139 THR cc_start: 0.6364 (OUTLIER) cc_final: 0.6020 (p) REVERT: n 87 TYR cc_start: 0.8140 (m-80) cc_final: 0.7160 (m-80) REVERT: r 33 THR cc_start: 0.9580 (m) cc_final: 0.9068 (p) REVERT: h 46 ASP cc_start: 0.8001 (m-30) cc_final: 0.7365 (m-30) REVERT: h 48 ILE cc_start: 0.8833 (mm) cc_final: 0.8427 (mp) REVERT: h 80 MET cc_start: 0.7455 (mmm) cc_final: 0.6479 (mmm) REVERT: l 9 LEU cc_start: 0.8539 (mt) cc_final: 0.8304 (tt) REVERT: l 37 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8588 (pp) REVERT: l 105 GLU cc_start: 0.4534 (OUTLIER) cc_final: 0.4183 (tt0) REVERT: A 588 ARG cc_start: 0.8476 (ttm170) cc_final: 0.7709 (mtm180) REVERT: 2 139 THR cc_start: 0.6349 (OUTLIER) cc_final: 0.6116 (p) REVERT: 5 16 GLU cc_start: 0.8043 (tt0) cc_final: 0.6982 (tm-30) REVERT: 7 24 LYS cc_start: 0.9178 (ttmm) cc_final: 0.8826 (ttmm) REVERT: 7 33 THR cc_start: 0.9678 (m) cc_final: 0.9246 (p) REVERT: 8 1 GLN cc_start: 0.8813 (pm20) cc_final: 0.8463 (pp30) REVERT: 3 33 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7759 (mm-30) REVERT: 3 80 MET cc_start: 0.6964 (mmm) cc_final: 0.6259 (mmm) REVERT: 3 82 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6564 (mmt90) REVERT: 3 82 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7237 (mp) REVERT: D 530 MET cc_start: 0.7873 (ptm) cc_final: 0.7364 (ptm) REVERT: D 648 GLU cc_start: 0.8412 (tp30) cc_final: 0.8088 (tp30) REVERT: D 659 ASP cc_start: 0.8007 (t0) cc_final: 0.7771 (t70) REVERT: N 87 TYR cc_start: 0.8583 (m-80) cc_final: 0.7997 (m-80) REVERT: M 46 GLU cc_start: 0.8787 (tt0) cc_final: 0.8439 (tm-30) REVERT: R 32 MET cc_start: 0.8836 (tpp) cc_final: 0.8524 (tpp) REVERT: R 33 THR cc_start: 0.9534 (m) cc_final: 0.9006 (p) REVERT: R 49 ASP cc_start: 0.8101 (t0) cc_final: 0.7714 (t0) REVERT: H 29 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7268 (t80) REVERT: H 48 ILE cc_start: 0.8717 (mm) cc_final: 0.8425 (mp) REVERT: L 9 LEU cc_start: 0.8639 (mt) cc_final: 0.8324 (tp) REVERT: L 90 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8410 (tm-30) REVERT: L 105 GLU cc_start: 0.4335 (OUTLIER) cc_final: 0.3977 (tt0) outliers start: 111 outliers final: 84 residues processed: 484 average time/residue: 0.2300 time to fit residues: 172.4561 Evaluate side-chains 469 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 375 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 111 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 63 LEU Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 13 LEU Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 82 ARG Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 2 optimal weight: 0.9990 chunk 363 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 228 optimal weight: 0.0970 chunk 183 optimal weight: 3.9990 chunk 328 optimal weight: 5.9990 chunk 169 optimal weight: 0.2980 chunk 356 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 80 ASN ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.057292 restraints weight = 106247.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.059069 restraints weight = 59283.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.060185 restraints weight = 43389.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060821 restraints weight = 36547.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.061151 restraints weight = 33211.388| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 33723 Z= 0.149 Angle : 0.737 10.680 46182 Z= 0.337 Chirality : 0.046 0.253 5664 Planarity : 0.004 0.062 5463 Dihedral : 9.734 108.563 8370 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.10 % Allowed : 14.72 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -1.02 (0.14), residues: 3777 helix: 0.99 (0.28), residues: 402 sheet: -0.31 (0.15), residues: 1212 loop : -1.23 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 4 53 TYR 0.017 0.001 TYR c 638 PHE 0.020 0.001 PHE H 98 TRP 0.013 0.001 TRP Q 50 HIS 0.004 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00335 (33462) covalent geometry : angle 0.68577 (45450) SS BOND : bond 0.00552 ( 51) SS BOND : angle 1.69392 ( 102) hydrogen bonds : bond 0.03092 ( 900) hydrogen bonds : angle 4.52395 ( 2448) link_ALPHA1-2 : bond 0.00454 ( 15) link_ALPHA1-2 : angle 1.82186 ( 45) link_ALPHA1-3 : bond 0.01532 ( 30) link_ALPHA1-3 : angle 2.16018 ( 90) link_ALPHA1-6 : bond 0.00992 ( 21) link_ALPHA1-6 : angle 1.64113 ( 63) link_BETA1-4 : bond 0.00540 ( 87) link_BETA1-4 : angle 2.49443 ( 261) link_NAG-ASN : bond 0.00315 ( 57) link_NAG-ASN : angle 2.47713 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 390 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 543 ASN cc_start: 0.8769 (t0) cc_final: 0.8542 (t0) REVERT: c 632 ASP cc_start: 0.8677 (t0) cc_final: 0.8402 (t0) REVERT: d 103 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8151 (pp30) REVERT: d 139 THR cc_start: 0.6066 (OUTLIER) cc_final: 0.5728 (p) REVERT: n 87 TYR cc_start: 0.8159 (m-80) cc_final: 0.7236 (m-80) REVERT: r 33 THR cc_start: 0.9587 (m) cc_final: 0.9066 (p) REVERT: q 76 ASP cc_start: 0.8064 (t0) cc_final: 0.7536 (p0) REVERT: h 46 ASP cc_start: 0.8016 (m-30) cc_final: 0.7365 (m-30) REVERT: h 48 ILE cc_start: 0.8853 (mm) cc_final: 0.8463 (mp) REVERT: h 80 MET cc_start: 0.7457 (mmm) cc_final: 0.6545 (mmm) REVERT: l 4 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.7048 (mmm) REVERT: l 9 LEU cc_start: 0.8638 (mt) cc_final: 0.8323 (tt) REVERT: l 37 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8684 (pp) REVERT: l 105 GLU cc_start: 0.4529 (OUTLIER) cc_final: 0.4172 (tt0) REVERT: A 588 ARG cc_start: 0.8506 (ttm170) cc_final: 0.7739 (mtm180) REVERT: 2 139 THR cc_start: 0.6041 (OUTLIER) cc_final: 0.5812 (p) REVERT: 7 24 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8794 (ttmm) REVERT: 7 33 THR cc_start: 0.9673 (m) cc_final: 0.9249 (p) REVERT: 8 1 GLN cc_start: 0.8850 (pm20) cc_final: 0.8482 (pp30) REVERT: 3 33 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7738 (mm-30) REVERT: 3 80 MET cc_start: 0.6834 (mmm) cc_final: 0.6291 (mmm) REVERT: 3 82 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6535 (mmt90) REVERT: 3 82 LEU cc_start: 0.7498 (mp) cc_final: 0.7289 (mp) REVERT: 4 24 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7757 (ttm110) REVERT: D 530 MET cc_start: 0.7937 (ptm) cc_final: 0.7435 (ptm) REVERT: D 648 GLU cc_start: 0.8412 (tp30) cc_final: 0.8089 (tp30) REVERT: D 659 ASP cc_start: 0.7976 (t0) cc_final: 0.7755 (t70) REVERT: M 13 LYS cc_start: 0.8425 (tppt) cc_final: 0.7762 (tppt) REVERT: M 46 GLU cc_start: 0.8794 (tt0) cc_final: 0.8441 (tm-30) REVERT: R 32 MET cc_start: 0.8845 (tpp) cc_final: 0.8522 (tpp) REVERT: R 49 ASP cc_start: 0.8091 (t0) cc_final: 0.7734 (t0) REVERT: H 29 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7309 (t80) REVERT: H 48 ILE cc_start: 0.8686 (mm) cc_final: 0.8364 (mp) REVERT: H 80 MET cc_start: 0.7075 (mmm) cc_final: 0.5841 (mmm) REVERT: L 4 MET cc_start: 0.7213 (mmm) cc_final: 0.6568 (mmm) REVERT: L 9 LEU cc_start: 0.8710 (mt) cc_final: 0.8405 (tp) outliers start: 103 outliers final: 81 residues processed: 471 average time/residue: 0.2353 time to fit residues: 171.4626 Evaluate side-chains 467 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 378 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 538 THR Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 103 GLN Chi-restraints excluded: chain d residue 111 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 63 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 13 LEU Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 83 THR Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 82 ARG Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 24 optimal weight: 0.9980 chunk 272 optimal weight: 0.7980 chunk 278 optimal weight: 0.0970 chunk 124 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 325 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 chunk 286 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 64 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.3514 r_free = 0.3514 target = 0.081782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057996 restraints weight = 105550.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.059780 restraints weight = 59016.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.060897 restraints weight = 43178.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061529 restraints weight = 36374.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061868 restraints weight = 33094.357| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33723 Z= 0.128 Angle : 0.732 11.645 46182 Z= 0.335 Chirality : 0.046 0.249 5664 Planarity : 0.004 0.063 5463 Dihedral : 9.338 107.124 8370 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.04 % Allowed : 14.94 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -0.83 (0.14), residues: 3777 helix: 1.32 (0.29), residues: 384 sheet: -0.19 (0.15), residues: 1194 loop : -1.11 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 4 53 TYR 0.017 0.001 TYR c 638 PHE 0.021 0.001 PHE H 98 TRP 0.012 0.001 TRP Q 50 HIS 0.003 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00283 (33462) covalent geometry : angle 0.68424 (45450) SS BOND : bond 0.00265 ( 51) SS BOND : angle 1.57856 ( 102) hydrogen bonds : bond 0.03043 ( 900) hydrogen bonds : angle 4.43957 ( 2448) link_ALPHA1-2 : bond 0.00447 ( 15) link_ALPHA1-2 : angle 1.78402 ( 45) link_ALPHA1-3 : bond 0.01561 ( 30) link_ALPHA1-3 : angle 2.08639 ( 90) link_ALPHA1-6 : bond 0.01023 ( 21) link_ALPHA1-6 : angle 1.62618 ( 63) link_BETA1-4 : bond 0.00558 ( 87) link_BETA1-4 : angle 2.45563 ( 261) link_NAG-ASN : bond 0.00298 ( 57) link_NAG-ASN : angle 2.36762 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 399 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 632 ASP cc_start: 0.8626 (t0) cc_final: 0.8362 (t0) REVERT: d 103 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8132 (pp30) REVERT: d 125 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9144 (tt) REVERT: d 139 THR cc_start: 0.6019 (OUTLIER) cc_final: 0.5684 (p) REVERT: n 87 TYR cc_start: 0.8059 (m-80) cc_final: 0.7248 (m-80) REVERT: r 33 THR cc_start: 0.9549 (m) cc_final: 0.9043 (p) REVERT: r 49 ASP cc_start: 0.8077 (t0) cc_final: 0.7687 (t0) REVERT: h 39 GLN cc_start: 0.7237 (tp40) cc_final: 0.6916 (tp40) REVERT: h 46 ASP cc_start: 0.7883 (m-30) cc_final: 0.7286 (m-30) REVERT: h 48 ILE cc_start: 0.8852 (mm) cc_final: 0.8328 (mp) REVERT: h 80 MET cc_start: 0.7487 (mmm) cc_final: 0.6599 (mmm) REVERT: l 4 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7103 (mmm) REVERT: l 9 LEU cc_start: 0.8690 (mt) cc_final: 0.8371 (tt) REVERT: l 105 GLU cc_start: 0.4646 (OUTLIER) cc_final: 0.4309 (tt0) REVERT: 2 139 THR cc_start: 0.6068 (OUTLIER) cc_final: 0.5790 (p) REVERT: 5 16 GLU cc_start: 0.8080 (tt0) cc_final: 0.7018 (tm-30) REVERT: 7 24 LYS cc_start: 0.9190 (ttmm) cc_final: 0.8834 (ttmm) REVERT: 7 33 THR cc_start: 0.9643 (m) cc_final: 0.9181 (p) REVERT: 8 1 GLN cc_start: 0.8883 (pm20) cc_final: 0.8511 (pp30) REVERT: 3 33 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7681 (mm-30) REVERT: 3 80 MET cc_start: 0.6700 (mmm) cc_final: 0.6177 (mmm) REVERT: 3 82 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6517 (mmt90) REVERT: D 530 MET cc_start: 0.7897 (ptm) cc_final: 0.7407 (ptm) REVERT: D 648 GLU cc_start: 0.8406 (tp30) cc_final: 0.8071 (tp30) REVERT: D 659 ASP cc_start: 0.7967 (t0) cc_final: 0.7764 (t70) REVERT: N 87 TYR cc_start: 0.8155 (m-80) cc_final: 0.7955 (m-80) REVERT: M 46 GLU cc_start: 0.8794 (tt0) cc_final: 0.8351 (tm-30) REVERT: R 33 THR cc_start: 0.9505 (m) cc_final: 0.8985 (p) REVERT: R 49 ASP cc_start: 0.8062 (t0) cc_final: 0.7724 (t0) REVERT: H 48 ILE cc_start: 0.8682 (mm) cc_final: 0.8367 (mp) REVERT: H 80 MET cc_start: 0.7236 (mmm) cc_final: 0.5982 (mmm) REVERT: H 82 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6828 (tp) REVERT: L 4 MET cc_start: 0.7299 (mmm) cc_final: 0.6838 (mmm) REVERT: L 9 LEU cc_start: 0.8745 (mt) cc_final: 0.8439 (tp) REVERT: L 105 GLU cc_start: 0.4378 (OUTLIER) cc_final: 0.3982 (tt0) outliers start: 101 outliers final: 79 residues processed: 479 average time/residue: 0.2355 time to fit residues: 173.2444 Evaluate side-chains 463 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 375 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 103 GLN Chi-restraints excluded: chain d residue 111 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 63 LEU Chi-restraints excluded: chain q residue 100 CYS Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 13 LEU Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 7 residue 80 GLU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 82 ARG Chi-restraints excluded: chain 4 residue 4 MET Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 119 optimal weight: 0.4980 chunk 358 optimal weight: 6.9990 chunk 254 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 355 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 543 ASN r 41 GLN ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.081664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.057831 restraints weight = 106586.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.059617 restraints weight = 59345.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060718 restraints weight = 43291.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061354 restraints weight = 36479.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061722 restraints weight = 33132.265| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33723 Z= 0.143 Angle : 0.772 25.597 46182 Z= 0.351 Chirality : 0.047 0.580 5664 Planarity : 0.004 0.064 5463 Dihedral : 9.182 106.755 8370 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.62 % Allowed : 15.66 % Favored : 81.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -0.77 (0.14), residues: 3777 helix: 1.42 (0.29), residues: 381 sheet: -0.01 (0.15), residues: 1152 loop : -1.15 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 4 53 TYR 0.019 0.001 TYR q 32 PHE 0.028 0.001 PHE q 91 TRP 0.016 0.001 TRP 2 112 HIS 0.005 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00316 (33462) covalent geometry : angle 0.71092 (45450) SS BOND : bond 0.00217 ( 51) SS BOND : angle 1.56299 ( 102) hydrogen bonds : bond 0.03049 ( 900) hydrogen bonds : angle 4.38912 ( 2448) link_ALPHA1-2 : bond 0.00428 ( 15) link_ALPHA1-2 : angle 1.76827 ( 45) link_ALPHA1-3 : bond 0.01563 ( 30) link_ALPHA1-3 : angle 2.10159 ( 90) link_ALPHA1-6 : bond 0.01027 ( 21) link_ALPHA1-6 : angle 1.60821 ( 63) link_BETA1-4 : bond 0.00748 ( 87) link_BETA1-4 : angle 2.57419 ( 261) link_NAG-ASN : bond 0.00303 ( 57) link_NAG-ASN : angle 3.33731 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 394 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 632 ASP cc_start: 0.8655 (t0) cc_final: 0.8387 (t0) REVERT: d 103 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8236 (pp30) REVERT: d 125 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9146 (tt) REVERT: d 139 THR cc_start: 0.6066 (OUTLIER) cc_final: 0.5702 (p) REVERT: n 87 TYR cc_start: 0.8040 (m-80) cc_final: 0.7206 (m-80) REVERT: r 33 THR cc_start: 0.9542 (m) cc_final: 0.8993 (p) REVERT: r 49 ASP cc_start: 0.8069 (t0) cc_final: 0.7687 (t0) REVERT: h 46 ASP cc_start: 0.7895 (m-30) cc_final: 0.7356 (m-30) REVERT: h 48 ILE cc_start: 0.8745 (mm) cc_final: 0.8343 (mp) REVERT: h 52 ASP cc_start: 0.7830 (t0) cc_final: 0.7367 (t0) REVERT: h 62 LYS cc_start: 0.9445 (mtmm) cc_final: 0.9199 (mtpp) REVERT: h 80 MET cc_start: 0.7425 (mmm) cc_final: 0.6456 (mmm) REVERT: l 9 LEU cc_start: 0.8694 (mt) cc_final: 0.8370 (tt) REVERT: l 105 GLU cc_start: 0.4646 (OUTLIER) cc_final: 0.4324 (tt0) REVERT: A 588 ARG cc_start: 0.8521 (ttm170) cc_final: 0.7764 (mtm180) REVERT: 2 139 THR cc_start: 0.6094 (OUTLIER) cc_final: 0.5825 (p) REVERT: 5 13 LYS cc_start: 0.8405 (mmmm) cc_final: 0.7998 (mmmt) REVERT: 5 16 GLU cc_start: 0.8071 (tt0) cc_final: 0.7127 (tm-30) REVERT: 7 33 THR cc_start: 0.9646 (m) cc_final: 0.9208 (p) REVERT: 8 1 GLN cc_start: 0.8917 (pm20) cc_final: 0.8525 (pp30) REVERT: 3 33 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7675 (mm-30) REVERT: 3 80 MET cc_start: 0.6768 (mmm) cc_final: 0.6191 (mmm) REVERT: 3 82 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6494 (mmt90) REVERT: 4 24 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7722 (ttm110) REVERT: D 530 MET cc_start: 0.7915 (ptm) cc_final: 0.7418 (ptm) REVERT: D 648 GLU cc_start: 0.8406 (tp30) cc_final: 0.8070 (tp30) REVERT: C 271 MET cc_start: 0.8588 (mmt) cc_final: 0.8221 (mmt) REVERT: N 87 TYR cc_start: 0.8154 (m-80) cc_final: 0.7904 (m-80) REVERT: M 46 GLU cc_start: 0.8724 (tt0) cc_final: 0.8357 (tm-30) REVERT: R 33 THR cc_start: 0.9466 (m) cc_final: 0.8990 (p) REVERT: R 49 ASP cc_start: 0.8072 (t0) cc_final: 0.7737 (t0) REVERT: H 48 ILE cc_start: 0.8676 (mm) cc_final: 0.8256 (mp) REVERT: H 80 MET cc_start: 0.7306 (mmm) cc_final: 0.6020 (mmm) REVERT: L 4 MET cc_start: 0.7231 (mmm) cc_final: 0.6741 (mmm) REVERT: L 9 LEU cc_start: 0.8784 (mt) cc_final: 0.8484 (tp) REVERT: L 24 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7479 (ttm170) REVERT: L 105 GLU cc_start: 0.4354 (OUTLIER) cc_final: 0.3974 (tt0) outliers start: 87 outliers final: 74 residues processed: 467 average time/residue: 0.2417 time to fit residues: 174.0379 Evaluate side-chains 453 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 372 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 103 GLN Chi-restraints excluded: chain d residue 111 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 63 LEU Chi-restraints excluded: chain q residue 100 CYS Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 13 LEU Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 82 ARG Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 269 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 331 optimal weight: 5.9990 chunk 252 optimal weight: 0.0060 chunk 268 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 72 optimal weight: 0.0670 chunk 293 optimal weight: 0.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 38 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.3503 r_free = 0.3503 target = 0.081272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.057415 restraints weight = 106448.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.059161 restraints weight = 59446.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.060253 restraints weight = 43506.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.060891 restraints weight = 36677.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.061240 restraints weight = 33346.697| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33723 Z= 0.157 Angle : 0.765 20.176 46182 Z= 0.350 Chirality : 0.046 0.306 5664 Planarity : 0.004 0.063 5463 Dihedral : 9.050 107.163 8370 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.68 % Allowed : 16.02 % Favored : 81.30 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -0.76 (0.14), residues: 3777 helix: 1.42 (0.29), residues: 381 sheet: -0.07 (0.15), residues: 1188 loop : -1.12 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 4 53 TYR 0.016 0.001 TYR c 638 PHE 0.026 0.001 PHE q 91 TRP 0.021 0.001 TRP 2 112 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00354 (33462) covalent geometry : angle 0.70910 (45450) SS BOND : bond 0.00239 ( 51) SS BOND : angle 1.59078 ( 102) hydrogen bonds : bond 0.03113 ( 900) hydrogen bonds : angle 4.41519 ( 2448) link_ALPHA1-2 : bond 0.00427 ( 15) link_ALPHA1-2 : angle 1.77112 ( 45) link_ALPHA1-3 : bond 0.01497 ( 30) link_ALPHA1-3 : angle 2.11842 ( 90) link_ALPHA1-6 : bond 0.01032 ( 21) link_ALPHA1-6 : angle 1.60252 ( 63) link_BETA1-4 : bond 0.00570 ( 87) link_BETA1-4 : angle 2.47237 ( 261) link_NAG-ASN : bond 0.00304 ( 57) link_NAG-ASN : angle 3.08138 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6304.12 seconds wall clock time: 109 minutes 56.85 seconds (6596.85 seconds total)