Starting phenix.real_space_refine on Mon Oct 13 10:40:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cde_7459/10_2025/6cde_7459_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cde_7459/10_2025/6cde_7459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6cde_7459/10_2025/6cde_7459_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cde_7459/10_2025/6cde_7459_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cde_7459/10_2025/6cde_7459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cde_7459/10_2025/6cde_7459.map" } resolution = 3.8 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= 0.004 sd= 0.093 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 177 5.16 5 C 20661 2.51 5 N 5319 2.21 5 O 6816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32973 Number of models: 1 Model: "" Number of chains: 81 Chain: "h" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "l" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 107} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "R" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 107} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "r" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "d" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "c" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "7" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "8" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "6" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "5" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "1" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "2" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "3" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "4" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 107} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 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: "J" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "V" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" 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: "Y" 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 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: "i" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "j" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 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: "t" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 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: "y" 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: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" 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: "AA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "BA" 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: "CA" 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: "DA" 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: "EA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "FA" 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: "GA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "IA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "JA" 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: "KA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "LA" 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: "MA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "1" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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 Time building chain proxies: 7.53, per 1000 atoms: 0.23 Number of scatterers: 32973 At special positions: 0 Unit cell: (163.24, 159, 154.76, 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 177 16.00 O 6816 8.00 N 5319 7.00 C 20661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.13 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.09 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.19 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 87 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.16 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.34 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.13 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.09 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 95 " distance=2.25 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 87 " distance=2.05 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.16 Simple disulfide: pdb=" SG CYS d 598 " - pdb=" SG CYS d 604 " distance=2.02 Simple disulfide: pdb=" SG CYS d 605 " - pdb=" SG CYS c 501 " distance=2.03 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.27 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 126 " - pdb=" SG CYS c 196 " distance=2.02 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.02 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.03 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.02 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.03 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 22 " - pdb=" SG CYS 7 95 " distance=2.40 Simple disulfide: pdb=" SG CYS 8 23 " - pdb=" SG CYS 8 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 87 " distance=2.05 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 98 " - pdb=" SG CYS 5 100A" distance=2.17 Simple disulfide: pdb=" SG CYS 1 598 " - pdb=" SG CYS 1 604 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 605 " - pdb=" SG CYS 2 501 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.42 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.13 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM31432 O5 NAG j 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32304 O5 NAGDA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30560 O5 NAG K 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31266 O5 NAG g 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30394 O5 NAG I 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32138 O5 NAGBA 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN P 5 " - " MAN P 6 " " MAN P 7 " - " MAN P 8 " " MAN U 5 " - " MAN U 6 " " MAN U 8 " - " MAN U 9 " " MAN g 4 " - " MAN g 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN o 5 " - " MAN o 6 " " MAN o 7 " - " MAN o 8 " " MAN t 5 " - " MAN t 6 " " MAN t 8 " - " MAN t 9 " " MANBA 4 " - " MANBA 5 " " MANCA 4 " - " MANCA 5 " " MANCA 5 " - " MANCA 6 " " MANFA 5 " - " MANFA 6 " " MANFA 7 " - " MANFA 8 " " MANIA 5 " - " MANIA 6 " " MANIA 8 " - " MANIA 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 7 " " MAN P 4 " - " MAN P 5 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 5 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 8 " " BMA k 3 " - " MAN k 4 " " BMA o 3 " - " MAN o 7 " " MAN o 4 " - " MAN o 5 " " BMA t 3 " - " MAN t 8 " " MAN t 4 " - " MAN t 5 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " " BMACA 3 " - " MANCA 4 " " MANCA 7 " - " MANCA 8 " " BMAEA 3 " - " MANEA 4 " " BMAFA 3 " - " MANFA 7 " " MANFA 4 " - " MANFA 5 " " BMAIA 3 " - " MANIA 8 " " MANIA 4 " - " MANIA 5 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA J 3 " - " MAN J 7 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 7 " " BMA W 3 " - " MAN W 4 " " BMA g 3 " - " MAN g 6 " " BMA i 3 " - " MAN i 7 " " BMA k 3 " - " MAN k 5 " " BMA o 3 " - " MAN o 4 " " BMA t 3 " - " MAN t 4 " " MAN t 4 " - " MAN t 7 " " BMA v 3 " - " MAN v 4 " " BMABA 3 " - " MANBA 6 " " BMACA 3 " - " MANCA 7 " " BMAEA 3 " - " MANEA 5 " " BMAFA 3 " - " MANFA 4 " " BMAIA 3 " - " MANIA 4 " " MANIA 4 " - " MANIA 7 " " BMAKA 3 " - " MANKA 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 9 1 " - " NAG 9 2 " " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " " NAGKA 1 " - " NAGKA 2 " " NAGKA 2 " - " BMAKA 3 " " NAGLA 1 " - " NAGLA 2 " " NAGLA 2 " - " BMALA 3 " " NAGMA 1 " - " NAGMA 2 " " NAGMA 2 " - " BMAMA 3 " NAG-ASN " NAG 0 1 " - " ASN 2 88 " " NAG 1 701 " - " ASN 1 618 " " NAG 2 653 " - " ASN 2 339 " " NAG 2 654 " - " ASN 2 355 " " NAG 9 1 " - " ASN 2 133 " " NAG A 1 " - " ASN D 637 " " NAG B 1 " - " ASN D 611 " " NAG C 653 " - " ASN C 339 " " NAG C 654 " - " ASN C 355 " " NAG D 701 " - " ASN D 618 " " NAG E 1 " - " ASN C 88 " " NAG F 1 " - " ASN C 133 " " NAG G 1 " - " ASN C 137 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 160 " " NAG K 1 " - " ASN C 197 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN d 637 " " NAG a 1 " - " ASN d 611 " " NAG b 1 " - " ASN c 88 " " NAG c 653 " - " ASN c 339 " " NAG c 654 " - " ASN c 355 " " NAG d 701 " - " ASN d 618 " " NAG e 1 " - " ASN c 133 " " NAG f 1 " - " ASN c 137 " " NAG g 1 " - " ASN c 156 " " NAG i 1 " - " ASN c 160 " " NAG j 1 " - " ASN c 197 " " NAG k 1 " - " ASN c 234 " " NAG o 1 " - " ASN c 262 " " NAG p 1 " - " ASN c 295 " " NAG s 1 " - " ASN c 301 " " NAG t 1 " - " ASN c 332 " " NAG u 1 " - " ASN c 363 " " NAG v 1 " - " ASN c 386 " " NAG w 1 " - " ASN c 392 " " NAG x 1 " - " ASN c 448 " " NAG y 1 " - " ASN 1 637 " " NAG z 1 " - " ASN 1 611 " " NAGAA 1 " - " ASN 2 137 " " NAGBA 1 " - " ASN 2 156 " " NAGCA 1 " - " ASN 2 160 " " NAGDA 1 " - " ASN 2 197 " " NAGEA 1 " - " ASN 2 234 " " NAGFA 1 " - " ASN 2 262 " " NAGGA 1 " - " ASN 2 295 " " NAGHA 1 " - " ASN 2 301 " " NAGIA 1 " - " ASN 2 332 " " NAGJA 1 " - " ASN 2 363 " " NAGKA 1 " - " ASN 2 386 " " NAGLA 1 " - " ASN 2 392 " " NAGMA 1 " - " ASN 2 448 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 84 sheets defined 13.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'M' and resid 86 through 90 removed outlier: 3.511A pdb=" N ASP M 89 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER M 90 " --> pdb=" O ALA M 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 86 through 90' Processing helix chain 'M' and resid 107 through 111 Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.684A pdb=" N GLN Q 64 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.678A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.798A pdb=" N PHE D 519 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.214A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 4.113A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.855A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 627 through 633 Processing helix chain 'D' and resid 638 through 663 removed outlier: 4.039A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.693A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.438A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'm' and resid 86 through 90 removed outlier: 3.511A pdb=" N ASP m 89 " --> pdb=" O THR m 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER m 90 " --> pdb=" O ALA m 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 86 through 90' Processing helix chain 'm' and resid 107 through 111 Processing helix chain 'q' and resid 61 through 64 removed outlier: 3.685A pdb=" N GLN q 64 " --> pdb=" O ARG q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 61 through 64' Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.678A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 515 through 520 removed outlier: 3.798A pdb=" N PHE d 519 " --> pdb=" O ILE d 515 " (cutoff:3.500A) Processing helix chain 'd' and resid 523 through 527 removed outlier: 4.213A pdb=" N GLY d 527 " --> pdb=" O GLY d 524 " (cutoff:3.500A) Processing helix chain 'd' and resid 529 through 534 removed outlier: 4.113A pdb=" N SER d 534 " --> pdb=" O MET d 530 " (cutoff:3.500A) Processing helix chain 'd' and resid 537 through 543 removed outlier: 3.854A pdb=" N ALA d 541 " --> pdb=" O LEU d 537 " (cutoff:3.500A) Processing helix chain 'd' and resid 570 through 595 Processing helix chain 'd' and resid 620 through 625 Processing helix chain 'd' and resid 627 through 633 Processing helix chain 'd' and resid 638 through 663 removed outlier: 4.038A pdb=" N LEU d 663 " --> pdb=" O ASP d 659 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 63 Processing helix chain 'c' and resid 99 through 115 removed outlier: 3.693A pdb=" N ILE c 109 " --> pdb=" O HIS c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 177 through 179 No H-bonds generated for 'chain 'c' and resid 177 through 179' Processing helix chain 'c' and resid 195 through 198 Processing helix chain 'c' and resid 335 through 354 removed outlier: 4.439A pdb=" N LYS c 351 " --> pdb=" O LYS c 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS c 352 " --> pdb=" O GLN c 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE c 353 " --> pdb=" O LEU c 349 " (cutoff:3.500A) Processing helix chain 'c' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR c 372 " --> pdb=" O ASP c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 476 through 481 Processing helix chain '7' and resid 86 through 90 removed outlier: 3.511A pdb=" N ASP 7 89 " --> pdb=" O THR 7 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER 7 90 " --> pdb=" O ALA 7 87 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 86 through 90' Processing helix chain '7' and resid 107 through 111 Processing helix chain '5' and resid 61 through 64 removed outlier: 3.684A pdb=" N GLN 5 64 " --> pdb=" O ARG 5 61 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 61 through 64' Processing helix chain '5' and resid 83 through 87 removed outlier: 3.678A pdb=" N THR 5 87 " --> pdb=" O PRO 5 84 " (cutoff:3.500A) Processing helix chain '1' and resid 515 through 520 removed outlier: 3.798A pdb=" N PHE 1 519 " --> pdb=" O ILE 1 515 " (cutoff:3.500A) Processing helix chain '1' and resid 523 through 527 removed outlier: 4.214A pdb=" N GLY 1 527 " --> pdb=" O GLY 1 524 " (cutoff:3.500A) Processing helix chain '1' and resid 529 through 534 removed outlier: 4.112A pdb=" N SER 1 534 " --> pdb=" O MET 1 530 " (cutoff:3.500A) Processing helix chain '1' and resid 537 through 543 removed outlier: 3.855A pdb=" N ALA 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 570 through 595 Processing helix chain '1' and resid 620 through 625 Processing helix chain '1' and resid 627 through 633 Processing helix chain '1' and resid 638 through 663 removed outlier: 4.038A pdb=" N LEU 1 663 " --> pdb=" O ASP 1 659 " (cutoff:3.500A) Processing helix chain '2' and resid 58 through 63 Processing helix chain '2' and resid 99 through 115 removed outlier: 3.693A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 177 through 179 No H-bonds generated for 'chain '2' and resid 177 through 179' Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 354 removed outlier: 4.437A pdb=" N LYS 2 351 " --> pdb=" O LYS 2 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS 2 352 " --> pdb=" O GLN 2 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE 2 353 " --> pdb=" O LEU 2 349 " (cutoff:3.500A) Processing helix chain '2' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR 2 372 " --> pdb=" O ASP 2 368 " (cutoff:3.500A) Processing helix chain '2' and resid 476 through 481 Processing sheet with id=AA1, first strand: chain 'h' and resid 10 through 11 removed outlier: 6.540A pdb=" N ASP h 10 " --> pdb=" O THR h 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'h' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'h' and resid 44 through 51 removed outlier: 6.581A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET h 34 " --> pdb=" O ALA h 50 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER h 93 " --> pdb=" O HIS h 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG h 94 " --> pdb=" O ASP h 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'l' and resid 5 through 7 removed outlier: 4.152A pdb=" N THR l 5 " --> pdb=" O LYS l 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS l 24 " --> pdb=" O THR l 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'l' and resid 33 through 38 removed outlier: 4.422A pdb=" N GLY l 84 " --> pdb=" O LEU l 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU l 104 " --> pdb=" O GLY l 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL M 12 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL M 128 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA M 91 " --> pdb=" O VAL M 128 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL M 12 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL M 128 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA M 91 " --> pdb=" O VAL M 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR M 33 " --> pdb=" O THR M 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 96 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 13 removed outlier: 5.736A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'N' and resid 19 through 22 Processing sheet with id=AB2, first strand: chain 'N' and resid 31 through 38 removed outlier: 3.882A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 5 through 7 removed outlier: 3.579A pdb=" N ASP R 69 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP R 34 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AB7, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.664A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.984A pdb=" N TYR Q 102 " --> pdb=" O ARG Q 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.532A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.875A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.513A pdb=" N THR C 244 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.127A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.198A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.385A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.790A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 304 through 312 removed outlier: 7.058A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.539A pdb=" N ASP H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AD4, first strand: chain 'H' and resid 44 through 51 removed outlier: 6.579A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.153A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 33 through 38 removed outlier: 4.422A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.507A pdb=" N VAL m 12 " --> pdb=" O THR m 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL m 128 " --> pdb=" O ALA m 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA m 91 " --> pdb=" O VAL m 128 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.507A pdb=" N VAL m 12 " --> pdb=" O THR m 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL m 128 " --> pdb=" O ALA m 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA m 91 " --> pdb=" O VAL m 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR m 33 " --> pdb=" O THR m 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA m 96 " --> pdb=" O SER m 35 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'm' and resid 71 through 72 Processing sheet with id=AE1, first strand: chain 'n' and resid 11 through 13 removed outlier: 5.743A pdb=" N VAL n 11 " --> pdb=" O ILE n 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'n' and resid 19 through 22 Processing sheet with id=AE3, first strand: chain 'n' and resid 31 through 38 removed outlier: 3.882A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'r' and resid 5 through 7 removed outlier: 3.580A pdb=" N ASP r 69 " --> pdb=" O SER r 66 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AE8, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.664A pdb=" N GLY q 49 " --> pdb=" O TRP q 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.983A pdb=" N TYR q 102 " --> pdb=" O ARG q 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 35 through 40 Processing sheet with id=AF2, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.532A pdb=" N LYS c 487 " --> pdb=" O LEU c 226 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 75 through 76 removed outlier: 3.875A pdb=" N VAL c 75 " --> pdb=" O CYS c 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE c 53 " --> pdb=" O CYS c 218 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 84 through 85 removed outlier: 3.514A pdb=" N THR c 244 " --> pdb=" O ILE c 84 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 91 through 94 removed outlier: 4.127A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 130 through 133 Processing sheet with id=AF7, first strand: chain 'c' and resid 181 through 183 Processing sheet with id=AF8, first strand: chain 'c' and resid 202 through 203 removed outlier: 7.198A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 271 through 273 removed outlier: 7.385A pdb=" N THR c 450 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N THR c 290 " --> pdb=" O ASN c 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN c 448 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N VAL c 292 " --> pdb=" O VAL c 446 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N VAL c 446 " --> pdb=" O VAL c 292 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ILE c 294 " --> pdb=" O ARG c 444 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ARG c 444 " --> pdb=" O ILE c 294 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE c 358 " --> pdb=" O GLU c 466 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE c 468 " --> pdb=" O ILE c 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG c 360 " --> pdb=" O PHE c 468 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 271 through 273 removed outlier: 6.790A pdb=" N GLN c 293 " --> pdb=" O SER c 334 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER c 334 " --> pdb=" O GLN c 293 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS c 330 " --> pdb=" O THR c 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE c 376 " --> pdb=" O PHE c 383 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'c' and resid 304 through 312 removed outlier: 7.068A pdb=" N GLN c 315 " --> pdb=" O ILE c 309 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '7' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL 7 12 " --> pdb=" O THR 7 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 7 128 " --> pdb=" O ALA 7 91 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 7 91 " --> pdb=" O VAL 7 128 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP 7 34 " --> pdb=" O TYR 7 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR 7 50 " --> pdb=" O TRP 7 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP 7 36 " --> pdb=" O ILE 7 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '7' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL 7 12 " --> pdb=" O THR 7 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 7 128 " --> pdb=" O ALA 7 91 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 7 91 " --> pdb=" O VAL 7 128 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR 7 33 " --> pdb=" O THR 7 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA 7 96 " --> pdb=" O SER 7 35 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '7' and resid 71 through 72 Processing sheet with id=AG6, first strand: chain '8' and resid 11 through 13 removed outlier: 5.730A pdb=" N VAL 8 11 " --> pdb=" O ILE 8 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain '8' and resid 19 through 22 Processing sheet with id=AG8, first strand: chain '8' and resid 31 through 38 removed outlier: 3.881A pdb=" N TYR 8 87 " --> pdb=" O TYR 8 36 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '6' and resid 5 through 7 removed outlier: 3.579A pdb=" N ASP 6 69 " --> pdb=" O SER 6 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '6' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU 6 11 " --> pdb=" O GLU 6 100 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP 6 34 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '6' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU 6 11 " --> pdb=" O GLU 6 100 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '5' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain '5' and resid 10 through 11 removed outlier: 3.664A pdb=" N GLY 5 49 " --> pdb=" O TRP 5 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG 5 38 " --> pdb=" O TRP 5 47 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP 5 47 " --> pdb=" O ARG 5 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE 5 40 " --> pdb=" O PHE 5 45 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE 5 45 " --> pdb=" O ILE 5 40 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '5' and resid 10 through 11 removed outlier: 3.983A pdb=" N TYR 5 102 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2' and resid 35 through 40 Processing sheet with id=AH7, first strand: chain '2' and resid 45 through 47 removed outlier: 3.532A pdb=" N LYS 2 487 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '2' and resid 75 through 76 removed outlier: 3.875A pdb=" N VAL 2 75 " --> pdb=" O CYS 2 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE 2 53 " --> pdb=" O CYS 2 218 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 84 through 85 removed outlier: 3.513A pdb=" N THR 2 244 " --> pdb=" O ILE 2 84 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '2' and resid 91 through 94 removed outlier: 4.127A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AI3, first strand: chain '2' and resid 181 through 183 Processing sheet with id=AI4, first strand: chain '2' and resid 202 through 203 removed outlier: 7.199A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain '2' and resid 271 through 273 removed outlier: 7.385A pdb=" N THR 2 450 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N THR 2 290 " --> pdb=" O ASN 2 448 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN 2 448 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N VAL 2 292 " --> pdb=" O VAL 2 446 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N VAL 2 446 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ILE 2 294 " --> pdb=" O ARG 2 444 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ARG 2 444 " --> pdb=" O ILE 2 294 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE 2 358 " --> pdb=" O GLU 2 466 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE 2 468 " --> pdb=" O ILE 2 358 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG 2 360 " --> pdb=" O PHE 2 468 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '2' and resid 271 through 273 removed outlier: 6.791A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS 2 330 " --> pdb=" O THR 2 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE 2 376 " --> pdb=" O PHE 2 383 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain '2' and resid 304 through 312 removed outlier: 7.058A pdb=" N GLN 2 315 " --> pdb=" O ILE 2 309 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '3' and resid 10 through 11 removed outlier: 6.539A pdb=" N ASP 3 10 " --> pdb=" O THR 3 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain '3' and resid 21 through 23 Processing sheet with id=AJ1, first strand: chain '3' and resid 44 through 51 removed outlier: 6.580A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA 3 50 " --> pdb=" O MET 3 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET 3 34 " --> pdb=" O ALA 3 50 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER 3 93 " --> pdb=" O HIS 3 35 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG 3 94 " --> pdb=" O ASP 3 101 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '4' and resid 5 through 7 removed outlier: 4.153A pdb=" N THR 4 5 " --> pdb=" O LYS 4 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS 4 24 " --> pdb=" O THR 4 5 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain '4' and resid 33 through 38 removed outlier: 4.422A pdb=" N GLY 4 84 " --> pdb=" O LEU 4 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU 4 104 " --> pdb=" O GLY 4 84 " (cutoff:3.500A) 882 hydrogen bonds defined for protein. 2223 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: 7.61 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9936 1.34 - 1.46: 9053 1.46 - 1.59: 14446 1.59 - 1.71: 0 1.71 - 1.83: 240 Bond restraints: 33675 Sorted by residual: bond pdb=" C1 MAN i 4 " pdb=" O5 MAN i 4 " ideal model delta sigma weight residual 1.399 1.480 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1 MAN J 4 " pdb=" O5 MAN J 4 " ideal model delta sigma weight residual 1.399 1.479 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1 MANCA 4 " pdb=" O5 MANCA 4 " ideal model delta sigma weight residual 1.399 1.479 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C5 BMAAA 3 " pdb=" O5 BMAAA 3 " ideal model delta sigma weight residual 1.417 1.493 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 BMA f 3 " pdb=" O5 BMA f 3 " ideal model delta sigma weight residual 1.417 1.493 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 33670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 43327 2.23 - 4.46: 1936 4.46 - 6.69: 394 6.69 - 8.92: 56 8.92 - 11.14: 19 Bond angle restraints: 45732 Sorted by residual: angle pdb=" N GLN R 89 " pdb=" CA GLN R 89 " pdb=" C GLN R 89 " ideal model delta sigma weight residual 108.41 98.37 10.04 1.63e+00 3.76e-01 3.80e+01 angle pdb=" C SER 1 615 " pdb=" N ASN 1 616 " pdb=" CA ASN 1 616 " ideal model delta sigma weight residual 122.46 129.36 -6.90 1.41e+00 5.03e-01 2.39e+01 angle pdb=" C SER D 615 " pdb=" N ASN D 616 " pdb=" CA ASN D 616 " ideal model delta sigma weight residual 122.46 129.35 -6.89 1.41e+00 5.03e-01 2.39e+01 angle pdb=" C SER d 615 " pdb=" N ASN d 616 " pdb=" CA ASN d 616 " ideal model delta sigma weight residual 122.46 129.34 -6.88 1.41e+00 5.03e-01 2.38e+01 angle pdb=" N PHE Q 100D" pdb=" CA PHE Q 100D" pdb=" C PHE Q 100D" ideal model delta sigma weight residual 109.81 120.28 -10.47 2.21e+00 2.05e-01 2.24e+01 ... (remaining 45727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 21475 23.24 - 46.48: 759 46.48 - 69.71: 186 69.71 - 92.95: 230 92.95 - 116.19: 132 Dihedral angle restraints: 22782 sinusoidal: 11763 harmonic: 11019 Sorted by residual: dihedral pdb=" CB CYS 2 54 " pdb=" SG CYS 2 54 " pdb=" SG CYS 2 74 " pdb=" CB CYS 2 74 " ideal model delta sinusoidal sigma weight residual -86.00 -171.53 85.53 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS c 54 " pdb=" SG CYS c 54 " pdb=" SG CYS c 74 " pdb=" CB CYS c 74 " ideal model delta sinusoidal sigma weight residual -86.00 -169.43 83.43 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -156.77 70.77 1 1.00e+01 1.00e-02 6.44e+01 ... (remaining 22779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 5688 0.327 - 0.653: 18 0.653 - 0.980: 9 0.980 - 1.307: 9 1.307 - 1.633: 6 Chirality restraints: 5730 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 332 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.67e+01 chirality pdb=" C1 NAG t 1 " pdb=" ND2 ASN c 332 " pdb=" C2 NAG t 1 " pdb=" O5 NAG t 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.66e+01 chirality pdb=" C1 NAGIA 1 " pdb=" ND2 ASN 2 332 " pdb=" C2 NAGIA 1 " pdb=" O5 NAGIA 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.65e+01 ... (remaining 5727 not shown) Planarity restraints: 5529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN c 392 " -0.073 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" CG ASN c 392 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN c 392 " -0.193 2.00e-02 2.50e+03 pdb=" ND2 ASN c 392 " 0.519 2.00e-02 2.50e+03 pdb=" C1 NAG w 1 " -0.344 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 392 " 0.073 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" CG ASN C 392 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 392 " 0.193 2.00e-02 2.50e+03 pdb=" ND2 ASN C 392 " -0.519 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 392 " 0.073 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" CG ASN 2 392 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 392 " 0.193 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 392 " -0.518 2.00e-02 2.50e+03 pdb=" C1 NAGLA 1 " 0.343 2.00e-02 2.50e+03 ... (remaining 5526 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 47 2.30 - 2.95: 15387 2.95 - 3.60: 42730 3.60 - 4.25: 71011 4.25 - 4.90: 116013 Nonbonded interactions: 245188 Sorted by model distance: nonbonded pdb=" O GLY 2 263 " pdb=" CG2 THR 2 450 " model vdw 1.655 3.460 nonbonded pdb=" O GLY C 263 " pdb=" CG2 THR C 450 " model vdw 1.664 3.460 nonbonded pdb=" O GLY c 263 " pdb=" CG2 THR c 450 " model vdw 1.664 3.460 nonbonded pdb=" O LYS c 502 " pdb=" CD2 LEU 1 661 " model vdw 1.865 3.460 nonbonded pdb=" CD2 LEU D 661 " pdb=" O LYS 2 502 " model vdw 1.918 3.460 ... (remaining 245183 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain '0' selection = chain '9' selection = chain 'DA' selection = chain 'E' selection = chain 'F' selection = chain 'GA' selection = chain 'K' selection = chain 'S' selection = chain 'b' selection = chain 'e' selection = chain 'j' selection = chain 'p' } ncs_group { reference = chain '1' selection = chain 'D' selection = chain 'd' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '6' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '7' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '8' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'HA' selection = chain 'JA' selection = chain 'LA' selection = chain 'MA' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'AA' selection = chain 'G' selection = chain 'KA' selection = chain 'W' selection = chain 'f' selection = chain 'v' } ncs_group { reference = chain 'BA' selection = chain 'I' selection = chain 'g' } ncs_group { reference = (chain 'CA' and (resid 1 or resid 4 through 8)) selection = (chain 'FA' and (resid 1 or resid 4 through 8)) selection = (chain 'IA' and (resid 2 or resid 5 through 9)) selection = (chain 'J' and (resid 1 or resid 4 through 8)) selection = (chain 'P' and (resid 1 or resid 4 through 8)) selection = (chain 'U' and (resid 2 or resid 5 through 9)) selection = (chain 'i' and (resid 1 or resid 4 through 8)) selection = (chain 'o' and (resid 1 or resid 4 through 8)) selection = (chain 't' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'EA' selection = chain 'O' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 32.560 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 0.010 0.391 33954 Z= 0.457 Angle : 1.633 61.575 46503 Z= 0.699 Chirality : 0.101 1.633 5730 Planarity : 0.006 0.067 5469 Dihedral : 17.575 116.188 15561 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.21 % Allowed : 3.78 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.12), residues: 3774 helix: -2.28 (0.20), residues: 405 sheet: -1.48 (0.14), residues: 1221 loop : -2.67 (0.11), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 4 61 TYR 0.025 0.003 TYR L 49 PHE 0.044 0.004 PHE 2 288 TRP 0.033 0.003 TRP c 479 HIS 0.010 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00845 (33675) covalent geometry : angle 1.11297 (45732) SS BOND : bond 0.10306 ( 57) SS BOND : angle 12.40989 ( 114) hydrogen bonds : bond 0.18497 ( 834) hydrogen bonds : angle 8.07383 ( 2223) Misc. bond : bond 0.00507 ( 3) link_ALPHA1-2 : bond 0.00455 ( 21) link_ALPHA1-2 : angle 1.91691 ( 63) link_ALPHA1-3 : bond 0.00927 ( 27) link_ALPHA1-3 : angle 3.05049 ( 81) link_ALPHA1-6 : bond 0.00802 ( 21) link_ALPHA1-6 : angle 1.86227 ( 63) link_BETA1-4 : bond 0.00954 ( 90) link_BETA1-4 : angle 3.75932 ( 270) link_NAG-ASN : bond 0.05560 ( 60) link_NAG-ASN : angle 15.77995 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 709 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 4 MET cc_start: 0.7185 (mtt) cc_final: 0.6452 (mmm) REVERT: l 24 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7855 (mttt) REVERT: l 27 GLN cc_start: 0.8328 (mt0) cc_final: 0.7847 (mt0) REVERT: l 30 ASN cc_start: 0.8361 (m110) cc_final: 0.8024 (m-40) REVERT: N 17 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7777 (mt0) REVERT: N 87 TYR cc_start: 0.8464 (m-80) cc_final: 0.8144 (m-10) REVERT: N 104 LEU cc_start: 0.8452 (tp) cc_final: 0.7841 (tp) REVERT: R 33 THR cc_start: 0.9351 (m) cc_final: 0.9085 (p) REVERT: Q 39 LEU cc_start: 0.9054 (tp) cc_final: 0.8740 (tt) REVERT: D 542 ARG cc_start: 0.8844 (ttm110) cc_final: 0.8496 (ttp-170) REVERT: D 571 TRP cc_start: 0.8222 (m100) cc_final: 0.7965 (m100) REVERT: D 657 GLU cc_start: 0.8837 (tp30) cc_final: 0.8614 (tp30) REVERT: C 475 MET cc_start: 0.8753 (tpt) cc_final: 0.8343 (tpp) REVERT: H 96 LYS cc_start: 0.8036 (mttt) cc_final: 0.7632 (tptt) REVERT: H 97 LEU cc_start: 0.8615 (mt) cc_final: 0.8359 (mt) REVERT: L 27 GLN cc_start: 0.8227 (mt0) cc_final: 0.7921 (mt0) REVERT: n 17 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7676 (mt0) REVERT: n 53 ASP cc_start: 0.7771 (m-30) cc_final: 0.7562 (m-30) REVERT: n 87 TYR cc_start: 0.8466 (m-80) cc_final: 0.8211 (m-80) REVERT: q 39 LEU cc_start: 0.9161 (tp) cc_final: 0.8913 (tt) REVERT: q 76 ASP cc_start: 0.8095 (p0) cc_final: 0.7776 (p0) REVERT: d 571 TRP cc_start: 0.8035 (m100) cc_final: 0.7653 (m100) REVERT: d 574 LYS cc_start: 0.8814 (mttp) cc_final: 0.8546 (mtpt) REVERT: d 647 GLU cc_start: 0.8456 (tt0) cc_final: 0.8202 (tt0) REVERT: d 657 GLU cc_start: 0.8937 (tp30) cc_final: 0.8545 (tp30) REVERT: d 659 ASP cc_start: 0.8647 (m-30) cc_final: 0.8396 (t0) REVERT: c 475 MET cc_start: 0.8729 (tpt) cc_final: 0.8401 (tpp) REVERT: 8 17 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7807 (mt0) REVERT: 8 49 TYR cc_start: 0.8410 (p90) cc_final: 0.8184 (p90) REVERT: 8 87 TYR cc_start: 0.8402 (m-80) cc_final: 0.8047 (m-80) REVERT: 6 33 THR cc_start: 0.9488 (m) cc_final: 0.9069 (p) REVERT: 5 39 LEU cc_start: 0.9231 (tp) cc_final: 0.8885 (tt) REVERT: 1 571 TRP cc_start: 0.8100 (m100) cc_final: 0.7849 (m100) REVERT: 1 574 LYS cc_start: 0.8737 (mttp) cc_final: 0.8492 (mtpt) REVERT: 1 657 GLU cc_start: 0.8956 (tp30) cc_final: 0.8641 (tp30) REVERT: 2 180 ASP cc_start: 0.8851 (m-30) cc_final: 0.8637 (m-30) REVERT: 2 475 MET cc_start: 0.8689 (tpt) cc_final: 0.8230 (tpp) REVERT: 4 24 LYS cc_start: 0.8356 (mtpp) cc_final: 0.7659 (mtpt) REVERT: 4 27 GLN cc_start: 0.8382 (mt0) cc_final: 0.7923 (mt0) outliers start: 7 outliers final: 4 residues processed: 716 average time/residue: 0.2460 time to fit residues: 269.4225 Evaluate side-chains 351 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 347 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain r residue 88 GLN Chi-restraints excluded: chain 7 residue 95 CYS Chi-restraints excluded: chain 6 residue 88 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 50 ASN D 543 ASN D 625 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 249 HIS C 293 GLN n 50 ASN d 543 ASN d 625 ASN ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 ASN c 103 GLN c 249 HIS c 293 GLN 8 50 ASN 1 543 ASN 1 625 ASN 2 249 HIS 2 293 GLN 3 61 GLN 4 90 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071758 restraints weight = 87913.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.071617 restraints weight = 64389.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072286 restraints weight = 47027.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073237 restraints weight = 39060.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073228 restraints weight = 34963.655| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33954 Z= 0.177 Angle : 0.842 12.867 46503 Z= 0.380 Chirality : 0.049 0.288 5730 Planarity : 0.005 0.043 5469 Dihedral : 15.493 89.952 8607 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.80 % Allowed : 8.89 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.13), residues: 3774 helix: -0.51 (0.25), residues: 426 sheet: -1.23 (0.14), residues: 1317 loop : -2.29 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 38 TYR 0.015 0.002 TYR 7 33 PHE 0.036 0.002 PHE 2 53 TRP 0.021 0.002 TRP c 112 HIS 0.005 0.001 HIS 4 93 Details of bonding type rmsd covalent geometry : bond 0.00387 (33675) covalent geometry : angle 0.76644 (45732) SS BOND : bond 0.00639 ( 57) SS BOND : angle 1.36684 ( 114) hydrogen bonds : bond 0.04215 ( 834) hydrogen bonds : angle 6.35779 ( 2223) Misc. bond : bond 0.00001 ( 3) link_ALPHA1-2 : bond 0.00505 ( 21) link_ALPHA1-2 : angle 1.82793 ( 63) link_ALPHA1-3 : bond 0.01391 ( 27) link_ALPHA1-3 : angle 2.68038 ( 81) link_ALPHA1-6 : bond 0.00771 ( 21) link_ALPHA1-6 : angle 2.01697 ( 63) link_BETA1-4 : bond 0.00787 ( 90) link_BETA1-4 : angle 2.84376 ( 270) link_NAG-ASN : bond 0.00604 ( 60) link_NAG-ASN : angle 3.83728 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 455 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 4 MET cc_start: 0.6759 (mtt) cc_final: 0.6485 (mmp) REVERT: l 24 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7800 (mttt) REVERT: l 27 ILE cc_start: 0.7948 (mt) cc_final: 0.7628 (mm) REVERT: l 30 ASN cc_start: 0.8332 (m110) cc_final: 0.8062 (m-40) REVERT: l 90 GLN cc_start: 0.7934 (tt0) cc_final: 0.7452 (tm-30) REVERT: M 64 LYS cc_start: 0.8597 (tptt) cc_final: 0.8381 (ttmm) REVERT: N 20 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7769 (mmm-85) REVERT: R 100 GLU cc_start: 0.6703 (tp30) cc_final: 0.6427 (tp30) REVERT: D 542 ARG cc_start: 0.8964 (ttm110) cc_final: 0.8513 (ttp-170) REVERT: D 633 LYS cc_start: 0.9264 (ptmt) cc_final: 0.8868 (mttp) REVERT: D 657 GLU cc_start: 0.8896 (tp30) cc_final: 0.8623 (tp30) REVERT: C 161 MET cc_start: 0.8315 (tpp) cc_final: 0.8095 (tpt) REVERT: C 264 SER cc_start: 0.9199 (t) cc_final: 0.8688 (p) REVERT: H 39 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7547 (pp30) REVERT: H 96 LYS cc_start: 0.7806 (mttt) cc_final: 0.7527 (tptt) REVERT: L 4 MET cc_start: 0.6829 (mtt) cc_final: 0.6328 (mmp) REVERT: L 6 GLN cc_start: 0.4800 (mt0) cc_final: 0.4571 (mt0) REVERT: L 24 LYS cc_start: 0.8140 (mttt) cc_final: 0.7347 (mtpt) REVERT: n 17 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8083 (mt0) REVERT: n 87 TYR cc_start: 0.8567 (m-80) cc_final: 0.8334 (m-10) REVERT: d 574 LYS cc_start: 0.8922 (mttp) cc_final: 0.8651 (mtpt) REVERT: d 633 LYS cc_start: 0.9291 (ptpt) cc_final: 0.8629 (mtmm) REVERT: d 657 GLU cc_start: 0.8935 (tp30) cc_final: 0.8574 (tp30) REVERT: c 264 SER cc_start: 0.9129 (t) cc_final: 0.8684 (p) REVERT: c 416 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9007 (pp) REVERT: 7 31 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8676 (t0) REVERT: 8 49 TYR cc_start: 0.8250 (p90) cc_final: 0.8048 (p90) REVERT: 8 100 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7846 (mm-30) REVERT: 6 100 GLU cc_start: 0.6839 (tp30) cc_final: 0.6472 (tp30) REVERT: 1 574 LYS cc_start: 0.8913 (mttp) cc_final: 0.8559 (mtpt) REVERT: 1 633 LYS cc_start: 0.9020 (ptpp) cc_final: 0.8800 (ptpp) REVERT: 1 657 GLU cc_start: 0.8934 (tp30) cc_final: 0.8658 (tp30) REVERT: 2 180 ASP cc_start: 0.8823 (m-30) cc_final: 0.8610 (m-30) REVERT: 2 264 SER cc_start: 0.9172 (t) cc_final: 0.8775 (p) REVERT: 2 416 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8978 (pp) REVERT: 4 4 MET cc_start: 0.6738 (mtt) cc_final: 0.6488 (mmp) REVERT: 4 27 GLN cc_start: 0.8397 (mt0) cc_final: 0.8049 (mt0) REVERT: 4 27 ILE cc_start: 0.7747 (mt) cc_final: 0.7441 (mm) REVERT: 4 70 ASP cc_start: 0.7658 (t0) cc_final: 0.7269 (t70) outliers start: 60 outliers final: 28 residues processed: 499 average time/residue: 0.2249 time to fit residues: 179.6750 Evaluate side-chains 386 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 355 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain R residue 51 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain d residue 576 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 7 residue 124 LYS Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 90 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 258 optimal weight: 8.9990 chunk 226 optimal weight: 2.9990 chunk 143 optimal weight: 30.0000 chunk 304 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 372 optimal weight: 30.0000 chunk 247 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 93 HIS R 36 GLN D 543 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 HIS ** r 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 64 GLN d 543 ASN ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 30 ASN 1 543 ASN ** 2 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 478 ASN 3 61 GLN 4 6 GLN 4 93 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.065365 restraints weight = 86549.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.065529 restraints weight = 57827.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.065872 restraints weight = 50531.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.066206 restraints weight = 44904.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.066345 restraints weight = 41215.796| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 33954 Z= 0.291 Angle : 0.859 11.515 46503 Z= 0.394 Chirality : 0.050 0.266 5730 Planarity : 0.004 0.076 5469 Dihedral : 13.363 89.784 8598 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.49 % Allowed : 11.50 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.13), residues: 3774 helix: 0.11 (0.25), residues: 426 sheet: -0.98 (0.14), residues: 1254 loop : -2.16 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 579 TYR 0.018 0.002 TYR 3 100 PHE 0.032 0.002 PHE 2 53 TRP 0.021 0.002 TRP D 571 HIS 0.007 0.002 HIS 2 105 Details of bonding type rmsd covalent geometry : bond 0.00665 (33675) covalent geometry : angle 0.78881 (45732) SS BOND : bond 0.00778 ( 57) SS BOND : angle 1.53394 ( 114) hydrogen bonds : bond 0.04318 ( 834) hydrogen bonds : angle 6.09828 ( 2223) Misc. bond : bond 0.00012 ( 3) link_ALPHA1-2 : bond 0.00493 ( 21) link_ALPHA1-2 : angle 1.81237 ( 63) link_ALPHA1-3 : bond 0.01547 ( 27) link_ALPHA1-3 : angle 2.86625 ( 81) link_ALPHA1-6 : bond 0.00753 ( 21) link_ALPHA1-6 : angle 1.91820 ( 63) link_BETA1-4 : bond 0.00687 ( 90) link_BETA1-4 : angle 2.75635 ( 270) link_NAG-ASN : bond 0.00806 ( 60) link_NAG-ASN : angle 3.68892 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 368 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 39 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7281 (pp30) REVERT: l 4 MET cc_start: 0.6920 (mtt) cc_final: 0.6605 (mmp) REVERT: l 30 ASN cc_start: 0.8425 (m110) cc_final: 0.8180 (m-40) REVERT: l 86 TYR cc_start: 0.6375 (m-80) cc_final: 0.6041 (m-80) REVERT: D 542 ARG cc_start: 0.8902 (ttm110) cc_final: 0.8603 (ttp-170) REVERT: D 633 LYS cc_start: 0.9270 (ptmt) cc_final: 0.8742 (mttp) REVERT: C 125 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9297 (tt) REVERT: C 161 MET cc_start: 0.8513 (tpp) cc_final: 0.8060 (tpt) REVERT: H 39 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7621 (pp30) REVERT: L 4 MET cc_start: 0.6847 (mtt) cc_final: 0.6294 (mmp) REVERT: L 6 GLN cc_start: 0.5028 (mt0) cc_final: 0.4760 (mt0) REVERT: d 574 LYS cc_start: 0.8956 (mttp) cc_final: 0.8653 (mtpt) REVERT: d 633 LYS cc_start: 0.9286 (ptpt) cc_final: 0.8833 (mtmm) REVERT: d 657 GLU cc_start: 0.8975 (tp30) cc_final: 0.8659 (tp30) REVERT: c 125 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9255 (tt) REVERT: c 161 MET cc_start: 0.8360 (tpp) cc_final: 0.8059 (tpp) REVERT: c 416 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9345 (pt) REVERT: 7 31 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8676 (t0) REVERT: 8 11 VAL cc_start: 0.8294 (m) cc_final: 0.7975 (p) REVERT: 1 574 LYS cc_start: 0.8932 (mttp) cc_final: 0.8534 (mtpt) REVERT: 1 657 GLU cc_start: 0.8938 (tp30) cc_final: 0.8735 (tp30) REVERT: 1 659 ASP cc_start: 0.9271 (OUTLIER) cc_final: 0.8692 (t0) REVERT: 2 125 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9308 (tt) REVERT: 2 416 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9102 (pp) REVERT: 3 39 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7186 (pp30) REVERT: 4 4 MET cc_start: 0.6656 (mtt) cc_final: 0.6313 (mmp) REVERT: 4 24 LYS cc_start: 0.8135 (mttt) cc_final: 0.7807 (mmtt) REVERT: 4 27 GLN cc_start: 0.8422 (mt0) cc_final: 0.8100 (mt0) REVERT: 4 27 ILE cc_start: 0.7939 (mt) cc_final: 0.7566 (mm) REVERT: 4 86 TYR cc_start: 0.6525 (m-80) cc_final: 0.6256 (m-80) REVERT: 4 90 GLN cc_start: 0.7208 (tt0) cc_final: 0.6623 (pp30) outliers start: 83 outliers final: 58 residues processed: 440 average time/residue: 0.2274 time to fit residues: 160.0989 Evaluate side-chains 389 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 324 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain R residue 51 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 104 ILE Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain r residue 36 GLN Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain d residue 576 LEU Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 396 ILE Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 546 SER Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 1 residue 620 SER Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 396 ILE Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 93 SER Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 193 optimal weight: 3.9990 chunk 352 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 368 optimal weight: 8.9990 chunk 367 optimal weight: 4.9990 chunk 263 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 343 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066493 restraints weight = 85924.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066788 restraints weight = 55942.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.067083 restraints weight = 49094.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.067453 restraints weight = 43550.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.067578 restraints weight = 39935.915| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33954 Z= 0.178 Angle : 0.761 14.734 46503 Z= 0.342 Chirality : 0.047 0.248 5730 Planarity : 0.004 0.038 5469 Dihedral : 11.716 85.904 8598 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.61 % Allowed : 12.37 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.13), residues: 3774 helix: 0.60 (0.26), residues: 426 sheet: -0.88 (0.14), residues: 1254 loop : -1.97 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 617 TYR 0.018 0.002 TYR 8 49 PHE 0.027 0.002 PHE 2 53 TRP 0.018 0.001 TRP D 571 HIS 0.004 0.001 HIS 2 374 Details of bonding type rmsd covalent geometry : bond 0.00399 (33675) covalent geometry : angle 0.69729 (45732) SS BOND : bond 0.00647 ( 57) SS BOND : angle 1.31068 ( 114) hydrogen bonds : bond 0.03624 ( 834) hydrogen bonds : angle 5.72862 ( 2223) Misc. bond : bond 0.00018 ( 3) link_ALPHA1-2 : bond 0.00487 ( 21) link_ALPHA1-2 : angle 1.69022 ( 63) link_ALPHA1-3 : bond 0.01528 ( 27) link_ALPHA1-3 : angle 2.75700 ( 81) link_ALPHA1-6 : bond 0.00857 ( 21) link_ALPHA1-6 : angle 1.71713 ( 63) link_BETA1-4 : bond 0.00581 ( 90) link_BETA1-4 : angle 2.56797 ( 270) link_NAG-ASN : bond 0.00502 ( 60) link_NAG-ASN : angle 3.11891 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 346 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 37 MET cc_start: 0.8602 (mmm) cc_final: 0.8327 (mmm) REVERT: h 39 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7687 (pp30) REVERT: l 27 GLN cc_start: 0.8300 (mt0) cc_final: 0.7914 (mt0) REVERT: l 48 ILE cc_start: 0.7149 (pt) cc_final: 0.6824 (pt) REVERT: D 633 LYS cc_start: 0.9218 (ptmt) cc_final: 0.8669 (mttp) REVERT: C 125 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9312 (tt) REVERT: C 161 MET cc_start: 0.8488 (tpp) cc_final: 0.8026 (tpt) REVERT: H 39 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7571 (pp30) REVERT: L 27 GLN cc_start: 0.8306 (mt0) cc_final: 0.7955 (mt0) REVERT: q 76 ASP cc_start: 0.8372 (t0) cc_final: 0.8131 (t0) REVERT: d 574 LYS cc_start: 0.8940 (mttp) cc_final: 0.8576 (mtpt) REVERT: d 633 LYS cc_start: 0.9276 (ptpt) cc_final: 0.8627 (mtmm) REVERT: d 657 GLU cc_start: 0.8900 (tp30) cc_final: 0.8547 (tp30) REVERT: c 125 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9239 (tt) REVERT: c 161 MET cc_start: 0.8432 (tpp) cc_final: 0.8035 (tpp) REVERT: c 416 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9244 (pt) REVERT: 7 31 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8694 (t0) REVERT: 8 11 VAL cc_start: 0.8271 (m) cc_final: 0.7962 (p) REVERT: 1 574 LYS cc_start: 0.8989 (mttp) cc_final: 0.8703 (mtpt) REVERT: 1 657 GLU cc_start: 0.8919 (tp30) cc_final: 0.8705 (tp30) REVERT: 2 125 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9279 (tt) REVERT: 2 416 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9033 (pp) REVERT: 3 39 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7422 (pp30) REVERT: 3 45 LEU cc_start: 0.6225 (tp) cc_final: 0.5980 (tp) REVERT: 4 4 MET cc_start: 0.6614 (mtt) cc_final: 0.6379 (mmp) REVERT: 4 27 GLN cc_start: 0.8396 (mt0) cc_final: 0.8160 (mt0) REVERT: 4 27 ILE cc_start: 0.7910 (mt) cc_final: 0.7600 (mm) outliers start: 87 outliers final: 49 residues processed: 418 average time/residue: 0.2097 time to fit residues: 144.2599 Evaluate side-chains 369 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 314 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain d residue 576 LEU Chi-restraints excluded: chain d residue 620 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 6 residue 22 PHE Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 10 optimal weight: 0.0370 chunk 244 optimal weight: 2.9990 chunk 191 optimal weight: 0.3980 chunk 201 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 343 optimal weight: 0.0170 chunk 346 optimal weight: 5.9990 overall best weight: 1.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 6 GLN d 575 GLN c 287 GLN 6 6 GLN ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.066357 restraints weight = 85507.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.066771 restraints weight = 59957.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067063 restraints weight = 48339.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.067439 restraints weight = 42683.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.067575 restraints weight = 39229.242| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33954 Z= 0.153 Angle : 0.743 19.479 46503 Z= 0.330 Chirality : 0.047 0.646 5730 Planarity : 0.004 0.048 5469 Dihedral : 10.954 84.724 8598 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.06 % Allowed : 12.04 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.13), residues: 3774 helix: 0.90 (0.26), residues: 426 sheet: -0.83 (0.14), residues: 1296 loop : -1.84 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.022 0.001 TYR M 33 PHE 0.023 0.002 PHE 2 53 TRP 0.016 0.001 TRP D 571 HIS 0.004 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00339 (33675) covalent geometry : angle 0.66793 (45732) SS BOND : bond 0.00484 ( 57) SS BOND : angle 1.26306 ( 114) hydrogen bonds : bond 0.03369 ( 834) hydrogen bonds : angle 5.51082 ( 2223) Misc. bond : bond 0.00012 ( 3) link_ALPHA1-2 : bond 0.00511 ( 21) link_ALPHA1-2 : angle 1.66398 ( 63) link_ALPHA1-3 : bond 0.01587 ( 27) link_ALPHA1-3 : angle 2.72248 ( 81) link_ALPHA1-6 : bond 0.00906 ( 21) link_ALPHA1-6 : angle 1.63033 ( 63) link_BETA1-4 : bond 0.00553 ( 90) link_BETA1-4 : angle 2.47281 ( 270) link_NAG-ASN : bond 0.00555 ( 60) link_NAG-ASN : angle 3.72723 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 339 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 37 MET cc_start: 0.8561 (mmm) cc_final: 0.8297 (mmm) REVERT: h 39 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7194 (pp30) REVERT: l 4 MET cc_start: 0.6769 (mtt) cc_final: 0.6559 (mmp) REVERT: l 48 ILE cc_start: 0.7321 (pt) cc_final: 0.6898 (pt) REVERT: l 90 GLN cc_start: 0.7862 (tt0) cc_final: 0.6996 (tm-30) REVERT: D 633 LYS cc_start: 0.9189 (ptmt) cc_final: 0.8648 (mttp) REVERT: C 125 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9306 (tt) REVERT: C 161 MET cc_start: 0.8566 (tpp) cc_final: 0.8096 (tpt) REVERT: L 90 GLN cc_start: 0.7819 (tt0) cc_final: 0.6622 (tm-30) REVERT: q 76 ASP cc_start: 0.8345 (t0) cc_final: 0.8030 (t0) REVERT: d 574 LYS cc_start: 0.8937 (mttp) cc_final: 0.8689 (mtpt) REVERT: d 633 LYS cc_start: 0.9283 (ptpt) cc_final: 0.8713 (mttp) REVERT: d 657 GLU cc_start: 0.8909 (tp30) cc_final: 0.8545 (tp30) REVERT: c 125 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9245 (tt) REVERT: c 161 MET cc_start: 0.8578 (tpp) cc_final: 0.8167 (tpp) REVERT: c 416 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9215 (pt) REVERT: 7 31 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8692 (t0) REVERT: 1 574 LYS cc_start: 0.8973 (mttp) cc_final: 0.8681 (mtpt) REVERT: 1 595 ILE cc_start: 0.9324 (pt) cc_final: 0.9038 (mt) REVERT: 1 657 GLU cc_start: 0.8915 (tp30) cc_final: 0.8675 (tp30) REVERT: 2 125 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9289 (tt) REVERT: 2 416 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9013 (pp) REVERT: 3 39 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7527 (pp30) REVERT: 4 4 MET cc_start: 0.6582 (mtt) cc_final: 0.6376 (mmp) REVERT: 4 24 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7977 (mmmt) REVERT: 4 27 GLN cc_start: 0.8403 (mt0) cc_final: 0.8112 (mt0) REVERT: 4 27 ILE cc_start: 0.7798 (mt) cc_final: 0.7522 (mm) outliers start: 102 outliers final: 60 residues processed: 428 average time/residue: 0.2091 time to fit residues: 147.9874 Evaluate side-chains 372 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 306 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain r residue 99 LEU Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain d residue 620 SER Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 277 ILE Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 194 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 329 optimal weight: 3.9990 chunk 355 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.094401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.066741 restraints weight = 85502.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.066994 restraints weight = 55950.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067299 restraints weight = 48744.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.067659 restraints weight = 43451.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.067787 restraints weight = 39896.195| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33954 Z= 0.157 Angle : 0.739 15.682 46503 Z= 0.329 Chirality : 0.048 0.724 5730 Planarity : 0.004 0.063 5469 Dihedral : 10.371 83.959 8598 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.64 % Allowed : 13.15 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.13), residues: 3774 helix: 1.06 (0.27), residues: 426 sheet: -0.70 (0.14), residues: 1284 loop : -1.77 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 4 54 TYR 0.030 0.001 TYR M 33 PHE 0.020 0.002 PHE 2 53 TRP 0.012 0.001 TRP m 47 HIS 0.004 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00354 (33675) covalent geometry : angle 0.66921 (45732) SS BOND : bond 0.00458 ( 57) SS BOND : angle 1.52063 ( 114) hydrogen bonds : bond 0.03308 ( 834) hydrogen bonds : angle 5.40040 ( 2223) Misc. bond : bond 0.00008 ( 3) link_ALPHA1-2 : bond 0.00502 ( 21) link_ALPHA1-2 : angle 1.67241 ( 63) link_ALPHA1-3 : bond 0.01592 ( 27) link_ALPHA1-3 : angle 2.69257 ( 81) link_ALPHA1-6 : bond 0.00985 ( 21) link_ALPHA1-6 : angle 1.69384 ( 63) link_BETA1-4 : bond 0.00544 ( 90) link_BETA1-4 : angle 2.41706 ( 270) link_NAG-ASN : bond 0.00509 ( 60) link_NAG-ASN : angle 3.44472 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 328 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 37 MET cc_start: 0.8597 (mmm) cc_final: 0.8355 (mmm) REVERT: h 39 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7196 (pp30) REVERT: l 27 GLN cc_start: 0.8287 (mt0) cc_final: 0.7978 (mt0) REVERT: l 90 GLN cc_start: 0.7786 (tt0) cc_final: 0.7008 (tm-30) REVERT: M 77 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.5762 (tp) REVERT: D 633 LYS cc_start: 0.9187 (ptmt) cc_final: 0.8584 (mtmm) REVERT: C 125 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9293 (tt) REVERT: C 161 MET cc_start: 0.8620 (tpp) cc_final: 0.8148 (tpt) REVERT: L 4 MET cc_start: 0.6842 (mtt) cc_final: 0.6394 (mmm) REVERT: L 24 LYS cc_start: 0.7988 (mttt) cc_final: 0.7623 (mmtt) REVERT: L 70 ASP cc_start: 0.7441 (t0) cc_final: 0.7184 (t70) REVERT: L 90 GLN cc_start: 0.8036 (tt0) cc_final: 0.7030 (tm-30) REVERT: m 77 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.5687 (tp) REVERT: d 574 LYS cc_start: 0.8940 (mttp) cc_final: 0.8676 (mtpt) REVERT: d 633 LYS cc_start: 0.9281 (ptpt) cc_final: 0.8701 (mttp) REVERT: d 657 GLU cc_start: 0.8887 (tp30) cc_final: 0.8615 (tp30) REVERT: c 125 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9243 (tt) REVERT: c 161 MET cc_start: 0.8639 (tpp) cc_final: 0.8230 (tpp) REVERT: c 416 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9231 (pt) REVERT: 7 77 LEU cc_start: 0.5831 (OUTLIER) cc_final: 0.5359 (tp) REVERT: 1 574 LYS cc_start: 0.8977 (mttp) cc_final: 0.8697 (mtpt) REVERT: 1 595 ILE cc_start: 0.9318 (pt) cc_final: 0.9053 (mt) REVERT: 1 657 GLU cc_start: 0.8878 (tp30) cc_final: 0.8638 (tp30) REVERT: 2 125 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9306 (tt) REVERT: 2 416 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9005 (pp) REVERT: 2 492 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7522 (mt-10) REVERT: 3 39 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7466 (pp30) REVERT: 4 27 GLN cc_start: 0.8404 (mt0) cc_final: 0.8070 (mt0) REVERT: 4 27 ILE cc_start: 0.7781 (mt) cc_final: 0.7525 (mm) outliers start: 88 outliers final: 64 residues processed: 402 average time/residue: 0.2140 time to fit residues: 142.0203 Evaluate side-chains 371 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 299 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 277 ILE Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 396 ILE Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 7 residue 124 LYS Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 546 SER Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 93 SER Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 0.0970 chunk 280 optimal weight: 10.0000 chunk 358 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 356 optimal weight: 20.0000 chunk 370 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.066195 restraints weight = 85801.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066253 restraints weight = 59776.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066683 restraints weight = 48966.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066981 restraints weight = 43903.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.067189 restraints weight = 40521.554| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33954 Z= 0.167 Angle : 0.746 17.194 46503 Z= 0.331 Chirality : 0.047 0.642 5730 Planarity : 0.004 0.080 5469 Dihedral : 10.018 83.847 8598 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.91 % Allowed : 13.09 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.14), residues: 3774 helix: 1.15 (0.26), residues: 426 sheet: -0.57 (0.14), residues: 1254 loop : -1.74 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 4 54 TYR 0.020 0.001 TYR 3 100 PHE 0.025 0.002 PHE R 70 TRP 0.011 0.001 TRP H 36 HIS 0.004 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00377 (33675) covalent geometry : angle 0.67850 (45732) SS BOND : bond 0.00489 ( 57) SS BOND : angle 1.58206 ( 114) hydrogen bonds : bond 0.03285 ( 834) hydrogen bonds : angle 5.33468 ( 2223) Misc. bond : bond 0.00004 ( 3) link_ALPHA1-2 : bond 0.00497 ( 21) link_ALPHA1-2 : angle 1.68214 ( 63) link_ALPHA1-3 : bond 0.01579 ( 27) link_ALPHA1-3 : angle 2.66676 ( 81) link_ALPHA1-6 : bond 0.01025 ( 21) link_ALPHA1-6 : angle 1.77163 ( 63) link_BETA1-4 : bond 0.00545 ( 90) link_BETA1-4 : angle 2.38994 ( 270) link_NAG-ASN : bond 0.00517 ( 60) link_NAG-ASN : angle 3.37895 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 317 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 37 MET cc_start: 0.8536 (mmm) cc_final: 0.8181 (mmm) REVERT: h 39 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7456 (pp30) REVERT: l 90 GLN cc_start: 0.7760 (tt0) cc_final: 0.6986 (tm-30) REVERT: M 77 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.5875 (tp) REVERT: N 104 LEU cc_start: 0.8754 (tp) cc_final: 0.8509 (tp) REVERT: D 633 LYS cc_start: 0.9207 (ptmt) cc_final: 0.8586 (mtmm) REVERT: C 125 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9300 (tt) REVERT: C 138 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8649 (mm) REVERT: C 150 MET cc_start: 0.7250 (pmm) cc_final: 0.6931 (pmm) REVERT: C 161 MET cc_start: 0.8655 (tpp) cc_final: 0.8193 (tpt) REVERT: H 10 ASP cc_start: 0.5440 (m-30) cc_final: 0.5006 (t0) REVERT: L 4 MET cc_start: 0.6888 (mtt) cc_final: 0.6282 (mmm) REVERT: L 90 GLN cc_start: 0.7838 (tt0) cc_final: 0.6887 (tm-30) REVERT: m 77 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6054 (tp) REVERT: d 574 LYS cc_start: 0.8952 (mttp) cc_final: 0.8677 (mtpt) REVERT: d 633 LYS cc_start: 0.9284 (ptpt) cc_final: 0.8858 (mttp) REVERT: d 657 GLU cc_start: 0.8897 (tp30) cc_final: 0.8604 (tp30) REVERT: c 125 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9240 (tt) REVERT: c 161 MET cc_start: 0.8660 (tpp) cc_final: 0.8143 (tpp) REVERT: c 416 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9256 (pt) REVERT: 7 73 LYS cc_start: 0.7826 (tttt) cc_final: 0.7202 (tttt) REVERT: 1 574 LYS cc_start: 0.8982 (mttp) cc_final: 0.8700 (mtpt) REVERT: 1 595 ILE cc_start: 0.9326 (pt) cc_final: 0.9070 (mt) REVERT: 1 657 GLU cc_start: 0.8893 (tp30) cc_final: 0.8632 (tp30) REVERT: 2 125 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9279 (tt) REVERT: 2 416 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8953 (pp) REVERT: 3 39 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7448 (pp30) REVERT: 4 27 GLN cc_start: 0.8401 (mt0) cc_final: 0.8091 (mt0) REVERT: 4 27 ILE cc_start: 0.7712 (mt) cc_final: 0.7438 (mm) outliers start: 97 outliers final: 67 residues processed: 401 average time/residue: 0.2069 time to fit residues: 136.8759 Evaluate side-chains 379 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 304 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain r residue 99 LEU Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 277 ILE Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 546 SER Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 93 SER Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 282 optimal weight: 0.8980 chunk 331 optimal weight: 3.9990 chunk 336 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 182 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 126 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 357 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.093087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.064993 restraints weight = 85791.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.065196 restraints weight = 59246.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.065522 restraints weight = 49737.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.065886 restraints weight = 43963.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.066025 restraints weight = 40489.720| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33954 Z= 0.220 Angle : 0.780 15.046 46503 Z= 0.350 Chirality : 0.048 0.634 5730 Planarity : 0.004 0.088 5469 Dihedral : 9.824 85.370 8598 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.76 % Allowed : 13.66 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.14), residues: 3774 helix: 1.09 (0.26), residues: 426 sheet: -0.53 (0.14), residues: 1254 loop : -1.70 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 54 TYR 0.020 0.002 TYR 7 33 PHE 0.025 0.002 PHE R 70 TRP 0.012 0.001 TRP H 36 HIS 0.004 0.001 HIS 2 374 Details of bonding type rmsd covalent geometry : bond 0.00501 (33675) covalent geometry : angle 0.71352 (45732) SS BOND : bond 0.00544 ( 57) SS BOND : angle 1.62450 ( 114) hydrogen bonds : bond 0.03520 ( 834) hydrogen bonds : angle 5.44246 ( 2223) Misc. bond : bond 0.00002 ( 3) link_ALPHA1-2 : bond 0.00465 ( 21) link_ALPHA1-2 : angle 1.74947 ( 63) link_ALPHA1-3 : bond 0.01527 ( 27) link_ALPHA1-3 : angle 2.69578 ( 81) link_ALPHA1-6 : bond 0.01074 ( 21) link_ALPHA1-6 : angle 1.94669 ( 63) link_BETA1-4 : bond 0.00540 ( 90) link_BETA1-4 : angle 2.37167 ( 270) link_NAG-ASN : bond 0.00578 ( 60) link_NAG-ASN : angle 3.44332 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 308 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 37 MET cc_start: 0.8614 (mmm) cc_final: 0.8248 (mmm) REVERT: h 39 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7242 (pp30) REVERT: l 27 GLN cc_start: 0.8305 (mt0) cc_final: 0.8065 (mt0) REVERT: l 90 GLN cc_start: 0.7852 (tt0) cc_final: 0.7048 (tm-30) REVERT: M 77 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5985 (tp) REVERT: D 612 SER cc_start: 0.8996 (t) cc_final: 0.8664 (t) REVERT: D 633 LYS cc_start: 0.9226 (ptmt) cc_final: 0.8628 (mtmm) REVERT: C 125 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9239 (tt) REVERT: C 138 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8698 (mm) REVERT: C 161 MET cc_start: 0.8729 (tpp) cc_final: 0.8214 (tpt) REVERT: L 4 MET cc_start: 0.6908 (mtt) cc_final: 0.6263 (mmm) REVERT: L 24 LYS cc_start: 0.8072 (mttt) cc_final: 0.7663 (mmmt) REVERT: L 27 GLN cc_start: 0.8381 (mt0) cc_final: 0.8054 (mt0) REVERT: L 90 GLN cc_start: 0.7927 (tt0) cc_final: 0.6902 (tm-30) REVERT: m 77 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6193 (tp) REVERT: d 574 LYS cc_start: 0.8976 (mttp) cc_final: 0.8710 (mtpt) REVERT: d 633 LYS cc_start: 0.9290 (ptpt) cc_final: 0.8874 (mttp) REVERT: d 657 GLU cc_start: 0.8943 (tp30) cc_final: 0.8632 (tp30) REVERT: c 125 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9222 (tt) REVERT: c 150 MET cc_start: 0.7093 (mpp) cc_final: 0.6860 (ptp) REVERT: c 161 MET cc_start: 0.8693 (tpp) cc_final: 0.8168 (tpp) REVERT: c 416 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9283 (pt) REVERT: 1 574 LYS cc_start: 0.9016 (mttp) cc_final: 0.8715 (mtpt) REVERT: 1 595 ILE cc_start: 0.9361 (pt) cc_final: 0.8990 (mt) REVERT: 1 657 GLU cc_start: 0.8923 (tp30) cc_final: 0.8640 (tp30) REVERT: 2 125 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9196 (tt) REVERT: 2 150 MET cc_start: 0.7180 (pmm) cc_final: 0.6825 (pmm) REVERT: 2 416 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9117 (pp) REVERT: 3 39 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7316 (pp30) REVERT: 4 27 GLN cc_start: 0.8480 (mt0) cc_final: 0.8232 (mt0) REVERT: 4 27 ILE cc_start: 0.7762 (mt) cc_final: 0.7509 (mm) REVERT: 4 45 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7651 (mmmt) outliers start: 92 outliers final: 72 residues processed: 388 average time/residue: 0.2136 time to fit residues: 138.7698 Evaluate side-chains 373 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain r residue 99 LEU Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain d residue 576 LEU Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 396 ILE Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 7 residue 124 LYS Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 25 GLU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 546 SER Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 261 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 93 SER Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 94 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 342 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 280 optimal weight: 7.9990 chunk 329 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 277 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN H 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 100 HIS ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.095000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.066951 restraints weight = 84774.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.066994 restraints weight = 60422.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.067563 restraints weight = 48176.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067855 restraints weight = 43949.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.067992 restraints weight = 40278.049| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33954 Z= 0.128 Angle : 0.728 13.875 46503 Z= 0.323 Chirality : 0.047 0.607 5730 Planarity : 0.003 0.057 5469 Dihedral : 9.232 82.107 8598 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.28 % Allowed : 14.35 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.14), residues: 3774 helix: 1.39 (0.27), residues: 426 sheet: -0.47 (0.14), residues: 1293 loop : -1.63 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 4 54 TYR 0.021 0.001 TYR 7 33 PHE 0.021 0.001 PHE R 70 TRP 0.014 0.001 TRP H 36 HIS 0.004 0.001 HIS 7 52 Details of bonding type rmsd covalent geometry : bond 0.00279 (33675) covalent geometry : angle 0.66479 (45732) SS BOND : bond 0.00413 ( 57) SS BOND : angle 1.45290 ( 114) hydrogen bonds : bond 0.03087 ( 834) hydrogen bonds : angle 5.18922 ( 2223) Misc. bond : bond 0.00008 ( 3) link_ALPHA1-2 : bond 0.00537 ( 21) link_ALPHA1-2 : angle 1.65907 ( 63) link_ALPHA1-3 : bond 0.01621 ( 27) link_ALPHA1-3 : angle 2.56547 ( 81) link_ALPHA1-6 : bond 0.01146 ( 21) link_ALPHA1-6 : angle 1.83306 ( 63) link_BETA1-4 : bond 0.00539 ( 90) link_BETA1-4 : angle 2.33093 ( 270) link_NAG-ASN : bond 0.00461 ( 60) link_NAG-ASN : angle 3.17858 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 337 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 37 MET cc_start: 0.8488 (mmm) cc_final: 0.8167 (mmm) REVERT: h 39 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7230 (pp30) REVERT: l 27 GLN cc_start: 0.8251 (mt0) cc_final: 0.8051 (mt0) REVERT: l 90 GLN cc_start: 0.7700 (tt0) cc_final: 0.6921 (tm-30) REVERT: M 77 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5637 (tp) REVERT: D 633 LYS cc_start: 0.9194 (ptmt) cc_final: 0.8729 (mtmm) REVERT: C 125 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9229 (tt) REVERT: C 138 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8703 (mm) REVERT: C 161 MET cc_start: 0.8685 (tpp) cc_final: 0.8202 (tpt) REVERT: H 10 ASP cc_start: 0.5454 (m-30) cc_final: 0.5205 (t0) REVERT: H 39 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7844 (pp30) REVERT: L 4 MET cc_start: 0.6953 (mtt) cc_final: 0.6392 (mmm) REVERT: L 24 LYS cc_start: 0.8080 (mttt) cc_final: 0.7628 (mmmt) REVERT: L 27 GLN cc_start: 0.8373 (mt0) cc_final: 0.8099 (mt0) REVERT: L 90 GLN cc_start: 0.7877 (tt0) cc_final: 0.6843 (tm-30) REVERT: m 77 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6080 (tp) REVERT: d 574 LYS cc_start: 0.8953 (mttp) cc_final: 0.8659 (mtpt) REVERT: d 633 LYS cc_start: 0.9301 (ptpt) cc_final: 0.8650 (mtmm) REVERT: d 657 GLU cc_start: 0.8877 (tp30) cc_final: 0.8532 (tp30) REVERT: c 125 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9229 (tt) REVERT: c 150 MET cc_start: 0.7043 (mpp) cc_final: 0.6767 (ptp) REVERT: c 161 MET cc_start: 0.8665 (tpp) cc_final: 0.8218 (tpp) REVERT: c 416 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9218 (pt) REVERT: 7 124 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7113 (mptt) REVERT: 5 39 LEU cc_start: 0.9102 (tp) cc_final: 0.8850 (tt) REVERT: 1 574 LYS cc_start: 0.8986 (mttp) cc_final: 0.8692 (mtpt) REVERT: 1 657 GLU cc_start: 0.8911 (tp30) cc_final: 0.8685 (tp30) REVERT: 2 125 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9240 (tt) REVERT: 2 150 MET cc_start: 0.7270 (pmm) cc_final: 0.6938 (pmm) REVERT: 2 416 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8982 (pp) REVERT: 3 39 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7370 (pp30) REVERT: 4 27 GLN cc_start: 0.8460 (mt0) cc_final: 0.8256 (mt0) REVERT: 4 45 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7649 (mmmt) outliers start: 76 outliers final: 56 residues processed: 403 average time/residue: 0.2165 time to fit residues: 143.4974 Evaluate side-chains 374 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 308 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 277 ILE Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain c residue 434 MET Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 7 residue 124 LYS Chi-restraints excluded: chain 8 residue 107 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 546 SER Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 261 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 93 SER Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 231 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 45 optimal weight: 0.0170 chunk 294 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.066267 restraints weight = 85940.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.066430 restraints weight = 58680.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.066813 restraints weight = 49015.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.067142 restraints weight = 43686.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.067303 restraints weight = 40310.880| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33954 Z= 0.157 Angle : 0.740 13.766 46503 Z= 0.330 Chirality : 0.046 0.593 5730 Planarity : 0.004 0.096 5469 Dihedral : 9.105 82.947 8598 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.31 % Allowed : 14.47 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.14), residues: 3774 helix: 1.42 (0.27), residues: 426 sheet: -0.42 (0.14), residues: 1290 loop : -1.60 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG 4 54 TYR 0.034 0.001 TYR 7 105 PHE 0.021 0.001 PHE R 70 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS 2 374 Details of bonding type rmsd covalent geometry : bond 0.00354 (33675) covalent geometry : angle 0.67767 (45732) SS BOND : bond 0.00475 ( 57) SS BOND : angle 1.45151 ( 114) hydrogen bonds : bond 0.03215 ( 834) hydrogen bonds : angle 5.16255 ( 2223) Misc. bond : bond 0.00003 ( 3) link_ALPHA1-2 : bond 0.00502 ( 21) link_ALPHA1-2 : angle 1.67080 ( 63) link_ALPHA1-3 : bond 0.01607 ( 27) link_ALPHA1-3 : angle 2.59154 ( 81) link_ALPHA1-6 : bond 0.01149 ( 21) link_ALPHA1-6 : angle 1.85473 ( 63) link_BETA1-4 : bond 0.00528 ( 90) link_BETA1-4 : angle 2.31247 ( 270) link_NAG-ASN : bond 0.00471 ( 60) link_NAG-ASN : angle 3.18994 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 313 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 37 MET cc_start: 0.8527 (mmm) cc_final: 0.8197 (mmm) REVERT: h 39 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7266 (pp30) REVERT: l 24 LYS cc_start: 0.8139 (mttt) cc_final: 0.7814 (mttt) REVERT: l 27 GLN cc_start: 0.8248 (mt0) cc_final: 0.8044 (mt0) REVERT: l 90 GLN cc_start: 0.7694 (tt0) cc_final: 0.6920 (tm-30) REVERT: M 77 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5811 (tp) REVERT: D 633 LYS cc_start: 0.9186 (ptmt) cc_final: 0.8726 (mtmm) REVERT: C 125 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9235 (tt) REVERT: C 138 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8742 (mm) REVERT: C 161 MET cc_start: 0.8730 (tpp) cc_final: 0.8230 (tpt) REVERT: L 4 MET cc_start: 0.6966 (mtt) cc_final: 0.6349 (mmm) REVERT: L 24 LYS cc_start: 0.8035 (mttt) cc_final: 0.7563 (mmmt) REVERT: L 27 GLN cc_start: 0.8353 (mt0) cc_final: 0.8088 (mt0) REVERT: L 90 GLN cc_start: 0.7930 (tt0) cc_final: 0.6858 (tm-30) REVERT: m 77 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6010 (tp) REVERT: d 574 LYS cc_start: 0.8956 (mttp) cc_final: 0.8661 (mtpt) REVERT: d 633 LYS cc_start: 0.9319 (ptpt) cc_final: 0.8677 (mtmm) REVERT: d 657 GLU cc_start: 0.8886 (tp30) cc_final: 0.8611 (tp30) REVERT: c 125 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9236 (tt) REVERT: c 150 MET cc_start: 0.7007 (mpp) cc_final: 0.6790 (ptp) REVERT: c 161 MET cc_start: 0.8722 (tpp) cc_final: 0.8263 (tpp) REVERT: 5 39 LEU cc_start: 0.9075 (tp) cc_final: 0.8811 (tt) REVERT: 1 574 LYS cc_start: 0.8981 (mttp) cc_final: 0.8682 (mtpt) REVERT: 1 657 GLU cc_start: 0.8936 (tp30) cc_final: 0.8716 (tp30) REVERT: 2 125 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9247 (tt) REVERT: 2 138 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8606 (mm) REVERT: 2 150 MET cc_start: 0.7351 (pmm) cc_final: 0.7061 (pmm) REVERT: 2 416 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8985 (pp) REVERT: 3 39 GLN cc_start: 0.7631 (tm-30) cc_final: 0.7311 (pp30) REVERT: 3 45 LEU cc_start: 0.6162 (tp) cc_final: 0.5900 (tp) REVERT: 4 45 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7613 (mmmt) REVERT: 4 90 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.6068 (tm-30) outliers start: 77 outliers final: 63 residues processed: 379 average time/residue: 0.2006 time to fit residues: 127.5586 Evaluate side-chains 370 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 298 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain d residue 595 ILE Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 154 LEU Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 277 ILE Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 396 ILE Chi-restraints excluded: chain c residue 434 MET Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 107 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 546 SER Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 261 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 93 SER Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 362 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 312 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 chunk 321 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 266 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.090968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062837 restraints weight = 87808.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.063140 restraints weight = 61300.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.063449 restraints weight = 50754.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.063762 restraints weight = 45340.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.063916 restraints weight = 41795.593| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 33954 Z= 0.384 Angle : 0.924 15.448 46503 Z= 0.426 Chirality : 0.052 0.648 5730 Planarity : 0.005 0.051 5469 Dihedral : 9.846 89.261 8598 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.79 % Allowed : 14.11 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.14), residues: 3774 helix: 0.79 (0.26), residues: 426 sheet: -0.66 (0.14), residues: 1305 loop : -1.72 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 4 54 TYR 0.045 0.003 TYR 7 33 PHE 0.042 0.003 PHE 4 89 TRP 0.023 0.003 TRP m 34 HIS 0.008 0.002 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00882 (33675) covalent geometry : angle 0.86242 (45732) SS BOND : bond 0.00783 ( 57) SS BOND : angle 1.81561 ( 114) hydrogen bonds : bond 0.04284 ( 834) hydrogen bonds : angle 5.77664 ( 2223) Misc. bond : bond 0.00011 ( 3) link_ALPHA1-2 : bond 0.00455 ( 21) link_ALPHA1-2 : angle 1.91923 ( 63) link_ALPHA1-3 : bond 0.01463 ( 27) link_ALPHA1-3 : angle 2.84586 ( 81) link_ALPHA1-6 : bond 0.01110 ( 21) link_ALPHA1-6 : angle 2.09331 ( 63) link_BETA1-4 : bond 0.00586 ( 90) link_BETA1-4 : angle 2.42225 ( 270) link_NAG-ASN : bond 0.00865 ( 60) link_NAG-ASN : angle 3.75692 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5014.96 seconds wall clock time: 88 minutes 23.08 seconds (5303.08 seconds total)