Starting phenix.real_space_refine on Fri Mar 6 00:18:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lg6_23312/03_2026/7lg6_23312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lg6_23312/03_2026/7lg6_23312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lg6_23312/03_2026/7lg6_23312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lg6_23312/03_2026/7lg6_23312.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lg6_23312/03_2026/7lg6_23312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lg6_23312/03_2026/7lg6_23312.map" } resolution = 3.28 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= 0.010 sd= 0.097 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 147 5.16 5 C 16638 2.51 5 N 4443 2.21 5 O 5322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26550 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3552 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 965 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1160 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "C" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "E" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3552 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "O" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 965 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 116} Chain: "Q" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1160 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "F" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3552 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "P" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 965 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 116} Chain: "R" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1160 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 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: "z" 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: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 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: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 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: "7" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.24, per 1000 atoms: 0.24 Number of scatterers: 26550 At special positions: 0 Unit cell: (159.65, 150.38, 157.59, 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 147 16.00 O 5322 8.00 N 4443 7.00 C 16638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.01 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " 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 B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS G 561 " distance=2.01 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 74 " - pdb=" SG CYS I 561 " distance=2.01 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.05 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN W 4 " - " MAN W 5 " " MAN X 4 " - " MAN X 5 " " MAN k 4 " - " MAN k 5 " " MAN l 4 " - " MAN l 5 " " MAN y 4 " - " MAN y 5 " " MAN z 4 " - " MAN z 5 " ALPHA1-3 " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA k 3 " - " MAN k 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " ALPHA1-6 " BMA W 3 " - " MAN W 6 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " " BMA k 3 " - " MAN k 6 " " BMA l 3 " - " MAN l 6 " " MAN l 6 " - " MAN l 8 " " BMA y 3 " - " MAN y 6 " " BMA z 3 " - " MAN z 6 " " MAN z 6 " - " MAN z 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " BETA1-6 " NAG 7 1 " - " FUC 7 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG f 1 " - " FUC f 2 " " NAG t 1 " - " FUC t 2 " NAG-ASN " NAG 0 1 " - " ASN F 295 " " NAG 1 1 " - " ASN F 332 " " NAG 2 1 " - " ASN F 386 " " NAG 3 1 " - " ASN F 392 " " NAG 4 1 " - " ASN F 448 " " NAG 5 1 " - " ASN F 301 " " NAG 6 1 " - " ASN F 363 " " NAG 7 1 " - " ASN I 611 " " NAG A 601 " - " ASN A 197 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 137 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG E 601 " - " ASN E 197 " " NAG E 602 " - " ASN E 339 " " NAG E 603 " - " ASN E 133 " " NAG E 604 " - " ASN E 137 " " NAG F 601 " - " ASN F 197 " " NAG F 602 " - " ASN F 339 " " NAG F 603 " - " ASN F 133 " " NAG F 604 " - " ASN F 137 " " NAG G 701 " - " ASN G 618 " " NAG G 702 " - " ASN G 637 " " NAG I 701 " - " ASN I 618 " " NAG I 702 " - " ASN I 637 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 160 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 295 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN A 448 " " NAG d 1 " - " ASN A 301 " " NAG e 1 " - " ASN A 363 " " NAG f 1 " - " ASN B 611 " " NAG g 1 " - " ASN E 88 " " NAG h 1 " - " ASN E 156 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 234 " " NAG k 1 " - " ASN E 262 " " NAG l 1 " - " ASN E 276 " " NAG m 1 " - " ASN E 295 " " NAG n 1 " - " ASN E 332 " " NAG o 1 " - " ASN E 386 " " NAG p 1 " - " ASN E 392 " " NAG q 1 " - " ASN E 448 " " NAG r 1 " - " ASN E 301 " " NAG s 1 " - " ASN E 363 " " NAG t 1 " - " ASN G 611 " " NAG u 1 " - " ASN F 88 " " NAG v 1 " - " ASN F 156 " " NAG w 1 " - " ASN F 160 " " NAG x 1 " - " ASN F 234 " " NAG y 1 " - " ASN F 262 " " NAG z 1 " - " ASN F 276 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5826 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 57 sheets defined 18.2% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.026A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 336 through 354 removed outlier: 5.865A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.953A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 561 through 568 removed outlier: 4.049A pdb=" N LEU B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.382A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.026A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 336 through 354 removed outlier: 5.865A pdb=" N LEU E 342 " --> pdb=" O TRP E 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.952A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 553 Processing helix chain 'G' and resid 561 through 568 removed outlier: 4.050A pdb=" N LEU G 565 " --> pdb=" O CYS G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 4.381A pdb=" N ASP G 624 " --> pdb=" O SER G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 633 Processing helix chain 'G' and resid 635 through 637 No H-bonds generated for 'chain 'G' and resid 635 through 637' Processing helix chain 'G' and resid 638 through 658 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.027A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'F' and resid 336 through 354 removed outlier: 5.865A pdb=" N LEU F 342 " --> pdb=" O TRP F 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.953A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 553 Processing helix chain 'I' and resid 561 through 568 removed outlier: 4.049A pdb=" N LEU I 565 " --> pdb=" O CYS I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 4.382A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 633 Processing helix chain 'I' and resid 635 through 637 No H-bonds generated for 'chain 'I' and resid 635 through 637' Processing helix chain 'I' and resid 638 through 658 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.339A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.021A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 9.995A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.606A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.789A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.471A pdb=" N ILE L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.371A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 7 removed outlier: 5.800A pdb=" N GLU C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 82B" --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.444A pdb=" N TRP C 35 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR C 50 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.339A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.021A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'E' and resid 201 through 203 Processing sheet with id=AC8, first strand: chain 'E' and resid 259 through 261 removed outlier: 9.995A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.897A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.606A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'O' and resid 56 through 59 removed outlier: 6.789A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE O 34 " --> pdb=" O ARG O 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'Q' and resid 10 through 13 removed outlier: 5.470A pdb=" N ILE Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.371A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 3 through 7 removed outlier: 5.800A pdb=" N GLU J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER J 82B" --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.444A pdb=" N TRP J 35 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AE3, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.339A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.020A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AE6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AE7, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AE8, first strand: chain 'F' and resid 201 through 203 Processing sheet with id=AE9, first strand: chain 'F' and resid 259 through 261 removed outlier: 9.995A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.897A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.606A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'P' and resid 56 through 59 removed outlier: 6.788A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG P 50 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE P 34 " --> pdb=" O ARG P 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'R' and resid 10 through 13 removed outlier: 5.471A pdb=" N ILE R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR R 49 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 10 through 13 Processing sheet with id=AF8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.371A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 removed outlier: 5.800A pdb=" N GLU K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER K 82B" --> pdb=" O GLU K 16 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.444A pdb=" N TRP K 35 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 11 through 12 1047 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5481 1.32 - 1.47: 9946 1.47 - 1.61: 11456 1.61 - 1.76: 54 1.76 - 1.91: 168 Bond restraints: 27105 Sorted by residual: bond pdb=" NE ARG D 3 " pdb=" CZ ARG D 3 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.16e+01 bond pdb=" NE ARG M 3 " pdb=" CZ ARG M 3 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.16e+01 bond pdb=" NE ARG N 3 " pdb=" CZ ARG N 3 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.14e+01 bond pdb=" CB ASP R 91 " pdb=" CG ASP R 91 " ideal model delta sigma weight residual 1.516 1.367 0.149 2.50e-02 1.60e+03 3.53e+01 bond pdb=" CB ASP Q 91 " pdb=" CG ASP Q 91 " ideal model delta sigma weight residual 1.516 1.368 0.148 2.50e-02 1.60e+03 3.52e+01 ... (remaining 27100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 33306 2.90 - 5.79: 3128 5.79 - 8.69: 358 8.69 - 11.58: 24 11.58 - 14.48: 6 Bond angle restraints: 36822 Sorted by residual: angle pdb=" C TRP P 72C" pdb=" N ARG P 72D" pdb=" CA ARG P 72D" ideal model delta sigma weight residual 120.28 134.76 -14.48 1.34e+00 5.57e-01 1.17e+02 angle pdb=" C TRP O 72C" pdb=" N ARG O 72D" pdb=" CA ARG O 72D" ideal model delta sigma weight residual 120.28 134.75 -14.47 1.34e+00 5.57e-01 1.17e+02 angle pdb=" C TRP H 72C" pdb=" N ARG H 72D" pdb=" CA ARG H 72D" ideal model delta sigma weight residual 120.28 134.75 -14.47 1.34e+00 5.57e-01 1.17e+02 angle pdb=" N SER G 613 " pdb=" CA SER G 613 " pdb=" C SER G 613 " ideal model delta sigma weight residual 114.62 102.94 11.68 1.14e+00 7.69e-01 1.05e+02 angle pdb=" N SER I 613 " pdb=" CA SER I 613 " pdb=" C SER I 613 " ideal model delta sigma weight residual 114.62 102.94 11.68 1.14e+00 7.69e-01 1.05e+02 ... (remaining 36817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 17288 21.21 - 42.41: 403 42.41 - 63.62: 105 63.62 - 84.83: 84 84.83 - 106.03: 39 Dihedral angle restraints: 17919 sinusoidal: 8859 harmonic: 9060 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 136.63 -43.63 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 136.63 -43.63 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 136.62 -43.62 1 1.00e+01 1.00e-02 2.65e+01 ... (remaining 17916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2885 0.101 - 0.203: 1042 0.203 - 0.304: 340 0.304 - 0.406: 159 0.406 - 0.507: 77 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 ... (remaining 4500 not shown) Planarity restraints: 4563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " -0.068 2.00e-02 2.50e+03 6.91e-02 5.98e+01 pdb=" CG ASN E 133 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG E 603 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 133 " 0.068 2.00e-02 2.50e+03 6.91e-02 5.97e+01 pdb=" CG ASN F 133 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN F 133 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN F 133 " -0.105 2.00e-02 2.50e+03 pdb=" C1 NAG F 603 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 133 " -0.068 2.00e-02 2.50e+03 6.91e-02 5.97e+01 pdb=" CG ASN A 133 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 133 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 133 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " -0.084 2.00e-02 2.50e+03 ... (remaining 4560 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 11239 2.92 - 3.41: 22833 3.41 - 3.91: 44050 3.91 - 4.40: 50557 4.40 - 4.90: 81424 Nonbonded interactions: 210103 Sorted by model distance: nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.421 3.120 nonbonded pdb=" NZ LYS F 46 " pdb=" OD2 ASP I 632 " model vdw 2.421 3.120 nonbonded pdb=" NZ LYS E 46 " pdb=" OD2 ASP G 632 " model vdw 2.421 3.120 nonbonded pdb=" N GLY F 431 " pdb=" O GLY F 431 " model vdw 2.423 2.496 nonbonded pdb=" N GLY A 431 " pdb=" O GLY A 431 " model vdw 2.423 2.496 ... (remaining 210098 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: 0.06 Found NCS groups: ncs_group { reference = (chain '0' and resid 1) selection = (chain '1' and resid 1) selection = (chain '2' and resid 1) selection = (chain '3' and resid 1) selection = (chain '4' and resid 1) selection = (chain '5' and resid 1) selection = (chain '6' and resid 1) selection = (chain '7' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 'q' and resid 1) selection = (chain 'r' and resid 1) selection = (chain 's' and resid 1) selection = (chain 't' and resid 1) selection = (chain 'u' and resid 1) selection = (chain 'w' and resid 1) selection = (chain 'x' and resid 1) } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'T' selection = chain 'h' selection = chain 'v' } ncs_group { reference = chain 'W' selection = chain 'k' selection = chain 'y' } ncs_group { reference = chain 'X' selection = chain 'l' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.090 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.023 0.149 27288 Z= 1.213 Angle : 1.832 14.479 37323 Z= 1.160 Chirality : 0.140 0.507 4503 Planarity : 0.009 0.038 4503 Dihedral : 12.385 106.035 11949 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.68 % Allowed : 3.57 % Favored : 95.75 % Rotamer: Outliers : 0.33 % Allowed : 0.76 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3105 helix: -0.80 (0.23), residues: 477 sheet: 0.93 (0.16), residues: 1116 loop : 0.24 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 350 TYR 0.048 0.009 TYR F 177 PHE 0.034 0.006 PHE N 98 TRP 0.057 0.011 TRP F 479 HIS 0.015 0.003 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.02283 (27105) covalent geometry : angle 1.79372 (36822) SS BOND : bond 0.00950 ( 48) SS BOND : angle 3.27140 ( 96) hydrogen bonds : bond 0.16743 ( 1002) hydrogen bonds : angle 7.75480 ( 2691) link_ALPHA1-2 : bond 0.08558 ( 6) link_ALPHA1-2 : angle 4.38696 ( 18) link_ALPHA1-3 : bond 0.07777 ( 9) link_ALPHA1-3 : angle 4.33422 ( 27) link_ALPHA1-6 : bond 0.05401 ( 9) link_ALPHA1-6 : angle 3.34445 ( 27) link_BETA1-4 : bond 0.07146 ( 48) link_BETA1-4 : angle 4.59270 ( 144) link_BETA1-6 : bond 0.08313 ( 3) link_BETA1-6 : angle 4.84408 ( 9) link_NAG-ASN : bond 0.07619 ( 60) link_NAG-ASN : angle 2.81522 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 637 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8518 (mtp85) REVERT: B 632 ASP cc_start: 0.8843 (t70) cc_final: 0.8600 (t0) REVERT: O 86 ASP cc_start: 0.8152 (m-30) cc_final: 0.7892 (m-30) REVERT: G 632 ASP cc_start: 0.8820 (t70) cc_final: 0.8591 (t0) REVERT: P 86 ASP cc_start: 0.8259 (m-30) cc_final: 0.8005 (m-30) REVERT: I 632 ASP cc_start: 0.8851 (t70) cc_final: 0.8579 (t0) outliers start: 9 outliers final: 3 residues processed: 646 average time/residue: 0.2045 time to fit residues: 196.1228 Evaluate side-chains 355 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 351 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain P residue 72 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN H 10 GLN D 92 ASN C 39 GLN E 195 ASN O 10 GLN Q 37 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN F 195 ASN N 92 ASN K 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.112866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.079509 restraints weight = 50122.334| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.13 r_work: 0.3022 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27288 Z= 0.165 Angle : 0.781 10.709 37323 Z= 0.391 Chirality : 0.047 0.298 4503 Planarity : 0.004 0.039 4503 Dihedral : 9.576 82.955 6182 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.83 % Favored : 95.72 % Rotamer: Outliers : 1.71 % Allowed : 6.91 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3105 helix: 0.59 (0.27), residues: 459 sheet: 1.02 (0.15), residues: 1119 loop : -0.34 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 480 TYR 0.020 0.002 TYR F 61 PHE 0.014 0.002 PHE D 98 TRP 0.032 0.002 TRP D 96 HIS 0.007 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00348 (27105) covalent geometry : angle 0.73204 (36822) SS BOND : bond 0.00376 ( 48) SS BOND : angle 1.34177 ( 96) hydrogen bonds : bond 0.05454 ( 1002) hydrogen bonds : angle 6.06593 ( 2691) link_ALPHA1-2 : bond 0.00473 ( 6) link_ALPHA1-2 : angle 2.20078 ( 18) link_ALPHA1-3 : bond 0.01043 ( 9) link_ALPHA1-3 : angle 1.78345 ( 27) link_ALPHA1-6 : bond 0.00504 ( 9) link_ALPHA1-6 : angle 1.70428 ( 27) link_BETA1-4 : bond 0.00503 ( 48) link_BETA1-4 : angle 2.67208 ( 144) link_BETA1-6 : bond 0.00757 ( 3) link_BETA1-6 : angle 1.34051 ( 9) link_NAG-ASN : bond 0.00513 ( 60) link_NAG-ASN : angle 2.94994 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 423 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8590 (mp10) cc_final: 0.8117 (mp10) REVERT: H 11 PHE cc_start: 0.7298 (m-80) cc_final: 0.6944 (m-80) REVERT: H 46 GLU cc_start: 0.7338 (tp30) cc_final: 0.6466 (tt0) REVERT: L 4 MET cc_start: 0.7356 (mmm) cc_final: 0.6989 (mmp) REVERT: B 632 ASP cc_start: 0.9121 (t70) cc_final: 0.8713 (t0) REVERT: B 652 GLN cc_start: 0.8320 (tp40) cc_final: 0.8108 (tp40) REVERT: D 81 GLU cc_start: 0.7923 (mp0) cc_final: 0.7557 (pm20) REVERT: D 82 ASP cc_start: 0.7537 (m-30) cc_final: 0.7328 (m-30) REVERT: D 90 GLN cc_start: 0.7564 (tp40) cc_final: 0.7166 (tp40) REVERT: C 13 ARG cc_start: 0.6832 (mtt-85) cc_final: 0.6093 (mpp-170) REVERT: C 48 ILE cc_start: 0.8985 (mt) cc_final: 0.8739 (tt) REVERT: C 72 ASP cc_start: 0.7256 (t0) cc_final: 0.6912 (p0) REVERT: C 77 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: E 65 LYS cc_start: 0.7366 (mttt) cc_final: 0.7153 (mtmm) REVERT: O 11 PHE cc_start: 0.7502 (m-80) cc_final: 0.7077 (m-80) REVERT: Q 4 MET cc_start: 0.6375 (mtt) cc_final: 0.5623 (mtt) REVERT: Q 86 TYR cc_start: 0.7754 (m-80) cc_final: 0.7494 (m-80) REVERT: Q 100 GLN cc_start: 0.7337 (mp10) cc_final: 0.7110 (mp10) REVERT: G 588 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7530 (ttm110) REVERT: G 632 ASP cc_start: 0.9101 (t70) cc_final: 0.8694 (t0) REVERT: M 81 GLU cc_start: 0.8075 (mp0) cc_final: 0.7804 (pm20) REVERT: J 13 ARG cc_start: 0.5987 (mmt90) cc_final: 0.5470 (mpp-170) REVERT: P 32 TYR cc_start: 0.8752 (m-10) cc_final: 0.8484 (m-10) REVERT: P 81 GLU cc_start: 0.8521 (tt0) cc_final: 0.8263 (tt0) REVERT: R 82 ASP cc_start: 0.6893 (m-30) cc_final: 0.6494 (m-30) REVERT: R 86 TYR cc_start: 0.7972 (m-80) cc_final: 0.7529 (m-80) REVERT: R 100 GLN cc_start: 0.7368 (mp10) cc_final: 0.7125 (mp10) REVERT: I 588 ARG cc_start: 0.8203 (tpt170) cc_final: 0.7384 (tpp80) REVERT: I 632 ASP cc_start: 0.9077 (t70) cc_final: 0.8658 (t0) REVERT: N 24 ARG cc_start: 0.8355 (mtp180) cc_final: 0.7913 (ttm110) REVERT: N 39 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7800 (mtmt) REVERT: N 81 GLU cc_start: 0.8025 (mp0) cc_final: 0.7816 (pm20) REVERT: K 48 ILE cc_start: 0.9019 (mt) cc_final: 0.8762 (tt) REVERT: K 72 ASP cc_start: 0.7341 (t0) cc_final: 0.7017 (p0) outliers start: 47 outliers final: 18 residues processed: 442 average time/residue: 0.1723 time to fit residues: 120.6789 Evaluate side-chains 351 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 332 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 275 optimal weight: 0.9990 chunk 252 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 297 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 146 optimal weight: 0.1980 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN K 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.070915 restraints weight = 51795.023| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.06 r_work: 0.2840 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 27288 Z= 0.276 Angle : 0.783 10.146 37323 Z= 0.393 Chirality : 0.049 0.307 4503 Planarity : 0.005 0.049 4503 Dihedral : 8.529 77.855 6168 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.22 % Favored : 94.11 % Rotamer: Outliers : 2.22 % Allowed : 8.26 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3105 helix: 0.33 (0.25), residues: 459 sheet: 0.79 (0.15), residues: 1122 loop : -0.72 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 480 TYR 0.021 0.002 TYR J 50 PHE 0.020 0.003 PHE J 78 TRP 0.031 0.002 TRP D 96 HIS 0.009 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00666 (27105) covalent geometry : angle 0.74413 (36822) SS BOND : bond 0.00522 ( 48) SS BOND : angle 1.27721 ( 96) hydrogen bonds : bond 0.05620 ( 1002) hydrogen bonds : angle 5.67195 ( 2691) link_ALPHA1-2 : bond 0.00455 ( 6) link_ALPHA1-2 : angle 2.17184 ( 18) link_ALPHA1-3 : bond 0.00811 ( 9) link_ALPHA1-3 : angle 1.51404 ( 27) link_ALPHA1-6 : bond 0.00515 ( 9) link_ALPHA1-6 : angle 1.80563 ( 27) link_BETA1-4 : bond 0.00631 ( 48) link_BETA1-4 : angle 2.22309 ( 144) link_BETA1-6 : bond 0.00674 ( 3) link_BETA1-6 : angle 1.04836 ( 9) link_NAG-ASN : bond 0.00349 ( 60) link_NAG-ASN : angle 2.75140 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 360 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7568 (t70) REVERT: L 4 MET cc_start: 0.7470 (mmm) cc_final: 0.6461 (mmp) REVERT: B 588 ARG cc_start: 0.8456 (tpt170) cc_final: 0.7657 (ttm110) REVERT: B 632 ASP cc_start: 0.9249 (t70) cc_final: 0.8842 (t0) REVERT: D 24 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7888 (ptm160) REVERT: D 81 GLU cc_start: 0.7947 (mp0) cc_final: 0.7621 (pm20) REVERT: C 37 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8807 (tt) REVERT: C 72 ASP cc_start: 0.7314 (t0) cc_final: 0.7083 (p0) REVERT: C 77 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: O 72 ASP cc_start: 0.7886 (t0) cc_final: 0.7628 (t70) REVERT: Q 87 TYR cc_start: 0.6627 (m-80) cc_final: 0.6232 (m-80) REVERT: Q 100 GLN cc_start: 0.7742 (mp10) cc_final: 0.7501 (mp10) REVERT: G 588 ARG cc_start: 0.8417 (tpt170) cc_final: 0.7695 (ttm110) REVERT: G 632 ASP cc_start: 0.9200 (t70) cc_final: 0.8848 (t0) REVERT: M 24 ARG cc_start: 0.8173 (mtp180) cc_final: 0.7826 (mmm-85) REVERT: M 81 GLU cc_start: 0.8029 (mp0) cc_final: 0.7778 (pm20) REVERT: P 32 TYR cc_start: 0.8991 (m-10) cc_final: 0.8682 (m-10) REVERT: P 46 GLU cc_start: 0.7669 (tt0) cc_final: 0.7234 (tp30) REVERT: P 72 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7711 (t70) REVERT: P 81 GLU cc_start: 0.8541 (tt0) cc_final: 0.8332 (tt0) REVERT: R 100 GLN cc_start: 0.7705 (mp10) cc_final: 0.7452 (mp10) REVERT: I 588 ARG cc_start: 0.8322 (tpt170) cc_final: 0.7648 (ttp-110) REVERT: I 632 ASP cc_start: 0.9196 (t70) cc_final: 0.8849 (t0) REVERT: N 24 ARG cc_start: 0.8388 (mtp180) cc_final: 0.7841 (ttm-80) REVERT: K 37 ILE cc_start: 0.9168 (mm) cc_final: 0.8739 (tt) REVERT: K 48 ILE cc_start: 0.9062 (mt) cc_final: 0.8789 (tt) outliers start: 61 outliers final: 50 residues processed: 392 average time/residue: 0.1765 time to fit residues: 107.9143 Evaluate side-chains 377 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 323 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 261 optimal weight: 5.9990 chunk 144 optimal weight: 0.4980 chunk 201 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 301 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN E 195 ASN Q 89 GLN M 92 ASN F 195 ASN R 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.072480 restraints weight = 51375.397| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.05 r_work: 0.2866 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27288 Z= 0.168 Angle : 0.683 10.180 37323 Z= 0.337 Chirality : 0.045 0.306 4503 Planarity : 0.004 0.044 4503 Dihedral : 7.655 70.555 6168 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.77 % Favored : 94.69 % Rotamer: Outliers : 2.15 % Allowed : 9.90 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3105 helix: 0.45 (0.26), residues: 477 sheet: 0.88 (0.16), residues: 1110 loop : -0.89 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 61 TYR 0.013 0.001 TYR F 61 PHE 0.028 0.002 PHE R 83 TRP 0.021 0.001 TRP N 96 HIS 0.005 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00394 (27105) covalent geometry : angle 0.64568 (36822) SS BOND : bond 0.00348 ( 48) SS BOND : angle 1.06758 ( 96) hydrogen bonds : bond 0.04709 ( 1002) hydrogen bonds : angle 5.38196 ( 2691) link_ALPHA1-2 : bond 0.00401 ( 6) link_ALPHA1-2 : angle 1.99147 ( 18) link_ALPHA1-3 : bond 0.00926 ( 9) link_ALPHA1-3 : angle 1.38701 ( 27) link_ALPHA1-6 : bond 0.00571 ( 9) link_ALPHA1-6 : angle 1.77048 ( 27) link_BETA1-4 : bond 0.00513 ( 48) link_BETA1-4 : angle 1.86259 ( 144) link_BETA1-6 : bond 0.00312 ( 3) link_BETA1-6 : angle 1.15348 ( 9) link_NAG-ASN : bond 0.00333 ( 60) link_NAG-ASN : angle 2.60031 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 355 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.7353 (mmm) cc_final: 0.6416 (mmp) REVERT: B 588 ARG cc_start: 0.8431 (tpt170) cc_final: 0.7631 (ttm110) REVERT: B 632 ASP cc_start: 0.9268 (t70) cc_final: 0.8864 (t0) REVERT: D 39 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7802 (mtmt) REVERT: D 81 GLU cc_start: 0.7934 (mp0) cc_final: 0.7670 (pm20) REVERT: C 37 ILE cc_start: 0.9140 (mm) cc_final: 0.8711 (tt) REVERT: C 66 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7380 (mtm110) REVERT: O 11 PHE cc_start: 0.7028 (m-80) cc_final: 0.6815 (m-80) REVERT: O 72 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7273 (t70) REVERT: Q 100 GLN cc_start: 0.7830 (mp10) cc_final: 0.7612 (mp10) REVERT: G 545 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8699 (tt) REVERT: G 588 ARG cc_start: 0.8382 (tpt170) cc_final: 0.7589 (ttm110) REVERT: G 632 ASP cc_start: 0.9207 (t70) cc_final: 0.8864 (t0) REVERT: M 24 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7778 (ptm160) REVERT: M 81 GLU cc_start: 0.8011 (mp0) cc_final: 0.7786 (pm20) REVERT: P 32 TYR cc_start: 0.8980 (m-10) cc_final: 0.8706 (m-10) REVERT: P 46 GLU cc_start: 0.7652 (tt0) cc_final: 0.7206 (tp30) REVERT: R 86 TYR cc_start: 0.7969 (m-80) cc_final: 0.7700 (m-80) REVERT: R 100 GLN cc_start: 0.7837 (mp10) cc_final: 0.7609 (mp10) REVERT: I 588 ARG cc_start: 0.8308 (tpt170) cc_final: 0.7644 (ttp-110) REVERT: I 632 ASP cc_start: 0.9199 (t70) cc_final: 0.8854 (t0) REVERT: N 24 ARG cc_start: 0.8368 (mtp180) cc_final: 0.7769 (ttm-80) REVERT: N 39 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7439 (ptpt) REVERT: N 79 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7792 (tt0) REVERT: N 81 GLU cc_start: 0.7675 (pm20) cc_final: 0.7142 (pm20) REVERT: N 93 ASP cc_start: 0.8316 (t0) cc_final: 0.7946 (m-30) REVERT: K 37 ILE cc_start: 0.9187 (mm) cc_final: 0.8687 (tt) outliers start: 59 outliers final: 40 residues processed: 383 average time/residue: 0.1749 time to fit residues: 105.5589 Evaluate side-chains 371 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 329 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 56 ILE Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** 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 = 0.3495 r_free = 0.3495 target = 0.101341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.067703 restraints weight = 52363.889| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.08 r_work: 0.2777 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 27288 Z= 0.384 Angle : 0.855 13.392 37323 Z= 0.420 Chirality : 0.051 0.305 4503 Planarity : 0.005 0.055 4503 Dihedral : 8.084 69.981 6168 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.41 % Favored : 93.01 % Rotamer: Outliers : 2.87 % Allowed : 10.33 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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 are not related in a simple way. whole: -0.52 (0.15), residues: 3105 helix: -0.10 (0.24), residues: 477 sheet: 0.67 (0.16), residues: 1110 loop : -1.21 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 480 TYR 0.022 0.002 TYR J 50 PHE 0.023 0.003 PHE E 53 TRP 0.035 0.003 TRP N 96 HIS 0.011 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00935 (27105) covalent geometry : angle 0.81861 (36822) SS BOND : bond 0.00602 ( 48) SS BOND : angle 1.61116 ( 96) hydrogen bonds : bond 0.05865 ( 1002) hydrogen bonds : angle 5.63256 ( 2691) link_ALPHA1-2 : bond 0.00455 ( 6) link_ALPHA1-2 : angle 2.28994 ( 18) link_ALPHA1-3 : bond 0.00638 ( 9) link_ALPHA1-3 : angle 1.80259 ( 27) link_ALPHA1-6 : bond 0.00608 ( 9) link_ALPHA1-6 : angle 2.00754 ( 27) link_BETA1-4 : bond 0.00484 ( 48) link_BETA1-4 : angle 2.05006 ( 144) link_BETA1-6 : bond 0.00777 ( 3) link_BETA1-6 : angle 1.05891 ( 9) link_NAG-ASN : bond 0.00564 ( 60) link_NAG-ASN : angle 2.86763 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 329 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 PHE cc_start: 0.7240 (m-80) cc_final: 0.6888 (m-80) REVERT: L 4 MET cc_start: 0.7442 (mmm) cc_final: 0.6309 (mmp) REVERT: L 23 CYS cc_start: 0.6628 (t) cc_final: 0.4856 (t) REVERT: L 27 GLN cc_start: 0.7260 (mt0) cc_final: 0.6701 (tt0) REVERT: L 61 ARG cc_start: 0.6358 (mtp180) cc_final: 0.5921 (mtp180) REVERT: L 82 ASP cc_start: 0.7285 (m-30) cc_final: 0.7049 (m-30) REVERT: B 632 ASP cc_start: 0.9332 (t70) cc_final: 0.8997 (t0) REVERT: D 81 GLU cc_start: 0.8073 (mp0) cc_final: 0.7725 (pm20) REVERT: C 37 ILE cc_start: 0.9149 (mm) cc_final: 0.8777 (tt) REVERT: O 72 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7392 (t70) REVERT: Q 17 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7288 (mp0) REVERT: Q 100 GLN cc_start: 0.7887 (mp10) cc_final: 0.7661 (mp10) REVERT: G 545 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8993 (tt) REVERT: G 588 ARG cc_start: 0.8445 (tpt170) cc_final: 0.7675 (ttm110) REVERT: M 72 THR cc_start: 0.8594 (m) cc_final: 0.8371 (p) REVERT: M 81 GLU cc_start: 0.7991 (mp0) cc_final: 0.7742 (pm20) REVERT: J 13 ARG cc_start: 0.6895 (mmt90) cc_final: 0.6059 (mpp-170) REVERT: P 72 ASP cc_start: 0.8317 (t70) cc_final: 0.8114 (t0) REVERT: R 100 GLN cc_start: 0.7992 (mp10) cc_final: 0.7779 (mp10) REVERT: I 588 ARG cc_start: 0.8352 (tpt170) cc_final: 0.7625 (ttp-110) REVERT: I 632 ASP cc_start: 0.9190 (t70) cc_final: 0.8838 (t0) REVERT: N 24 ARG cc_start: 0.8385 (mtp180) cc_final: 0.7892 (ttm110) REVERT: N 39 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7852 (ptpp) REVERT: N 93 ASP cc_start: 0.8232 (t0) cc_final: 0.7939 (m-30) REVERT: K 52 ASN cc_start: 0.8792 (t0) cc_final: 0.8546 (t0) outliers start: 79 outliers final: 68 residues processed: 378 average time/residue: 0.1736 time to fit residues: 102.8295 Evaluate side-chains 371 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 301 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 56 ILE Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 240 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 258 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 299 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** F 195 ASN ** 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 = 0.3560 r_free = 0.3560 target = 0.105634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073334 restraints weight = 51263.029| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.37 r_work: 0.2833 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27288 Z= 0.125 Angle : 0.652 10.625 37323 Z= 0.321 Chirality : 0.044 0.301 4503 Planarity : 0.004 0.049 4503 Dihedral : 7.159 61.897 6168 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.51 % Favored : 94.11 % Rotamer: Outliers : 1.38 % Allowed : 12.66 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3105 helix: 0.43 (0.26), residues: 480 sheet: 0.88 (0.16), residues: 1080 loop : -1.11 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 103 TYR 0.012 0.001 TYR F 61 PHE 0.020 0.001 PHE H 63 TRP 0.023 0.001 TRP D 96 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00273 (27105) covalent geometry : angle 0.61745 (36822) SS BOND : bond 0.00296 ( 48) SS BOND : angle 1.14275 ( 96) hydrogen bonds : bond 0.04381 ( 1002) hydrogen bonds : angle 5.23061 ( 2691) link_ALPHA1-2 : bond 0.00362 ( 6) link_ALPHA1-2 : angle 1.94740 ( 18) link_ALPHA1-3 : bond 0.01022 ( 9) link_ALPHA1-3 : angle 1.23012 ( 27) link_ALPHA1-6 : bond 0.00620 ( 9) link_ALPHA1-6 : angle 1.67931 ( 27) link_BETA1-4 : bond 0.00497 ( 48) link_BETA1-4 : angle 1.59855 ( 144) link_BETA1-6 : bond 0.00224 ( 3) link_BETA1-6 : angle 1.26202 ( 9) link_NAG-ASN : bond 0.00354 ( 60) link_NAG-ASN : angle 2.51459 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 PHE cc_start: 0.7152 (m-80) cc_final: 0.6894 (m-80) REVERT: L 4 MET cc_start: 0.7278 (mmm) cc_final: 0.6300 (mmp) REVERT: L 23 CYS cc_start: 0.6646 (t) cc_final: 0.5168 (t) REVERT: L 27 GLN cc_start: 0.7166 (mt0) cc_final: 0.6617 (tt0) REVERT: L 61 ARG cc_start: 0.6408 (mtp180) cc_final: 0.6000 (mtp180) REVERT: B 588 ARG cc_start: 0.8455 (tpt170) cc_final: 0.7611 (ttm110) REVERT: B 632 ASP cc_start: 0.9312 (t70) cc_final: 0.8950 (t0) REVERT: D 81 GLU cc_start: 0.8132 (mp0) cc_final: 0.7859 (pm20) REVERT: C 37 ILE cc_start: 0.9102 (mm) cc_final: 0.8685 (tt) REVERT: C 38 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7449 (ttm-80) REVERT: C 86 ASP cc_start: 0.7365 (m-30) cc_final: 0.7154 (m-30) REVERT: E 150 MET cc_start: 0.8595 (mmm) cc_final: 0.8350 (mmt) REVERT: Q 100 GLN cc_start: 0.7971 (mp10) cc_final: 0.7729 (mp10) REVERT: G 563 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7428 (pt0) REVERT: G 588 ARG cc_start: 0.8408 (tpt170) cc_final: 0.7572 (ttm110) REVERT: G 632 ASP cc_start: 0.9222 (t70) cc_final: 0.8862 (t0) REVERT: M 81 GLU cc_start: 0.8078 (mp0) cc_final: 0.7792 (pm20) REVERT: F 122 LEU cc_start: 0.8408 (mt) cc_final: 0.7896 (pp) REVERT: P 11 PHE cc_start: 0.7295 (m-80) cc_final: 0.7019 (m-80) REVERT: P 32 TYR cc_start: 0.9032 (m-10) cc_final: 0.8764 (m-10) REVERT: P 46 GLU cc_start: 0.7529 (tt0) cc_final: 0.7249 (tp30) REVERT: R 61 ARG cc_start: 0.6019 (mtm-85) cc_final: 0.5726 (ttp-110) REVERT: R 100 GLN cc_start: 0.8036 (mp10) cc_final: 0.7825 (mp10) REVERT: I 588 ARG cc_start: 0.8328 (tpt170) cc_final: 0.7621 (ttp-110) REVERT: I 632 ASP cc_start: 0.9164 (t70) cc_final: 0.8853 (t0) REVERT: N 24 ARG cc_start: 0.8343 (mtp180) cc_final: 0.7717 (ttm-80) REVERT: N 39 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7788 (ptpp) outliers start: 38 outliers final: 28 residues processed: 359 average time/residue: 0.1845 time to fit residues: 102.6199 Evaluate side-chains 343 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 315 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 74 SER Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 56 ILE Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 176 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 222 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.071460 restraints weight = 51566.516| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.04 r_work: 0.2847 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27288 Z= 0.169 Angle : 0.668 11.239 37323 Z= 0.326 Chirality : 0.045 0.309 4503 Planarity : 0.004 0.051 4503 Dihedral : 6.830 57.685 6168 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.57 % Favored : 93.20 % Rotamer: Outliers : 1.49 % Allowed : 12.70 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 3105 helix: 0.55 (0.26), residues: 480 sheet: 0.88 (0.16), residues: 1080 loop : -1.18 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 103 TYR 0.014 0.001 TYR J 50 PHE 0.015 0.002 PHE H 63 TRP 0.025 0.001 TRP D 96 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00401 (27105) covalent geometry : angle 0.63525 (36822) SS BOND : bond 0.00317 ( 48) SS BOND : angle 1.07275 ( 96) hydrogen bonds : bond 0.04464 ( 1002) hydrogen bonds : angle 5.17548 ( 2691) link_ALPHA1-2 : bond 0.00360 ( 6) link_ALPHA1-2 : angle 1.96014 ( 18) link_ALPHA1-3 : bond 0.00915 ( 9) link_ALPHA1-3 : angle 1.39461 ( 27) link_ALPHA1-6 : bond 0.00517 ( 9) link_ALPHA1-6 : angle 1.72159 ( 27) link_BETA1-4 : bond 0.00480 ( 48) link_BETA1-4 : angle 1.63039 ( 144) link_BETA1-6 : bond 0.00272 ( 3) link_BETA1-6 : angle 1.18418 ( 9) link_NAG-ASN : bond 0.00333 ( 60) link_NAG-ASN : angle 2.48176 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 322 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7997 (tpp) cc_final: 0.7794 (mtm) REVERT: H 11 PHE cc_start: 0.7093 (m-80) cc_final: 0.6845 (m-80) REVERT: L 27 GLN cc_start: 0.7240 (mt0) cc_final: 0.6734 (tt0) REVERT: B 588 ARG cc_start: 0.8446 (tpt170) cc_final: 0.7654 (ttm110) REVERT: B 632 ASP cc_start: 0.9296 (t70) cc_final: 0.8935 (t0) REVERT: D 81 GLU cc_start: 0.8087 (mp0) cc_final: 0.7805 (pm20) REVERT: C 37 ILE cc_start: 0.9083 (mm) cc_final: 0.8661 (tt) REVERT: C 66 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7996 (ttm170) REVERT: E 122 LEU cc_start: 0.8473 (mt) cc_final: 0.8013 (pp) REVERT: E 150 MET cc_start: 0.8601 (mmm) cc_final: 0.8367 (mmt) REVERT: O 72 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7361 (t70) REVERT: Q 17 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7294 (mt-10) REVERT: Q 100 GLN cc_start: 0.8003 (mp10) cc_final: 0.7776 (mp10) REVERT: G 545 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8775 (tt) REVERT: G 563 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7516 (pt0) REVERT: G 588 ARG cc_start: 0.8396 (tpt170) cc_final: 0.7617 (ttm110) REVERT: G 632 ASP cc_start: 0.9217 (t70) cc_final: 0.8869 (t0) REVERT: M 39 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7873 (mtmm) REVERT: M 81 GLU cc_start: 0.8047 (mp0) cc_final: 0.7763 (pm20) REVERT: P 32 TYR cc_start: 0.9045 (m-10) cc_final: 0.8765 (m-10) REVERT: P 46 GLU cc_start: 0.7469 (tt0) cc_final: 0.7248 (tp30) REVERT: R 4 MET cc_start: 0.6870 (mtt) cc_final: 0.5960 (mtt) REVERT: R 61 ARG cc_start: 0.6119 (mtm-85) cc_final: 0.5861 (ttp-110) REVERT: R 88 CYS cc_start: 0.6368 (p) cc_final: 0.5728 (p) REVERT: I 588 ARG cc_start: 0.8322 (tpt170) cc_final: 0.7645 (ttp-110) REVERT: I 632 ASP cc_start: 0.9121 (t70) cc_final: 0.8794 (t0) REVERT: N 24 ARG cc_start: 0.8356 (mtp180) cc_final: 0.7739 (ttm-80) REVERT: N 39 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7858 (ptpp) REVERT: N 105 GLU cc_start: 0.7407 (pp20) cc_final: 0.7079 (pp20) outliers start: 41 outliers final: 33 residues processed: 348 average time/residue: 0.1808 time to fit residues: 98.1408 Evaluate side-chains 339 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 304 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 56 ILE Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 262 optimal weight: 0.0870 chunk 240 optimal weight: 4.9990 chunk 166 optimal weight: 30.0000 chunk 249 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.105345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.072225 restraints weight = 51705.501| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.03 r_work: 0.2861 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27288 Z= 0.144 Angle : 0.646 10.476 37323 Z= 0.317 Chirality : 0.045 0.306 4503 Planarity : 0.004 0.053 4503 Dihedral : 6.489 51.349 6168 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.15 % Favored : 93.66 % Rotamer: Outliers : 1.71 % Allowed : 12.70 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3105 helix: 0.69 (0.26), residues: 480 sheet: 0.94 (0.16), residues: 1080 loop : -1.19 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 103 TYR 0.013 0.001 TYR K 50 PHE 0.014 0.001 PHE H 63 TRP 0.024 0.001 TRP N 94 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00333 (27105) covalent geometry : angle 0.61356 (36822) SS BOND : bond 0.00311 ( 48) SS BOND : angle 1.06679 ( 96) hydrogen bonds : bond 0.04237 ( 1002) hydrogen bonds : angle 5.07814 ( 2691) link_ALPHA1-2 : bond 0.00343 ( 6) link_ALPHA1-2 : angle 1.91035 ( 18) link_ALPHA1-3 : bond 0.01007 ( 9) link_ALPHA1-3 : angle 1.27339 ( 27) link_ALPHA1-6 : bond 0.00528 ( 9) link_ALPHA1-6 : angle 1.59459 ( 27) link_BETA1-4 : bond 0.00493 ( 48) link_BETA1-4 : angle 1.53635 ( 144) link_BETA1-6 : bond 0.00308 ( 3) link_BETA1-6 : angle 1.28576 ( 9) link_NAG-ASN : bond 0.00325 ( 60) link_NAG-ASN : angle 2.41633 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8052 (pp) REVERT: H 11 PHE cc_start: 0.6996 (m-80) cc_final: 0.6681 (m-80) REVERT: H 46 GLU cc_start: 0.7716 (tp30) cc_final: 0.7504 (tp30) REVERT: L 4 MET cc_start: 0.6858 (mmm) cc_final: 0.6468 (mmp) REVERT: L 27 GLN cc_start: 0.7286 (mt0) cc_final: 0.6761 (tt0) REVERT: L 31 ARG cc_start: 0.7938 (mtp85) cc_final: 0.6928 (mtm-85) REVERT: L 61 ARG cc_start: 0.6426 (mtp180) cc_final: 0.5975 (mtp180) REVERT: B 588 ARG cc_start: 0.8439 (tpt170) cc_final: 0.7642 (ttm110) REVERT: B 632 ASP cc_start: 0.9291 (t70) cc_final: 0.8929 (t0) REVERT: D 4 MET cc_start: 0.6854 (ptp) cc_final: 0.6647 (ptp) REVERT: D 24 ARG cc_start: 0.8182 (mtp180) cc_final: 0.7853 (ptm160) REVERT: D 81 GLU cc_start: 0.8130 (mp0) cc_final: 0.7860 (pm20) REVERT: C 37 ILE cc_start: 0.9043 (mm) cc_final: 0.8601 (tt) REVERT: E 122 LEU cc_start: 0.8444 (mt) cc_final: 0.8065 (pp) REVERT: E 150 MET cc_start: 0.8601 (mmm) cc_final: 0.8387 (mmt) REVERT: O 72 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7190 (t70) REVERT: Q 17 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7162 (mt-10) REVERT: Q 23 CYS cc_start: 0.6371 (t) cc_final: 0.6036 (t) REVERT: Q 27 GLN cc_start: 0.7424 (mt0) cc_final: 0.6916 (tt0) REVERT: Q 100 GLN cc_start: 0.8007 (mp10) cc_final: 0.7788 (mp10) REVERT: G 545 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8779 (tt) REVERT: G 563 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7550 (pt0) REVERT: G 588 ARG cc_start: 0.8386 (tpt170) cc_final: 0.7610 (ttm110) REVERT: G 632 ASP cc_start: 0.9220 (t70) cc_final: 0.8876 (t0) REVERT: M 39 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7786 (ptpp) REVERT: M 81 GLU cc_start: 0.8115 (mp0) cc_final: 0.7841 (pm20) REVERT: P 32 TYR cc_start: 0.9012 (m-10) cc_final: 0.8737 (m-10) REVERT: P 46 GLU cc_start: 0.7453 (tt0) cc_final: 0.7232 (tp30) REVERT: P 72 ASP cc_start: 0.8180 (t70) cc_final: 0.7866 (t0) REVERT: R 4 MET cc_start: 0.6683 (mtt) cc_final: 0.5685 (mtt) REVERT: R 61 ARG cc_start: 0.6246 (mtm-85) cc_final: 0.5968 (ttp-110) REVERT: R 88 CYS cc_start: 0.6412 (p) cc_final: 0.5648 (p) REVERT: I 530 MET cc_start: 0.8876 (mmm) cc_final: 0.8333 (mtt) REVERT: I 588 ARG cc_start: 0.8303 (tpt170) cc_final: 0.7631 (ttp-110) REVERT: I 632 ASP cc_start: 0.9195 (t70) cc_final: 0.8834 (t0) REVERT: N 24 ARG cc_start: 0.8345 (mtp180) cc_final: 0.7733 (ttm-80) REVERT: N 39 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7841 (ptpp) REVERT: K 13 ARG cc_start: 0.6852 (mmt90) cc_final: 0.6411 (mtm-85) outliers start: 47 outliers final: 40 residues processed: 346 average time/residue: 0.1834 time to fit residues: 98.7983 Evaluate side-chains 351 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 56 ILE Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 149 optimal weight: 0.7980 chunk 186 optimal weight: 0.0370 chunk 51 optimal weight: 0.0370 chunk 91 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.106470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073552 restraints weight = 51676.169| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.02 r_work: 0.2887 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27288 Z= 0.118 Angle : 0.624 10.309 37323 Z= 0.305 Chirality : 0.044 0.303 4503 Planarity : 0.004 0.053 4503 Dihedral : 5.915 59.231 6168 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.15 % Favored : 93.66 % Rotamer: Outliers : 1.53 % Allowed : 12.99 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 3105 helix: 0.90 (0.26), residues: 480 sheet: 0.94 (0.16), residues: 1116 loop : -1.17 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 103 TYR 0.011 0.001 TYR K 50 PHE 0.013 0.001 PHE H 63 TRP 0.029 0.001 TRP N 94 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00259 (27105) covalent geometry : angle 0.59315 (36822) SS BOND : bond 0.00274 ( 48) SS BOND : angle 0.96676 ( 96) hydrogen bonds : bond 0.03923 ( 1002) hydrogen bonds : angle 4.96573 ( 2691) link_ALPHA1-2 : bond 0.00350 ( 6) link_ALPHA1-2 : angle 1.85109 ( 18) link_ALPHA1-3 : bond 0.01077 ( 9) link_ALPHA1-3 : angle 1.20758 ( 27) link_ALPHA1-6 : bond 0.00522 ( 9) link_ALPHA1-6 : angle 1.44999 ( 27) link_BETA1-4 : bond 0.00510 ( 48) link_BETA1-4 : angle 1.46687 ( 144) link_BETA1-6 : bond 0.00228 ( 3) link_BETA1-6 : angle 1.45766 ( 9) link_NAG-ASN : bond 0.00336 ( 60) link_NAG-ASN : angle 2.34675 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 333 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 11 PHE cc_start: 0.7026 (m-80) cc_final: 0.6682 (m-80) REVERT: H 46 GLU cc_start: 0.7683 (tp30) cc_final: 0.7478 (tp30) REVERT: L 27 GLN cc_start: 0.7350 (mt0) cc_final: 0.6858 (tt0) REVERT: L 31 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7045 (mtm-85) REVERT: L 61 ARG cc_start: 0.6394 (mtp180) cc_final: 0.5840 (mtp180) REVERT: B 588 ARG cc_start: 0.8407 (tpt170) cc_final: 0.7607 (ttm110) REVERT: B 632 ASP cc_start: 0.9287 (t70) cc_final: 0.8947 (t0) REVERT: D 24 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7834 (ptm160) REVERT: D 81 GLU cc_start: 0.8090 (mp0) cc_final: 0.7846 (pm20) REVERT: C 37 ILE cc_start: 0.9038 (mm) cc_final: 0.8573 (tt) REVERT: E 150 MET cc_start: 0.8540 (mmm) cc_final: 0.8321 (mmt) REVERT: O 46 GLU cc_start: 0.7506 (tt0) cc_final: 0.7187 (tp30) REVERT: O 72 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7139 (t70) REVERT: Q 17 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7199 (mt-10) REVERT: Q 31 ARG cc_start: 0.7854 (mtp85) cc_final: 0.6959 (mtm-85) REVERT: G 545 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8787 (tt) REVERT: G 563 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7542 (pt0) REVERT: G 588 ARG cc_start: 0.8411 (tpt170) cc_final: 0.7632 (ttm110) REVERT: G 632 ASP cc_start: 0.9225 (t70) cc_final: 0.8876 (t0) REVERT: M 39 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7754 (ptpp) REVERT: M 81 GLU cc_start: 0.8089 (mp0) cc_final: 0.7807 (pm20) REVERT: P 32 TYR cc_start: 0.8970 (m-10) cc_final: 0.8691 (m-10) REVERT: P 46 GLU cc_start: 0.7422 (tt0) cc_final: 0.7135 (tp30) REVERT: R 31 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7039 (mtm110) REVERT: R 61 ARG cc_start: 0.6299 (mtm-85) cc_final: 0.6018 (ttp-110) REVERT: I 530 MET cc_start: 0.8862 (mmm) cc_final: 0.8202 (mtt) REVERT: I 588 ARG cc_start: 0.8292 (tpt170) cc_final: 0.7643 (ttp-110) REVERT: I 632 ASP cc_start: 0.9217 (t70) cc_final: 0.8866 (t0) REVERT: N 24 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7699 (ttm-80) REVERT: N 39 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7807 (ptpp) REVERT: N 105 GLU cc_start: 0.7380 (pp20) cc_final: 0.7012 (pp20) outliers start: 42 outliers final: 35 residues processed: 358 average time/residue: 0.1867 time to fit residues: 103.3350 Evaluate side-chains 349 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 312 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 93 TYR Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 53 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.106241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.073261 restraints weight = 51537.231| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.02 r_work: 0.2885 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27288 Z= 0.133 Angle : 0.634 10.234 37323 Z= 0.310 Chirality : 0.044 0.304 4503 Planarity : 0.004 0.053 4503 Dihedral : 5.524 46.879 6168 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.12 % Favored : 93.69 % Rotamer: Outliers : 1.38 % Allowed : 13.43 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 3105 helix: 0.93 (0.26), residues: 480 sheet: 0.95 (0.16), residues: 1116 loop : -1.19 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 103 TYR 0.014 0.001 TYR Q 87 PHE 0.012 0.001 PHE H 63 TRP 0.032 0.001 TRP N 94 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00306 (27105) covalent geometry : angle 0.60336 (36822) SS BOND : bond 0.00282 ( 48) SS BOND : angle 1.16279 ( 96) hydrogen bonds : bond 0.03957 ( 1002) hydrogen bonds : angle 4.95084 ( 2691) link_ALPHA1-2 : bond 0.00355 ( 6) link_ALPHA1-2 : angle 1.86790 ( 18) link_ALPHA1-3 : bond 0.01026 ( 9) link_ALPHA1-3 : angle 1.24685 ( 27) link_ALPHA1-6 : bond 0.00448 ( 9) link_ALPHA1-6 : angle 1.50801 ( 27) link_BETA1-4 : bond 0.00495 ( 48) link_BETA1-4 : angle 1.47074 ( 144) link_BETA1-6 : bond 0.00283 ( 3) link_BETA1-6 : angle 1.23268 ( 9) link_NAG-ASN : bond 0.00314 ( 60) link_NAG-ASN : angle 2.34360 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 324 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: H 11 PHE cc_start: 0.6975 (m-80) cc_final: 0.6716 (m-80) REVERT: L 27 GLN cc_start: 0.7348 (mt0) cc_final: 0.6902 (tt0) REVERT: L 31 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7001 (mtm-85) REVERT: L 61 ARG cc_start: 0.6437 (mtp180) cc_final: 0.5870 (mtp180) REVERT: B 588 ARG cc_start: 0.8400 (tpt170) cc_final: 0.7597 (ttm110) REVERT: B 632 ASP cc_start: 0.9335 (t70) cc_final: 0.9008 (t0) REVERT: D 24 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7829 (ptm160) REVERT: D 81 GLU cc_start: 0.8095 (mp0) cc_final: 0.7848 (pm20) REVERT: C 37 ILE cc_start: 0.9045 (mm) cc_final: 0.8576 (tt) REVERT: E 150 MET cc_start: 0.8540 (mmm) cc_final: 0.8329 (mmt) REVERT: O 46 GLU cc_start: 0.7500 (tt0) cc_final: 0.7189 (tp30) REVERT: O 72 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7162 (t70) REVERT: Q 4 MET cc_start: 0.7721 (mmm) cc_final: 0.7134 (mtt) REVERT: Q 17 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7212 (mt-10) REVERT: Q 27 GLN cc_start: 0.7446 (mt0) cc_final: 0.6968 (tt0) REVERT: Q 31 ARG cc_start: 0.7837 (mtp85) cc_final: 0.6953 (mtm-85) REVERT: G 545 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8771 (tt) REVERT: G 563 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7556 (pt0) REVERT: G 588 ARG cc_start: 0.8413 (tpt170) cc_final: 0.7628 (ttm110) REVERT: M 39 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7755 (ptpp) REVERT: M 81 GLU cc_start: 0.8073 (mp0) cc_final: 0.7728 (pm20) REVERT: P 32 TYR cc_start: 0.8970 (m-10) cc_final: 0.8686 (m-10) REVERT: P 46 GLU cc_start: 0.7420 (tt0) cc_final: 0.7144 (tp30) REVERT: R 4 MET cc_start: 0.7233 (mmm) cc_final: 0.6789 (mtt) REVERT: R 31 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7034 (mtm110) REVERT: R 61 ARG cc_start: 0.6269 (mtm-85) cc_final: 0.5995 (ttp-110) REVERT: I 530 MET cc_start: 0.8853 (mmm) cc_final: 0.8380 (mtt) REVERT: I 588 ARG cc_start: 0.8305 (tpt170) cc_final: 0.7648 (ttp-110) REVERT: I 632 ASP cc_start: 0.9238 (t70) cc_final: 0.8885 (t0) REVERT: N 24 ARG cc_start: 0.8355 (mtp180) cc_final: 0.7701 (ttm-80) REVERT: N 105 GLU cc_start: 0.7340 (pp20) cc_final: 0.6974 (pp20) outliers start: 38 outliers final: 35 residues processed: 346 average time/residue: 0.1895 time to fit residues: 101.7371 Evaluate side-chains 353 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 316 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 93 TYR Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 157 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 256 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 146 optimal weight: 0.3980 chunk 219 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.108778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.075838 restraints weight = 51659.551| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.13 r_work: 0.2953 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27288 Z= 0.138 Angle : 0.636 10.156 37323 Z= 0.311 Chirality : 0.044 0.303 4503 Planarity : 0.004 0.054 4503 Dihedral : 5.289 34.439 6168 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.15 % Favored : 93.66 % Rotamer: Outliers : 1.53 % Allowed : 13.25 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 3105 helix: 0.92 (0.26), residues: 480 sheet: 1.01 (0.16), residues: 1101 loop : -1.21 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 103 TYR 0.019 0.001 TYR L 87 PHE 0.012 0.001 PHE H 63 TRP 0.032 0.001 TRP N 94 HIS 0.007 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00319 (27105) covalent geometry : angle 0.60634 (36822) SS BOND : bond 0.00282 ( 48) SS BOND : angle 1.16714 ( 96) hydrogen bonds : bond 0.03991 ( 1002) hydrogen bonds : angle 4.92444 ( 2691) link_ALPHA1-2 : bond 0.00368 ( 6) link_ALPHA1-2 : angle 1.85196 ( 18) link_ALPHA1-3 : bond 0.01044 ( 9) link_ALPHA1-3 : angle 1.32377 ( 27) link_ALPHA1-6 : bond 0.00478 ( 9) link_ALPHA1-6 : angle 1.48286 ( 27) link_BETA1-4 : bond 0.00479 ( 48) link_BETA1-4 : angle 1.42760 ( 144) link_BETA1-6 : bond 0.00220 ( 3) link_BETA1-6 : angle 1.24000 ( 9) link_NAG-ASN : bond 0.00311 ( 60) link_NAG-ASN : angle 2.29515 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5700.92 seconds wall clock time: 98 minutes 38.74 seconds (5918.74 seconds total)