Starting phenix.real_space_refine on Sun Aug 24 15:08:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uls_42364/08_2025/8uls_42364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uls_42364/08_2025/8uls_42364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uls_42364/08_2025/8uls_42364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uls_42364/08_2025/8uls_42364.map" model { file = "/net/cci-nas-00/data/ceres_data/8uls_42364/08_2025/8uls_42364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uls_42364/08_2025/8uls_42364.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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 129 5.16 5 C 13113 2.51 5 N 3510 2.21 5 O 4207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20959 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3523 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1049 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3523 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1049 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3523 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1049 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1075 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 133} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "I" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1075 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 133} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1075 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 133} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 810 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "M" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 810 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "N" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 810 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" 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: "R" 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 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: 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: "q" 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: "r" 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: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.27, per 1000 atoms: 0.25 Number of scatterers: 20959 At special positions: 0 Unit cell: (138.944, 144.768, 119.808, 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 129 16.00 O 4207 8.00 N 3510 7.00 C 13113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.01 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.01 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 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 D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.01 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " " BMA e 3 " - " MAN e 4 " " BMA i 3 " - " MAN i 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA R 3 " - " MAN R 5 " " BMA W 3 " - " MAN W 4 " " BMA e 3 " - " MAN e 5 " " BMA j 3 " - " MAN j 4 " " BMA r 3 " - " MAN r 5 " " BMA w 3 " - " MAN w 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " 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 l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 355 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 339 " " NAG E 604 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG G 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 197 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 301 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 392 " " NAG Y 1 " - " ASN A 448 " " NAG Z 1 " - " ASN C 88 " " NAG a 1 " - " ASN C 156 " " NAG b 1 " - " ASN C 160 " " NAG c 1 " - " ASN C 197 " " NAG d 1 " - " ASN C 262 " " NAG e 1 " - " ASN C 276 " " NAG f 1 " - " ASN C 295 " " NAG g 1 " - " ASN C 301 " " NAG h 1 " - " ASN C 332 " " NAG i 1 " - " ASN C 363 " " NAG j 1 " - " ASN C 386 " " NAG k 1 " - " ASN C 392 " " NAG l 1 " - " ASN C 448 " " NAG m 1 " - " ASN E 88 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 160 " " NAG p 1 " - " ASN E 197 " " NAG q 1 " - " ASN E 262 " " NAG r 1 " - " ASN E 276 " " NAG s 1 " - " ASN E 295 " " NAG t 1 " - " ASN E 301 " " NAG u 1 " - " ASN E 332 " " NAG v 1 " - " ASN E 363 " " NAG w 1 " - " ASN E 386 " " NAG x 1 " - " ASN E 392 " " NAG y 1 " - " ASN E 448 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 883.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 33 sheets defined 18.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.057A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.653A pdb=" N ARG A 151 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.062A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.656A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.917A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.763A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.056A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.652A pdb=" N ARG C 151 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.061A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 481 removed outlier: 3.657A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 536 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.916A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.763A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.056A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.652A pdb=" N ARG E 151 " --> pdb=" O ASP E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.061A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 481 removed outlier: 3.656A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.917A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.763A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.852A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.851A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.851A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.689A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.546A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.825A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.586A pdb=" N CYS A 131 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.272A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 261 current: chain 'A' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 287 current: chain 'A' and resid 316 through 322 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 322 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.757A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.547A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.824A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.724A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.586A pdb=" N CYS C 131 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.270A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 287 current: chain 'C' and resid 316 through 322 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 322 current: chain 'C' and resid 381 through 385 removed outlier: 4.195A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 413 through 421 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB6, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.657A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.547A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.825A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.586A pdb=" N CYS E 131 " --> pdb=" O LYS E 189 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.271A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 261 current: chain 'E' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 287 current: chain 'E' and resid 316 through 322 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 316 through 322 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.608A pdb=" N GLU H 10 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL H 35E" --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N HIS H 50 " --> pdb=" O VAL H 35E" (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.607A pdb=" N GLU I 10 " --> pdb=" O ILE I 110 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL I 35E" --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N HIS I 50 " --> pdb=" O VAL I 35E" (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.608A pdb=" N GLU J 10 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL J 35E" --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N HIS J 50 " --> pdb=" O VAL J 35E" (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.765A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.622A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.766A pdb=" N PHE M 71 " --> pdb=" O CYS M 23 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 10 through 13 removed outlier: 5.622A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.766A pdb=" N PHE N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 13 removed outlier: 5.623A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1629 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: 3.52 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3545 1.32 - 1.45: 6019 1.45 - 1.57: 11650 1.57 - 1.69: 3 1.69 - 1.82: 180 Bond restraints: 21397 Sorted by residual: bond pdb=" CA SER C 388 " pdb=" CB SER C 388 " ideal model delta sigma weight residual 1.536 1.484 0.052 1.42e-02 4.96e+03 1.36e+01 bond pdb=" CA SER A 364 " pdb=" CB SER A 364 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.55e-02 4.16e+03 1.23e+01 bond pdb=" CA SER E 388 " pdb=" CB SER E 388 " ideal model delta sigma weight residual 1.536 1.486 0.050 1.42e-02 4.96e+03 1.23e+01 bond pdb=" CA SER E 364 " pdb=" CB SER E 364 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.55e-02 4.16e+03 1.15e+01 bond pdb=" CA SER C 447 " pdb=" CB SER C 447 " ideal model delta sigma weight residual 1.534 1.481 0.054 1.60e-02 3.91e+03 1.12e+01 ... (remaining 21392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.33: 29015 5.33 - 10.67: 34 10.67 - 16.00: 0 16.00 - 21.33: 0 21.33 - 26.66: 3 Bond angle restraints: 29052 Sorted by residual: angle pdb=" C CYS C 296 " pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " ideal model delta sigma weight residual 109.51 82.85 26.66 1.71e+00 3.42e-01 2.43e+02 angle pdb=" C CYS E 296 " pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " ideal model delta sigma weight residual 109.51 82.94 26.57 1.71e+00 3.42e-01 2.41e+02 angle pdb=" C CYS A 296 " pdb=" CA CYS A 296 " pdb=" CB CYS A 296 " ideal model delta sigma weight residual 109.46 83.45 26.01 1.84e+00 2.95e-01 2.00e+02 angle pdb=" CA GLY E 354 " pdb=" C GLY E 354 " pdb=" O GLY E 354 " ideal model delta sigma weight residual 122.22 117.92 4.30 6.50e-01 2.37e+00 4.37e+01 angle pdb=" CA PRO A 291 " pdb=" N PRO A 291 " pdb=" CD PRO A 291 " ideal model delta sigma weight residual 112.00 103.48 8.52 1.40e+00 5.10e-01 3.70e+01 ... (remaining 29047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 13013 21.25 - 42.50: 891 42.50 - 63.76: 178 63.76 - 85.01: 107 85.01 - 106.26: 60 Dihedral angle restraints: 14249 sinusoidal: 7169 harmonic: 7080 Sorted by residual: dihedral pdb=" C CYS C 296 " pdb=" N CYS C 296 " pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " ideal model delta harmonic sigma weight residual -122.60 -90.33 -32.27 0 2.50e+00 1.60e-01 1.67e+02 dihedral pdb=" C CYS E 296 " pdb=" N CYS E 296 " pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " ideal model delta harmonic sigma weight residual -122.60 -90.50 -32.10 0 2.50e+00 1.60e-01 1.65e+02 dihedral pdb=" C CYS A 296 " pdb=" N CYS A 296 " pdb=" CA CYS A 296 " pdb=" CB CYS A 296 " ideal model delta harmonic sigma weight residual -122.60 -91.04 -31.56 0 2.50e+00 1.60e-01 1.59e+02 ... (remaining 14246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 3461 0.150 - 0.301: 102 0.301 - 0.451: 9 0.451 - 0.601: 2 0.601 - 0.752: 3 Chirality restraints: 3577 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.88e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.84e+02 chirality pdb=" C1 MAN r 4 " pdb=" O3 BMA r 3 " pdb=" C2 MAN r 4 " pdb=" O5 MAN r 4 " both_signs ideal model delta sigma weight residual False 2.40 2.09 0.31 2.00e-02 2.50e+03 2.42e+02 ... (remaining 3574 not shown) Planarity restraints: 3597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG s 2 " -0.312 2.00e-02 2.50e+03 2.71e-01 9.21e+02 pdb=" C7 NAG s 2 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG s 2 " -0.050 2.00e-02 2.50e+03 pdb=" N2 NAG s 2 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG s 2 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " -0.309 2.00e-02 2.50e+03 2.70e-01 9.08e+02 pdb=" C7 NAG f 2 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " 0.476 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.309 2.00e-02 2.50e+03 2.69e-01 9.07e+02 pdb=" C7 NAG S 2 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.047 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.476 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.185 2.00e-02 2.50e+03 ... (remaining 3594 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 742 2.71 - 3.26: 19882 3.26 - 3.81: 33587 3.81 - 4.35: 43342 4.35 - 4.90: 73581 Nonbonded interactions: 171134 Sorted by model distance: nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.172 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.172 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.172 3.040 nonbonded pdb=" NE2 GLN A 258 " pdb=" O VAL A 371 " model vdw 2.217 3.120 ... (remaining 171129 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'c' selection = chain 'd' selection = chain 'l' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'e' selection = chain 'r' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'i' selection = chain 'j' selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.920 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.006 0.101 21549 Z= 0.336 Angle : 1.027 26.663 29475 Z= 0.524 Chirality : 0.066 0.752 3577 Planarity : 0.022 0.271 3543 Dihedral : 17.246 106.260 9590 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.13 % Favored : 95.75 % Rotamer: Outliers : 0.52 % Allowed : 1.04 % Favored : 98.45 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.03 % 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: -0.87 (0.17), residues: 2421 helix: 0.83 (0.27), residues: 405 sheet: -0.83 (0.19), residues: 714 loop : -0.81 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 617 TYR 0.010 0.001 TYR H 33 PHE 0.027 0.001 PHE C 391 TRP 0.013 0.001 TRP J 100H HIS 0.004 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00536 (21397) covalent geometry : angle 0.87879 (29052) SS BOND : bond 0.00670 ( 33) SS BOND : angle 1.62261 ( 66) hydrogen bonds : bond 0.19816 ( 603) hydrogen bonds : angle 8.55401 ( 1629) link_ALPHA1-3 : bond 0.04798 ( 5) link_ALPHA1-3 : angle 3.27756 ( 15) link_ALPHA1-6 : bond 0.03646 ( 6) link_ALPHA1-6 : angle 4.41523 ( 18) link_BETA1-4 : bond 0.04726 ( 54) link_BETA1-4 : angle 5.81876 ( 162) link_NAG-ASN : bond 0.01319 ( 54) link_NAG-ASN : angle 3.90132 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 394 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7721 (m90) cc_final: 0.7447 (m90) REVERT: A 207 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8168 (mmtm) REVERT: A 429 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7860 (mmm-85) REVERT: C 66 HIS cc_start: 0.7786 (m90) cc_final: 0.7428 (m90) REVERT: E 66 HIS cc_start: 0.7694 (m90) cc_final: 0.7379 (m90) REVERT: F 542 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7780 (mtm180) REVERT: L 42 LYS cc_start: 0.8291 (mmmm) cc_final: 0.8015 (mmtm) outliers start: 11 outliers final: 7 residues processed: 402 average time/residue: 0.1506 time to fit residues: 93.8725 Evaluate side-chains 313 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 306 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 33 ASN E 33 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 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 = 0.3413 r_free = 0.3413 target = 0.124560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102111 restraints weight = 26896.478| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.14 r_work: 0.2991 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 21549 Z= 0.235 Angle : 0.736 10.342 29475 Z= 0.340 Chirality : 0.048 0.263 3577 Planarity : 0.005 0.077 3543 Dihedral : 12.575 79.388 5101 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.54 % Allowed : 9.51 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.72 (0.17), residues: 2421 helix: 1.51 (0.27), residues: 390 sheet: -0.94 (0.19), residues: 759 loop : -0.75 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 53 TYR 0.026 0.002 TYR D 638 PHE 0.018 0.002 PHE E 53 TRP 0.011 0.002 TRP C 338 HIS 0.007 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00566 (21397) covalent geometry : angle 0.68378 (29052) SS BOND : bond 0.00332 ( 33) SS BOND : angle 0.84748 ( 66) hydrogen bonds : bond 0.04592 ( 603) hydrogen bonds : angle 6.13560 ( 1629) link_ALPHA1-3 : bond 0.00930 ( 5) link_ALPHA1-3 : angle 2.02750 ( 15) link_ALPHA1-6 : bond 0.00289 ( 6) link_ALPHA1-6 : angle 1.76292 ( 18) link_BETA1-4 : bond 0.00506 ( 54) link_BETA1-4 : angle 2.73210 ( 162) link_NAG-ASN : bond 0.00545 ( 54) link_NAG-ASN : angle 2.51744 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 346 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8004 (m90) cc_final: 0.7704 (m90) REVERT: B 543 ASN cc_start: 0.8694 (m110) cc_final: 0.8469 (m110) REVERT: B 626 MET cc_start: 0.8474 (tpp) cc_final: 0.7909 (ttm) REVERT: C 65 LYS cc_start: 0.8871 (mmtt) cc_final: 0.7955 (tttt) REVERT: C 66 HIS cc_start: 0.8156 (m90) cc_final: 0.7737 (m90) REVERT: C 151 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7560 (ttt90) REVERT: D 626 MET cc_start: 0.8505 (tpp) cc_final: 0.8021 (ttm) REVERT: E 66 HIS cc_start: 0.7986 (m90) cc_final: 0.7672 (m90) REVERT: F 542 ARG cc_start: 0.8461 (mtp180) cc_final: 0.8198 (mtm180) REVERT: I 100 ASP cc_start: 0.8604 (t70) cc_final: 0.8385 (t0) REVERT: J 83 ARG cc_start: 0.8536 (mtm110) cc_final: 0.8318 (mtp180) REVERT: L 42 LYS cc_start: 0.8612 (mmmm) cc_final: 0.8370 (mmtm) REVERT: M 50 ASP cc_start: 0.8711 (m-30) cc_final: 0.8430 (m-30) REVERT: N 50 ASP cc_start: 0.8713 (m-30) cc_final: 0.8377 (m-30) outliers start: 54 outliers final: 33 residues processed: 372 average time/residue: 0.1737 time to fit residues: 95.3309 Evaluate side-chains 354 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 321 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 33 ASN E 33 ASN F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100904 restraints weight = 26766.829| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.14 r_work: 0.2980 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21549 Z= 0.166 Angle : 0.658 13.028 29475 Z= 0.303 Chirality : 0.046 0.257 3577 Planarity : 0.004 0.056 3543 Dihedral : 10.312 69.239 5097 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.12 % Allowed : 12.10 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.68 (0.17), residues: 2421 helix: 1.72 (0.27), residues: 390 sheet: -0.92 (0.18), residues: 750 loop : -0.78 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 53 TYR 0.015 0.001 TYR D 638 PHE 0.017 0.002 PHE C 391 TRP 0.008 0.001 TRP J 100H HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00388 (21397) covalent geometry : angle 0.60791 (29052) SS BOND : bond 0.00234 ( 33) SS BOND : angle 0.55905 ( 66) hydrogen bonds : bond 0.04137 ( 603) hydrogen bonds : angle 5.64455 ( 1629) link_ALPHA1-3 : bond 0.01032 ( 5) link_ALPHA1-3 : angle 1.60726 ( 15) link_ALPHA1-6 : bond 0.00425 ( 6) link_ALPHA1-6 : angle 1.63271 ( 18) link_BETA1-4 : bond 0.00483 ( 54) link_BETA1-4 : angle 2.28292 ( 162) link_NAG-ASN : bond 0.00696 ( 54) link_NAG-ASN : angle 2.58775 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8025 (m90) cc_final: 0.7736 (m90) REVERT: A 264 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8663 (p) REVERT: B 626 MET cc_start: 0.8483 (tpp) cc_final: 0.7883 (ttm) REVERT: C 65 LYS cc_start: 0.8875 (mmtt) cc_final: 0.7932 (tttt) REVERT: C 66 HIS cc_start: 0.8161 (m90) cc_final: 0.7733 (m90) REVERT: D 617 ARG cc_start: 0.8459 (ttm170) cc_final: 0.8214 (ttm170) REVERT: E 66 HIS cc_start: 0.7958 (m90) cc_final: 0.7641 (m90) REVERT: F 542 ARG cc_start: 0.8482 (mtp180) cc_final: 0.8223 (mtm180) REVERT: H 35 ARG cc_start: 0.8897 (mtp85) cc_final: 0.8575 (mtp85) REVERT: I 100 ASP cc_start: 0.8618 (t70) cc_final: 0.8358 (t0) REVERT: J 83 ARG cc_start: 0.8554 (mtm110) cc_final: 0.8324 (mtp180) REVERT: L 42 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8360 (mmtm) REVERT: N 50 ASP cc_start: 0.8649 (m-30) cc_final: 0.8335 (m-30) outliers start: 45 outliers final: 27 residues processed: 349 average time/residue: 0.1813 time to fit residues: 94.1548 Evaluate side-chains 338 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 310 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 0.0020 chunk 173 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 33 ASN C 428 GLN E 33 ASN F 543 ASN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.103361 restraints weight = 26685.275| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.12 r_work: 0.3014 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21549 Z= 0.147 Angle : 0.634 13.726 29475 Z= 0.291 Chirality : 0.046 0.282 3577 Planarity : 0.004 0.044 3543 Dihedral : 8.594 60.181 5092 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.88 % Allowed : 14.17 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.58 (0.17), residues: 2421 helix: 1.83 (0.27), residues: 390 sheet: -0.85 (0.19), residues: 744 loop : -0.72 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 71 TYR 0.015 0.001 TYR D 638 PHE 0.013 0.001 PHE C 391 TRP 0.009 0.001 TRP A 35 HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00342 (21397) covalent geometry : angle 0.57894 (29052) SS BOND : bond 0.00196 ( 33) SS BOND : angle 0.48320 ( 66) hydrogen bonds : bond 0.03776 ( 603) hydrogen bonds : angle 5.38866 ( 1629) link_ALPHA1-3 : bond 0.01081 ( 5) link_ALPHA1-3 : angle 1.73968 ( 15) link_ALPHA1-6 : bond 0.00516 ( 6) link_ALPHA1-6 : angle 1.56432 ( 18) link_BETA1-4 : bond 0.00494 ( 54) link_BETA1-4 : angle 2.09572 ( 162) link_NAG-ASN : bond 0.00542 ( 54) link_NAG-ASN : angle 2.81732 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 316 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8049 (m90) cc_final: 0.7735 (m90) REVERT: B 626 MET cc_start: 0.8430 (tpp) cc_final: 0.7985 (ttm) REVERT: C 65 LYS cc_start: 0.8878 (mmtt) cc_final: 0.7895 (tttt) REVERT: C 66 HIS cc_start: 0.8175 (m90) cc_final: 0.7741 (m90) REVERT: E 66 HIS cc_start: 0.7958 (m90) cc_final: 0.7579 (m90) REVERT: F 542 ARG cc_start: 0.8454 (mtp180) cc_final: 0.8209 (mtm180) REVERT: F 626 MET cc_start: 0.8536 (tpp) cc_final: 0.7756 (ttm) REVERT: H 35 ARG cc_start: 0.8900 (mtp85) cc_final: 0.8657 (mtp85) REVERT: I 100 ASP cc_start: 0.8643 (t70) cc_final: 0.8389 (t0) REVERT: L 7 SER cc_start: 0.8880 (m) cc_final: 0.8594 (p) REVERT: L 18 ARG cc_start: 0.7962 (ptm-80) cc_final: 0.7746 (ptm-80) REVERT: L 42 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8361 (mmtm) REVERT: L 50 ASP cc_start: 0.8691 (m-30) cc_final: 0.8307 (m-30) REVERT: M 7 SER cc_start: 0.8929 (m) cc_final: 0.8570 (p) REVERT: N 7 SER cc_start: 0.8800 (m) cc_final: 0.8527 (p) REVERT: N 50 ASP cc_start: 0.8604 (m-30) cc_final: 0.8299 (m-30) outliers start: 40 outliers final: 24 residues processed: 332 average time/residue: 0.1744 time to fit residues: 86.2435 Evaluate side-chains 326 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 54 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 232 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 177 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 293 GLN C 293 GLN E 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100108 restraints weight = 26979.509| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.19 r_work: 0.2770 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 21549 Z= 0.243 Angle : 0.688 11.754 29475 Z= 0.320 Chirality : 0.048 0.322 3577 Planarity : 0.004 0.043 3543 Dihedral : 8.192 59.930 5090 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.26 % Allowed : 15.44 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.70 (0.17), residues: 2421 helix: 1.72 (0.27), residues: 390 sheet: -0.98 (0.18), residues: 744 loop : -0.77 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 71 TYR 0.016 0.002 TYR D 638 PHE 0.018 0.002 PHE C 391 TRP 0.010 0.002 TRP H 103 HIS 0.008 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00589 (21397) covalent geometry : angle 0.63318 (29052) SS BOND : bond 0.00333 ( 33) SS BOND : angle 0.55722 ( 66) hydrogen bonds : bond 0.04185 ( 603) hydrogen bonds : angle 5.49375 ( 1629) link_ALPHA1-3 : bond 0.00958 ( 5) link_ALPHA1-3 : angle 1.91067 ( 15) link_ALPHA1-6 : bond 0.00537 ( 6) link_ALPHA1-6 : angle 1.58202 ( 18) link_BETA1-4 : bond 0.00407 ( 54) link_BETA1-4 : angle 2.06211 ( 162) link_NAG-ASN : bond 0.00742 ( 54) link_NAG-ASN : angle 3.05133 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7966 (m90) cc_final: 0.7555 (m90) REVERT: A 207 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8328 (mmtm) REVERT: A 264 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 543 ASN cc_start: 0.8798 (m110) cc_final: 0.8467 (m110) REVERT: B 626 MET cc_start: 0.8488 (tpp) cc_final: 0.8087 (ttm) REVERT: C 65 LYS cc_start: 0.8866 (mmtt) cc_final: 0.7801 (tttt) REVERT: C 66 HIS cc_start: 0.8135 (m90) cc_final: 0.7582 (m90) REVERT: C 151 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7705 (ttt180) REVERT: D 543 ASN cc_start: 0.8769 (m110) cc_final: 0.8421 (m110) REVERT: E 66 HIS cc_start: 0.7945 (m90) cc_final: 0.7502 (m90) REVERT: F 626 MET cc_start: 0.8611 (tpp) cc_final: 0.8254 (ttm) REVERT: H 35 ARG cc_start: 0.8847 (mtp85) cc_final: 0.8481 (mtp85) REVERT: I 71 GLU cc_start: 0.8350 (tt0) cc_final: 0.7601 (tt0) REVERT: I 100 ASP cc_start: 0.8649 (t70) cc_final: 0.8380 (t0) REVERT: L 7 SER cc_start: 0.8784 (m) cc_final: 0.8433 (p) REVERT: L 42 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8222 (mmtm) REVERT: M 7 SER cc_start: 0.8833 (m) cc_final: 0.8419 (p) REVERT: N 7 SER cc_start: 0.8801 (m) cc_final: 0.8434 (p) REVERT: N 50 ASP cc_start: 0.8581 (m-30) cc_final: 0.8214 (m-30) outliers start: 48 outliers final: 34 residues processed: 335 average time/residue: 0.1754 time to fit residues: 87.8597 Evaluate side-chains 334 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 299 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 226 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 33 ASN F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103094 restraints weight = 26623.890| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.17 r_work: 0.2849 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21549 Z= 0.138 Angle : 0.623 12.472 29475 Z= 0.288 Chirality : 0.046 0.279 3577 Planarity : 0.004 0.045 3543 Dihedral : 7.446 57.721 5090 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.07 % Allowed : 15.96 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.61 (0.17), residues: 2421 helix: 1.78 (0.27), residues: 390 sheet: -0.89 (0.19), residues: 744 loop : -0.73 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.014 0.001 TYR F 638 PHE 0.014 0.001 PHE M 21 TRP 0.010 0.001 TRP J 100H HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00321 (21397) covalent geometry : angle 0.56787 (29052) SS BOND : bond 0.00191 ( 33) SS BOND : angle 0.43553 ( 66) hydrogen bonds : bond 0.03670 ( 603) hydrogen bonds : angle 5.28109 ( 1629) link_ALPHA1-3 : bond 0.01213 ( 5) link_ALPHA1-3 : angle 1.67911 ( 15) link_ALPHA1-6 : bond 0.00728 ( 6) link_ALPHA1-6 : angle 1.39095 ( 18) link_BETA1-4 : bond 0.00469 ( 54) link_BETA1-4 : angle 1.84528 ( 162) link_NAG-ASN : bond 0.00512 ( 54) link_NAG-ASN : angle 2.96166 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 312 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7974 (m90) cc_final: 0.7570 (m90) REVERT: A 164 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: A 207 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8313 (mmtm) REVERT: A 264 SER cc_start: 0.9184 (OUTLIER) cc_final: 0.8640 (p) REVERT: B 626 MET cc_start: 0.8454 (tpp) cc_final: 0.8082 (ttm) REVERT: C 65 LYS cc_start: 0.8877 (mmtt) cc_final: 0.7883 (tttt) REVERT: C 66 HIS cc_start: 0.8166 (m90) cc_final: 0.7630 (m90) REVERT: C 151 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7617 (ttt180) REVERT: E 66 HIS cc_start: 0.7954 (m90) cc_final: 0.7506 (m90) REVERT: E 164 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: F 626 MET cc_start: 0.8631 (tpp) cc_final: 0.8176 (ttm) REVERT: H 35 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8596 (mtp85) REVERT: I 100 ASP cc_start: 0.8710 (t70) cc_final: 0.8430 (t0) REVERT: L 7 SER cc_start: 0.8849 (m) cc_final: 0.8504 (p) REVERT: L 42 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8309 (mmtm) REVERT: L 50 ASP cc_start: 0.8568 (m-30) cc_final: 0.8168 (m-30) REVERT: M 7 SER cc_start: 0.8865 (m) cc_final: 0.8462 (p) REVERT: M 77 ASN cc_start: 0.8552 (t0) cc_final: 0.8218 (t0) REVERT: N 7 SER cc_start: 0.8806 (m) cc_final: 0.8496 (p) REVERT: N 50 ASP cc_start: 0.8547 (m-30) cc_final: 0.8226 (m-30) outliers start: 44 outliers final: 25 residues processed: 332 average time/residue: 0.1790 time to fit residues: 89.2994 Evaluate side-chains 324 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 233 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 192 optimal weight: 0.0040 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104375 restraints weight = 26662.175| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.19 r_work: 0.3028 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21549 Z= 0.123 Angle : 0.620 13.082 29475 Z= 0.284 Chirality : 0.045 0.371 3577 Planarity : 0.004 0.042 3543 Dihedral : 7.037 57.188 5090 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.84 % Allowed : 16.53 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.52 (0.17), residues: 2421 helix: 1.88 (0.27), residues: 390 sheet: -0.85 (0.19), residues: 759 loop : -0.66 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 71 TYR 0.015 0.001 TYR D 638 PHE 0.013 0.001 PHE C 391 TRP 0.009 0.001 TRP J 100H HIS 0.005 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00279 (21397) covalent geometry : angle 0.55567 (29052) SS BOND : bond 0.00171 ( 33) SS BOND : angle 0.41751 ( 66) hydrogen bonds : bond 0.03494 ( 603) hydrogen bonds : angle 5.13006 ( 1629) link_ALPHA1-3 : bond 0.01182 ( 5) link_ALPHA1-3 : angle 1.58145 ( 15) link_ALPHA1-6 : bond 0.00748 ( 6) link_ALPHA1-6 : angle 1.36069 ( 18) link_BETA1-4 : bond 0.00482 ( 54) link_BETA1-4 : angle 1.74573 ( 162) link_NAG-ASN : bond 0.00482 ( 54) link_NAG-ASN : angle 3.31171 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 307 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8028 (m90) cc_final: 0.7648 (m90) REVERT: A 207 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8344 (mmtm) REVERT: A 264 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8678 (p) REVERT: B 626 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8226 (ttm) REVERT: C 65 LYS cc_start: 0.8872 (mmtt) cc_final: 0.7957 (tttt) REVERT: C 66 HIS cc_start: 0.8155 (m90) cc_final: 0.7671 (m90) REVERT: C 95 MET cc_start: 0.9122 (ptm) cc_final: 0.8892 (ptm) REVERT: C 151 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7569 (ttt90) REVERT: C 164 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: E 66 HIS cc_start: 0.8032 (m90) cc_final: 0.7619 (m90) REVERT: F 626 MET cc_start: 0.8561 (tpp) cc_final: 0.8068 (ttt) REVERT: H 35 ARG cc_start: 0.8926 (mtp85) cc_final: 0.8671 (mtp85) REVERT: I 100 ASP cc_start: 0.8731 (t70) cc_final: 0.8467 (t0) REVERT: L 7 SER cc_start: 0.8863 (m) cc_final: 0.8545 (p) REVERT: L 42 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8394 (mmtm) REVERT: L 50 ASP cc_start: 0.8610 (m-30) cc_final: 0.8248 (m-30) REVERT: M 7 SER cc_start: 0.8866 (m) cc_final: 0.8555 (p) REVERT: N 7 SER cc_start: 0.8814 (m) cc_final: 0.8542 (p) REVERT: N 50 ASP cc_start: 0.8603 (m-30) cc_final: 0.8324 (m-30) outliers start: 39 outliers final: 24 residues processed: 324 average time/residue: 0.1892 time to fit residues: 90.5890 Evaluate side-chains 327 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 54 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 149 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 24 optimal weight: 0.0040 chunk 26 optimal weight: 0.0970 chunk 234 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 211 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105741 restraints weight = 26430.994| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.14 r_work: 0.3043 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21549 Z= 0.110 Angle : 0.603 12.576 29475 Z= 0.275 Chirality : 0.046 0.654 3577 Planarity : 0.004 0.045 3543 Dihedral : 6.796 57.391 5090 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.88 % Allowed : 16.76 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.46 (0.17), residues: 2421 helix: 1.95 (0.27), residues: 390 sheet: -0.80 (0.19), residues: 759 loop : -0.64 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 71 TYR 0.016 0.001 TYR N 36 PHE 0.013 0.001 PHE M 21 TRP 0.010 0.001 TRP J 100H HIS 0.005 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00246 (21397) covalent geometry : angle 0.54678 (29052) SS BOND : bond 0.00147 ( 33) SS BOND : angle 0.38764 ( 66) hydrogen bonds : bond 0.03346 ( 603) hydrogen bonds : angle 5.00162 ( 1629) link_ALPHA1-3 : bond 0.01194 ( 5) link_ALPHA1-3 : angle 1.49630 ( 15) link_ALPHA1-6 : bond 0.00769 ( 6) link_ALPHA1-6 : angle 1.33147 ( 18) link_BETA1-4 : bond 0.00487 ( 54) link_BETA1-4 : angle 1.68143 ( 162) link_NAG-ASN : bond 0.00457 ( 54) link_NAG-ASN : angle 3.04973 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 306 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7992 (m90) cc_final: 0.7626 (m90) REVERT: A 207 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8384 (mmtm) REVERT: A 264 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8673 (p) REVERT: C 65 LYS cc_start: 0.8869 (mmtt) cc_final: 0.7959 (tttt) REVERT: C 66 HIS cc_start: 0.8136 (m90) cc_final: 0.7634 (m90) REVERT: C 95 MET cc_start: 0.9123 (ptm) cc_final: 0.8880 (ptm) REVERT: E 66 HIS cc_start: 0.8013 (m90) cc_final: 0.7573 (m90) REVERT: F 568 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7080 (pt) REVERT: F 626 MET cc_start: 0.8540 (tpp) cc_final: 0.8062 (ttt) REVERT: I 100 ASP cc_start: 0.8745 (t70) cc_final: 0.8462 (t0) REVERT: L 7 SER cc_start: 0.8858 (m) cc_final: 0.8545 (p) REVERT: L 42 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8402 (mmtm) REVERT: L 50 ASP cc_start: 0.8550 (m-30) cc_final: 0.8162 (m-30) REVERT: M 7 SER cc_start: 0.8852 (m) cc_final: 0.8527 (p) REVERT: N 7 SER cc_start: 0.8828 (m) cc_final: 0.8545 (p) REVERT: N 50 ASP cc_start: 0.8551 (m-30) cc_final: 0.8277 (m-30) outliers start: 40 outliers final: 24 residues processed: 327 average time/residue: 0.1836 time to fit residues: 89.4343 Evaluate side-chains 321 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 213 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN D 653 GLN F 653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.101671 restraints weight = 26838.848| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.18 r_work: 0.2828 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 21549 Z= 0.207 Angle : 0.654 12.538 29475 Z= 0.304 Chirality : 0.047 0.427 3577 Planarity : 0.004 0.043 3543 Dihedral : 6.954 59.655 5090 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.12 % Allowed : 16.76 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.53 (0.17), residues: 2421 helix: 1.88 (0.27), residues: 390 sheet: -0.85 (0.19), residues: 738 loop : -0.68 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 71 TYR 0.016 0.002 TYR F 638 PHE 0.017 0.002 PHE C 391 TRP 0.014 0.001 TRP A 35 HIS 0.007 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00500 (21397) covalent geometry : angle 0.60423 (29052) SS BOND : bond 0.00294 ( 33) SS BOND : angle 0.48987 ( 66) hydrogen bonds : bond 0.03859 ( 603) hydrogen bonds : angle 5.17289 ( 1629) link_ALPHA1-3 : bond 0.01017 ( 5) link_ALPHA1-3 : angle 1.74016 ( 15) link_ALPHA1-6 : bond 0.00725 ( 6) link_ALPHA1-6 : angle 1.38754 ( 18) link_BETA1-4 : bond 0.00444 ( 54) link_BETA1-4 : angle 1.74046 ( 162) link_NAG-ASN : bond 0.00546 ( 54) link_NAG-ASN : angle 2.95706 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 304 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8004 (m90) cc_final: 0.7582 (m90) REVERT: A 164 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: A 207 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8359 (mmtm) REVERT: A 264 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8731 (p) REVERT: B 543 ASN cc_start: 0.8773 (m110) cc_final: 0.8458 (m110) REVERT: C 65 LYS cc_start: 0.8890 (mmtt) cc_final: 0.7894 (tttt) REVERT: C 66 HIS cc_start: 0.8174 (m90) cc_final: 0.7806 (m90) REVERT: C 151 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7649 (ttt180) REVERT: C 164 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: E 66 HIS cc_start: 0.8018 (m90) cc_final: 0.7541 (m90) REVERT: F 626 MET cc_start: 0.8687 (tpp) cc_final: 0.8243 (ttm) REVERT: H 35 ARG cc_start: 0.8850 (mtp85) cc_final: 0.8544 (mtp85) REVERT: I 100 ASP cc_start: 0.8735 (t70) cc_final: 0.8441 (t0) REVERT: L 7 SER cc_start: 0.8859 (m) cc_final: 0.8517 (p) REVERT: L 42 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8334 (mmtm) REVERT: L 50 ASP cc_start: 0.8605 (m-30) cc_final: 0.8182 (m-30) REVERT: M 7 SER cc_start: 0.8811 (m) cc_final: 0.8438 (p) REVERT: N 7 SER cc_start: 0.8812 (m) cc_final: 0.8481 (p) REVERT: N 50 ASP cc_start: 0.8637 (m-30) cc_final: 0.8327 (m-30) outliers start: 45 outliers final: 32 residues processed: 328 average time/residue: 0.1717 time to fit residues: 83.9529 Evaluate side-chains 338 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 229 optimal weight: 0.5980 chunk 158 optimal weight: 0.0050 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN E 33 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104870 restraints weight = 26701.962| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.18 r_work: 0.3013 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21549 Z= 0.118 Angle : 0.604 12.421 29475 Z= 0.279 Chirality : 0.044 0.357 3577 Planarity : 0.004 0.046 3543 Dihedral : 6.674 58.493 5090 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.65 % Allowed : 17.37 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.45 (0.17), residues: 2421 helix: 2.00 (0.27), residues: 390 sheet: -0.83 (0.19), residues: 753 loop : -0.62 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 71 TYR 0.016 0.001 TYR D 638 PHE 0.012 0.001 PHE M 21 TRP 0.011 0.001 TRP J 100H HIS 0.005 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00269 (21397) covalent geometry : angle 0.55220 (29052) SS BOND : bond 0.00171 ( 33) SS BOND : angle 0.37614 ( 66) hydrogen bonds : bond 0.03432 ( 603) hydrogen bonds : angle 5.02318 ( 1629) link_ALPHA1-3 : bond 0.01145 ( 5) link_ALPHA1-3 : angle 1.45994 ( 15) link_ALPHA1-6 : bond 0.00787 ( 6) link_ALPHA1-6 : angle 1.30017 ( 18) link_BETA1-4 : bond 0.00468 ( 54) link_BETA1-4 : angle 1.63043 ( 162) link_NAG-ASN : bond 0.00488 ( 54) link_NAG-ASN : angle 2.91703 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7999 (m90) cc_final: 0.7613 (m90) REVERT: A 164 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: A 207 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8384 (mmtm) REVERT: A 264 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8704 (p) REVERT: C 65 LYS cc_start: 0.8874 (mmtt) cc_final: 0.7938 (tttt) REVERT: C 66 HIS cc_start: 0.8179 (m90) cc_final: 0.7676 (m90) REVERT: C 151 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7526 (ttt90) REVERT: C 164 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: E 66 HIS cc_start: 0.8034 (m90) cc_final: 0.7582 (m90) REVERT: F 535 MET cc_start: 0.8198 (mtm) cc_final: 0.7877 (mtm) REVERT: F 626 MET cc_start: 0.8557 (tpp) cc_final: 0.7957 (ttm) REVERT: H 35 ARG cc_start: 0.8911 (mtp85) cc_final: 0.8428 (mtp85) REVERT: I 100 ASP cc_start: 0.8746 (t70) cc_final: 0.8447 (t0) REVERT: L 7 SER cc_start: 0.8872 (m) cc_final: 0.8557 (p) REVERT: L 42 LYS cc_start: 0.8664 (mmmm) cc_final: 0.8386 (mmtm) REVERT: L 50 ASP cc_start: 0.8571 (m-30) cc_final: 0.8161 (m-30) REVERT: M 7 SER cc_start: 0.8837 (m) cc_final: 0.8525 (p) REVERT: N 7 SER cc_start: 0.8821 (m) cc_final: 0.8534 (p) REVERT: N 50 ASP cc_start: 0.8612 (m-30) cc_final: 0.8345 (m-30) outliers start: 35 outliers final: 27 residues processed: 319 average time/residue: 0.1803 time to fit residues: 84.9737 Evaluate side-chains 327 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 110 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 226 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104878 restraints weight = 26630.436| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.18 r_work: 0.3036 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 21549 Z= 0.216 Angle : 0.902 59.199 29475 Z= 0.484 Chirality : 0.051 1.032 3577 Planarity : 0.004 0.048 3543 Dihedral : 6.672 58.496 5090 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.51 % Allowed : 17.80 % Favored : 80.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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: -0.45 (0.17), residues: 2421 helix: 1.99 (0.27), residues: 390 sheet: -0.83 (0.19), residues: 753 loop : -0.62 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 71 TYR 0.016 0.001 TYR D 638 PHE 0.012 0.001 PHE M 21 TRP 0.010 0.001 TRP J 100H HIS 0.005 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00467 (21397) covalent geometry : angle 0.87183 (29052) SS BOND : bond 0.00170 ( 33) SS BOND : angle 0.37528 ( 66) hydrogen bonds : bond 0.03438 ( 603) hydrogen bonds : angle 5.02191 ( 1629) link_ALPHA1-3 : bond 0.01032 ( 5) link_ALPHA1-3 : angle 1.38575 ( 15) link_ALPHA1-6 : bond 0.00778 ( 6) link_ALPHA1-6 : angle 1.30353 ( 18) link_BETA1-4 : bond 0.00435 ( 54) link_BETA1-4 : angle 1.63732 ( 162) link_NAG-ASN : bond 0.00522 ( 54) link_NAG-ASN : angle 2.95232 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5585.43 seconds wall clock time: 96 minutes 46.07 seconds (5806.07 seconds total)