Starting phenix.real_space_refine on Wed Jun 18 06:00:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uls_42364/06_2025/8uls_42364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uls_42364/06_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_42364/06_2025/8uls_42364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uls_42364/06_2025/8uls_42364.map" model { file = "/net/cci-nas-00/data/ceres_data/8uls_42364/06_2025/8uls_42364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uls_42364/06_2025/8uls_42364.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 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: 13.79, per 1000 atoms: 0.66 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: 7.11 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.78 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: 7.13 Time building geometry restraints manager: 7.95 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: 0.00 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: 4.270 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: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 51.280 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.310 ------------------------------------------------------------------------------- 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 : 9.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP J 100H HIS 0.004 0.001 HIS I 50 PHE 0.027 0.001 PHE C 391 TYR 0.010 0.001 TYR H 33 ARG 0.005 0.001 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.01319 ( 54) link_NAG-ASN : angle 3.90132 ( 162) 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_ALPHA1-3 : bond 0.04798 ( 5) link_ALPHA1-3 : angle 3.27756 ( 15) hydrogen bonds : bond 0.19816 ( 603) hydrogen bonds : angle 8.55401 ( 1629) SS BOND : bond 0.00670 ( 33) SS BOND : angle 1.62261 ( 66) covalent geometry : bond 0.00536 (21397) covalent geometry : angle 0.87879 (29052) *********************** 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 : 2.193 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: 0.8170 (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: 0.7781 (mtm180) REVERT: L 42 LYS cc_start: 0.8291 (mmmm) cc_final: 0.8014 (mmtm) outliers start: 11 outliers final: 7 residues processed: 402 average time/residue: 0.3508 time to fit residues: 219.4766 Evaluate side-chains 314 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 307 time to evaluate : 2.388 ------------------------------------------------------------------------------- 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 202 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 140 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.121890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.099172 restraints weight = 26958.903| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.15 r_work: 0.2980 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 21549 Z= 0.273 Angle : 0.747 10.717 29475 Z= 0.347 Chirality : 0.048 0.288 3577 Planarity : 0.005 0.075 3543 Dihedral : 13.127 81.592 5101 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.12 % Allowed : 9.51 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2421 helix: 1.47 (0.27), residues: 390 sheet: -0.97 (0.19), residues: 759 loop : -0.77 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.008 0.001 HIS I 50 PHE 0.022 0.002 PHE C 391 TYR 0.032 0.002 TYR D 638 ARG 0.006 0.001 ARG J 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00693 ( 54) link_NAG-ASN : angle 2.68482 ( 162) link_ALPHA1-6 : bond 0.00255 ( 6) link_ALPHA1-6 : angle 1.89012 ( 18) link_BETA1-4 : bond 0.00511 ( 54) link_BETA1-4 : angle 2.73503 ( 162) link_ALPHA1-3 : bond 0.00751 ( 5) link_ALPHA1-3 : angle 1.89680 ( 15) hydrogen bonds : bond 0.04974 ( 603) hydrogen bonds : angle 6.28509 ( 1629) SS BOND : bond 0.00372 ( 33) SS BOND : angle 0.95434 ( 66) covalent geometry : bond 0.00659 (21397) covalent geometry : angle 0.69187 (29052) *********************** 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 391 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 346 time to evaluate : 2.326 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: 0.8003 (m90) cc_final: 0.7724 (m90) REVERT: A 264 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8666 (p) REVERT: B 543 ASN cc_start: 0.8724 (m110) cc_final: 0.8490 (m110) REVERT: B 626 MET cc_start: 0.8501 (tpp) cc_final: 0.7960 (ttm) REVERT: C 65 LYS cc_start: 0.8866 (mmtt) cc_final: 0.7934 (tttt) REVERT: C 66 HIS cc_start: 0.8149 (m90) cc_final: 0.7721 (m90) REVERT: E 66 HIS cc_start: 0.7988 (m90) cc_final: 0.7670 (m90) REVERT: F 542 ARG cc_start: 0.8463 (mtp180) cc_final: 0.8201 (mtm180) REVERT: I 100 ASP cc_start: 0.8596 (t70) cc_final: 0.8377 (t0) REVERT: J 83 ARG cc_start: 0.8565 (mtm110) cc_final: 0.8313 (mtp180) REVERT: L 42 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8377 (mmtm) REVERT: M 50 ASP cc_start: 0.8749 (m-30) cc_final: 0.8525 (m-30) REVERT: N 50 ASP cc_start: 0.8747 (m-30) cc_final: 0.8434 (m-30) outliers start: 45 outliers final: 29 residues processed: 370 average time/residue: 0.3792 time to fit residues: 208.6425 Evaluate side-chains 353 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 323 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL 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 264 SER Chi-restraints excluded: chain A residue 325 ASP 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 E residue 172 VAL 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 568 LEU Chi-restraints excluded: chain F residue 620 SER 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 54 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 232 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 157 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.123525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101052 restraints weight = 26586.913| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.14 r_work: 0.2798 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 21549 Z= 0.206 Angle : 0.672 9.678 29475 Z= 0.312 Chirality : 0.048 0.271 3577 Planarity : 0.005 0.056 3543 Dihedral : 10.340 68.701 5097 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 2.21 % Allowed : 12.57 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2421 helix: 1.60 (0.27), residues: 390 sheet: -1.05 (0.18), residues: 765 loop : -0.79 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.007 0.001 HIS I 50 PHE 0.018 0.002 PHE C 391 TYR 0.022 0.001 TYR D 638 ARG 0.009 0.001 ARG E 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 54) link_NAG-ASN : angle 2.32747 ( 162) link_ALPHA1-6 : bond 0.00409 ( 6) link_ALPHA1-6 : angle 1.65793 ( 18) link_BETA1-4 : bond 0.00495 ( 54) link_BETA1-4 : angle 2.28941 ( 162) link_ALPHA1-3 : bond 0.01070 ( 5) link_ALPHA1-3 : angle 1.71456 ( 15) hydrogen bonds : bond 0.04377 ( 603) hydrogen bonds : angle 5.72157 ( 1629) SS BOND : bond 0.00293 ( 33) SS BOND : angle 0.64558 ( 66) covalent geometry : bond 0.00493 (21397) covalent geometry : angle 0.62766 (29052) *********************** 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 383 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 336 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8027 (m90) cc_final: 0.7650 (m90) REVERT: B 543 ASN cc_start: 0.8682 (m110) cc_final: 0.8385 (m110) REVERT: B 626 MET cc_start: 0.8500 (tpp) cc_final: 0.8074 (ttm) REVERT: C 65 LYS cc_start: 0.8852 (mmtt) cc_final: 0.7793 (tttt) REVERT: C 66 HIS cc_start: 0.8119 (m90) cc_final: 0.7569 (m90) REVERT: D 617 ARG cc_start: 0.8438 (ttm170) cc_final: 0.8173 (ttm170) REVERT: E 66 HIS cc_start: 0.7893 (m90) cc_final: 0.7489 (m90) REVERT: F 542 ARG cc_start: 0.8342 (mtp180) cc_final: 0.8063 (mtm180) REVERT: H 35 ARG cc_start: 0.8826 (mtp85) cc_final: 0.8477 (mtp85) REVERT: I 35 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8576 (mtp85) REVERT: I 100 ASP cc_start: 0.8596 (t70) cc_final: 0.8336 (t0) REVERT: L 42 LYS cc_start: 0.8469 (mmmm) cc_final: 0.8250 (mmtm) REVERT: M 7 SER cc_start: 0.8876 (m) cc_final: 0.8461 (p) REVERT: M 50 ASP cc_start: 0.8649 (m-30) cc_final: 0.8237 (m-30) REVERT: N 50 ASP cc_start: 0.8586 (m-30) cc_final: 0.8209 (m-30) outliers start: 47 outliers final: 31 residues processed: 357 average time/residue: 0.3606 time to fit residues: 192.7156 Evaluate side-chains 346 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 315 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 325 ASP Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 84 SER 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 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 54 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 130 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.124328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.101791 restraints weight = 26738.298| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.14 r_work: 0.2968 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21549 Z= 0.167 Angle : 0.648 13.565 29475 Z= 0.299 Chirality : 0.046 0.325 3577 Planarity : 0.004 0.045 3543 Dihedral : 8.846 60.433 5095 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.17 % Allowed : 13.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.17), residues: 2421 helix: 1.75 (0.27), residues: 390 sheet: -1.00 (0.18), residues: 759 loop : -0.72 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 35 HIS 0.006 0.001 HIS H 50 PHE 0.016 0.002 PHE C 391 TYR 0.017 0.001 TYR D 638 ARG 0.006 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 54) link_NAG-ASN : angle 2.75071 ( 162) link_ALPHA1-6 : bond 0.00500 ( 6) link_ALPHA1-6 : angle 1.58441 ( 18) link_BETA1-4 : bond 0.00469 ( 54) link_BETA1-4 : angle 2.12427 ( 162) link_ALPHA1-3 : bond 0.01089 ( 5) link_ALPHA1-3 : angle 1.82472 ( 15) hydrogen bonds : bond 0.03985 ( 603) hydrogen bonds : angle 5.49758 ( 1629) SS BOND : bond 0.00235 ( 33) SS BOND : angle 0.52060 ( 66) covalent geometry : bond 0.00396 (21397) covalent geometry : angle 0.59612 (29052) *********************** 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 363 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 7.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8075 (m90) cc_final: 0.7779 (m90) REVERT: A 264 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8705 (p) REVERT: C 65 LYS cc_start: 0.8851 (mmtt) cc_final: 0.7888 (tttt) REVERT: C 66 HIS cc_start: 0.8192 (m90) cc_final: 0.7764 (m90) REVERT: E 66 HIS cc_start: 0.7986 (m90) cc_final: 0.7635 (m90) REVERT: F 626 MET cc_start: 0.8595 (tpp) cc_final: 0.8138 (ttm) REVERT: H 35 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8588 (mtp85) REVERT: I 100 ASP cc_start: 0.8671 (t70) cc_final: 0.8418 (t0) REVERT: L 7 SER cc_start: 0.8882 (m) cc_final: 0.8595 (p) REVERT: L 42 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8370 (mmtm) REVERT: L 50 ASP cc_start: 0.8724 (m-30) cc_final: 0.8313 (m-30) REVERT: M 7 SER cc_start: 0.8914 (m) cc_final: 0.8577 (p) REVERT: N 7 SER cc_start: 0.8833 (m) cc_final: 0.8553 (p) REVERT: N 50 ASP cc_start: 0.8618 (m-30) cc_final: 0.8309 (m-30) outliers start: 46 outliers final: 30 residues processed: 338 average time/residue: 0.3630 time to fit residues: 192.9094 Evaluate side-chains 337 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 306 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 264 SER 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 C residue 340 GLU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 340 GLU 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 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 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 14 SER 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 208 optimal weight: 0.1980 chunk 160 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 209 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.120439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.097650 restraints weight = 26958.048| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.16 r_work: 0.2932 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 21549 Z= 0.229 Angle : 0.684 13.141 29475 Z= 0.318 Chirality : 0.047 0.283 3577 Planarity : 0.004 0.044 3543 Dihedral : 8.361 59.555 5090 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.82 % Allowed : 14.60 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2421 helix: 1.66 (0.27), residues: 390 sheet: -1.07 (0.18), residues: 759 loop : -0.74 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 35 HIS 0.007 0.001 HIS J 50 PHE 0.018 0.002 PHE C 391 TYR 0.015 0.002 TYR D 638 ARG 0.006 0.001 ARG I 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 54) link_NAG-ASN : angle 3.05849 ( 162) link_ALPHA1-6 : bond 0.00541 ( 6) link_ALPHA1-6 : angle 1.59010 ( 18) link_BETA1-4 : bond 0.00456 ( 54) link_BETA1-4 : angle 2.07407 ( 162) link_ALPHA1-3 : bond 0.01024 ( 5) link_ALPHA1-3 : angle 1.93149 ( 15) hydrogen bonds : bond 0.04186 ( 603) hydrogen bonds : angle 5.51078 ( 1629) SS BOND : bond 0.00317 ( 33) SS BOND : angle 0.55929 ( 66) covalent geometry : bond 0.00553 (21397) covalent geometry : angle 0.62843 (29052) *********************** 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 372 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 312 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8088 (m90) cc_final: 0.7760 (m90) REVERT: A 207 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8497 (mmtm) REVERT: A 264 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 543 ASN cc_start: 0.8822 (m110) cc_final: 0.8576 (m110) REVERT: C 65 LYS cc_start: 0.8885 (mmtt) cc_final: 0.7928 (tttt) REVERT: C 66 HIS cc_start: 0.8208 (m90) cc_final: 0.7761 (m90) REVERT: C 151 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7661 (ttt180) REVERT: C 164 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: D 543 ASN cc_start: 0.8782 (m110) cc_final: 0.8525 (m110) REVERT: E 66 HIS cc_start: 0.8051 (m90) cc_final: 0.7705 (m90) REVERT: E 457 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: F 626 MET cc_start: 0.8610 (tpp) cc_final: 0.8193 (ttm) REVERT: H 35 ARG cc_start: 0.8996 (mtp85) cc_final: 0.8635 (mtp85) REVERT: I 100 ASP cc_start: 0.8713 (t70) cc_final: 0.8453 (t0) REVERT: L 7 SER cc_start: 0.8870 (m) cc_final: 0.8583 (p) REVERT: L 42 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8349 (mmtm) REVERT: M 7 SER cc_start: 0.8861 (m) cc_final: 0.8540 (p) REVERT: N 7 SER cc_start: 0.8837 (m) cc_final: 0.8547 (p) REVERT: N 50 ASP cc_start: 0.8665 (m-30) cc_final: 0.8373 (m-30) outliers start: 60 outliers final: 39 residues processed: 341 average time/residue: 0.3572 time to fit residues: 183.0691 Evaluate side-chains 338 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 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 90 THR 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 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 340 GLU Chi-restraints excluded: chain E residue 457 ASP 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 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 112 SER 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 14 SER 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 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 139 optimal weight: 2.9990 chunk 217 optimal weight: 0.2980 chunk 219 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.123205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.100622 restraints weight = 26758.427| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.18 r_work: 0.2754 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 21549 Z= 0.197 Angle : 0.658 11.604 29475 Z= 0.305 Chirality : 0.047 0.407 3577 Planarity : 0.004 0.042 3543 Dihedral : 7.792 59.034 5090 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.97 % Allowed : 15.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2421 helix: 1.68 (0.27), residues: 390 sheet: -1.22 (0.19), residues: 702 loop : -0.72 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 100H HIS 0.007 0.001 HIS H 50 PHE 0.017 0.002 PHE C 391 TYR 0.017 0.001 TYR B 638 ARG 0.007 0.001 ARG I 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 54) link_NAG-ASN : angle 3.05105 ( 162) link_ALPHA1-6 : bond 0.00688 ( 6) link_ALPHA1-6 : angle 1.45260 ( 18) link_BETA1-4 : bond 0.00451 ( 54) link_BETA1-4 : angle 1.91212 ( 162) link_ALPHA1-3 : bond 0.01094 ( 5) link_ALPHA1-3 : angle 1.85275 ( 15) hydrogen bonds : bond 0.04019 ( 603) hydrogen bonds : angle 5.43550 ( 1629) SS BOND : bond 0.00280 ( 33) SS BOND : angle 0.51444 ( 66) covalent geometry : bond 0.00471 (21397) covalent geometry : angle 0.60275 (29052) *********************** 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 376 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 313 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8015 (m90) cc_final: 0.7589 (m90) REVERT: A 164 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: A 264 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8648 (p) REVERT: C 65 LYS cc_start: 0.8855 (mmtt) cc_final: 0.7777 (tttt) REVERT: C 66 HIS cc_start: 0.8163 (m90) cc_final: 0.7766 (m90) REVERT: C 151 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7691 (ttt180) REVERT: E 66 HIS cc_start: 0.7978 (m90) cc_final: 0.7493 (m90) REVERT: E 164 GLU cc_start: 0.8279 (pm20) cc_final: 0.8074 (pm20) REVERT: E 273 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7106 (ptp-110) REVERT: F 626 MET cc_start: 0.8673 (tpp) cc_final: 0.8356 (ttm) REVERT: H 35 ARG cc_start: 0.8835 (mtp85) cc_final: 0.8468 (mtp85) REVERT: I 71 GLU cc_start: 0.8278 (tt0) cc_final: 0.7533 (tt0) REVERT: I 100 ASP cc_start: 0.8686 (t70) cc_final: 0.8399 (t0) REVERT: L 7 SER cc_start: 0.8824 (m) cc_final: 0.8465 (p) REVERT: L 42 LYS cc_start: 0.8467 (mmmm) cc_final: 0.8248 (mmtm) REVERT: M 7 SER cc_start: 0.8788 (m) cc_final: 0.8385 (p) REVERT: M 77 ASN cc_start: 0.8524 (t0) cc_final: 0.8143 (t0) REVERT: N 7 SER cc_start: 0.8776 (m) cc_final: 0.8423 (p) REVERT: N 50 ASP cc_start: 0.8566 (m-30) cc_final: 0.8201 (m-30) outliers start: 63 outliers final: 37 residues processed: 348 average time/residue: 0.3570 time to fit residues: 186.4751 Evaluate side-chains 340 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 C residue 114 GLN 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 606 THR 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 273 ARG Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 340 GLU 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 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 112 SER 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 14 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 67 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 C 33 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.101935 restraints weight = 26702.663| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.19 r_work: 0.2850 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21549 Z= 0.152 Angle : 0.640 12.011 29475 Z= 0.295 Chirality : 0.046 0.371 3577 Planarity : 0.004 0.043 3543 Dihedral : 7.440 58.381 5090 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.59 % Allowed : 16.10 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2421 helix: 1.78 (0.27), residues: 390 sheet: -1.01 (0.19), residues: 753 loop : -0.72 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 100H HIS 0.006 0.001 HIS H 50 PHE 0.016 0.001 PHE C 391 TYR 0.014 0.001 TYR D 638 ARG 0.007 0.001 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 54) link_NAG-ASN : angle 3.19825 ( 162) link_ALPHA1-6 : bond 0.00742 ( 6) link_ALPHA1-6 : angle 1.38479 ( 18) link_BETA1-4 : bond 0.00459 ( 54) link_BETA1-4 : angle 1.80518 ( 162) link_ALPHA1-3 : bond 0.01149 ( 5) link_ALPHA1-3 : angle 1.72570 ( 15) hydrogen bonds : bond 0.03783 ( 603) hydrogen bonds : angle 5.30690 ( 1629) SS BOND : bond 0.00218 ( 33) SS BOND : angle 0.46020 ( 66) covalent geometry : bond 0.00358 (21397) covalent geometry : angle 0.58016 (29052) *********************** 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 370 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8063 (m90) cc_final: 0.7662 (m90) REVERT: A 164 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: A 207 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8448 (mmtm) REVERT: A 264 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8709 (p) REVERT: C 65 LYS cc_start: 0.8870 (mmtt) cc_final: 0.7905 (tttt) REVERT: C 66 HIS cc_start: 0.8211 (m90) cc_final: 0.7852 (m90) REVERT: C 151 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7665 (ttt180) REVERT: D 634 GLU cc_start: 0.7857 (tt0) cc_final: 0.7517 (mt-10) REVERT: E 66 HIS cc_start: 0.8032 (m90) cc_final: 0.7585 (m90) REVERT: E 67 ASN cc_start: 0.9094 (m-40) cc_final: 0.8739 (t0) REVERT: E 164 GLU cc_start: 0.8296 (pm20) cc_final: 0.8094 (pm20) REVERT: E 273 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7132 (ptp-110) REVERT: E 457 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7688 (m-30) REVERT: H 35 ARG cc_start: 0.8907 (mtp85) cc_final: 0.8552 (mtp85) REVERT: I 100 ASP cc_start: 0.8760 (t70) cc_final: 0.8487 (t0) REVERT: L 7 SER cc_start: 0.8848 (m) cc_final: 0.8515 (p) REVERT: L 42 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8317 (mmtm) REVERT: L 50 ASP cc_start: 0.8620 (m-30) cc_final: 0.8260 (m-30) REVERT: M 7 SER cc_start: 0.8875 (m) cc_final: 0.8517 (p) REVERT: N 7 SER cc_start: 0.8805 (m) cc_final: 0.8499 (p) REVERT: N 50 ASP cc_start: 0.8603 (m-30) cc_final: 0.8275 (m-30) outliers start: 55 outliers final: 39 residues processed: 344 average time/residue: 0.3589 time to fit residues: 184.3644 Evaluate side-chains 349 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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 114 GLN 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 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 114 GLN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 457 ASP 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 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 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 14 SER 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 14 SER Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 43 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 138 optimal weight: 0.0670 chunk 227 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- 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 ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102027 restraints weight = 26856.919| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.25 r_work: 0.2970 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21549 Z= 0.169 Angle : 0.653 13.577 29475 Z= 0.300 Chirality : 0.048 0.723 3577 Planarity : 0.004 0.044 3543 Dihedral : 7.315 58.676 5090 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.59 % Allowed : 15.96 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2421 helix: 1.81 (0.27), residues: 390 sheet: -0.99 (0.19), residues: 753 loop : -0.69 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 427 HIS 0.006 0.001 HIS H 50 PHE 0.016 0.002 PHE C 391 TYR 0.014 0.001 TYR D 638 ARG 0.007 0.001 ARG I 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 54) link_NAG-ASN : angle 3.36701 ( 162) link_ALPHA1-6 : bond 0.00743 ( 6) link_ALPHA1-6 : angle 1.37782 ( 18) link_BETA1-4 : bond 0.00450 ( 54) link_BETA1-4 : angle 1.77345 ( 162) link_ALPHA1-3 : bond 0.01110 ( 5) link_ALPHA1-3 : angle 1.71753 ( 15) hydrogen bonds : bond 0.03797 ( 603) hydrogen bonds : angle 5.29448 ( 1629) SS BOND : bond 0.00239 ( 33) SS BOND : angle 0.46449 ( 66) covalent geometry : bond 0.00403 (21397) covalent geometry : angle 0.58995 (29052) *********************** 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 370 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8113 (m90) cc_final: 0.7755 (m90) REVERT: A 164 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: A 207 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8483 (mmtm) REVERT: A 264 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8771 (p) REVERT: C 65 LYS cc_start: 0.8858 (mmtt) cc_final: 0.7950 (tttt) REVERT: C 66 HIS cc_start: 0.8241 (m90) cc_final: 0.7926 (m90) REVERT: C 151 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7681 (ttt180) REVERT: C 164 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: D 634 GLU cc_start: 0.7868 (tt0) cc_final: 0.7457 (mt-10) REVERT: E 66 HIS cc_start: 0.8094 (m90) cc_final: 0.7682 (m90) REVERT: E 67 ASN cc_start: 0.9037 (m-40) cc_final: 0.8685 (t0) REVERT: E 164 GLU cc_start: 0.8329 (pm20) cc_final: 0.8104 (pm20) REVERT: E 273 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7194 (ptp-110) REVERT: E 457 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: H 35 ARG cc_start: 0.8965 (mtp85) cc_final: 0.8632 (mtp85) REVERT: I 100 ASP cc_start: 0.8808 (t70) cc_final: 0.8538 (t0) REVERT: L 7 SER cc_start: 0.8849 (m) cc_final: 0.8546 (p) REVERT: L 42 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8310 (mmtm) REVERT: L 50 ASP cc_start: 0.8636 (m-30) cc_final: 0.8302 (m-30) REVERT: M 7 SER cc_start: 0.8882 (m) cc_final: 0.8567 (p) REVERT: N 7 SER cc_start: 0.8802 (m) cc_final: 0.8531 (p) REVERT: N 50 ASP cc_start: 0.8714 (m-30) cc_final: 0.8423 (m-30) outliers start: 55 outliers final: 43 residues processed: 347 average time/residue: 0.3758 time to fit residues: 193.3361 Evaluate side-chains 358 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 310 time to evaluate : 2.192 ------------------------------------------------------------------------------- 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 114 GLN 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 51 THR 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 201 ILE 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 114 GLN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 457 ASP 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 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 I residue 112 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 112 SER 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 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 14 SER Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.097381 restraints weight = 27014.942| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.21 r_work: 0.2729 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 21549 Z= 0.323 Angle : 0.750 12.336 29475 Z= 0.354 Chirality : 0.050 0.446 3577 Planarity : 0.005 0.046 3543 Dihedral : 7.826 58.599 5090 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.59 % Allowed : 16.20 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2421 helix: 1.60 (0.27), residues: 390 sheet: -1.27 (0.19), residues: 660 loop : -0.82 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 103 HIS 0.009 0.002 HIS I 50 PHE 0.023 0.002 PHE C 391 TYR 0.017 0.002 TYR F 638 ARG 0.008 0.001 ARG I 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 54) link_NAG-ASN : angle 3.20307 ( 162) link_ALPHA1-6 : bond 0.00711 ( 6) link_ALPHA1-6 : angle 1.45862 ( 18) link_BETA1-4 : bond 0.00427 ( 54) link_BETA1-4 : angle 1.91601 ( 162) link_ALPHA1-3 : bond 0.00877 ( 5) link_ALPHA1-3 : angle 2.09220 ( 15) hydrogen bonds : bond 0.04581 ( 603) hydrogen bonds : angle 5.60979 ( 1629) SS BOND : bond 0.00456 ( 33) SS BOND : angle 0.63214 ( 66) covalent geometry : bond 0.00786 (21397) covalent geometry : angle 0.69858 (29052) *********************** 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 356 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 2.466 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8098 (m90) cc_final: 0.7653 (m90) REVERT: A 164 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: A 207 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8356 (mmtm) REVERT: A 264 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.8795 (p) REVERT: A 273 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7602 (ptp-110) REVERT: B 543 ASN cc_start: 0.8890 (m110) cc_final: 0.8566 (m110) REVERT: C 65 LYS cc_start: 0.8877 (mmtt) cc_final: 0.7790 (tttt) REVERT: C 151 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7857 (ttt180) REVERT: C 161 MET cc_start: 0.8702 (mmm) cc_final: 0.8388 (tpp) REVERT: C 164 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: D 543 ASN cc_start: 0.8858 (m110) cc_final: 0.8604 (m110) REVERT: E 164 GLU cc_start: 0.8349 (pm20) cc_final: 0.8117 (pm20) REVERT: E 273 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7257 (ptp-110) REVERT: E 457 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: H 35 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8502 (mtp85) REVERT: H 71 GLU cc_start: 0.8336 (tt0) cc_final: 0.7410 (tt0) REVERT: L 7 SER cc_start: 0.8771 (m) cc_final: 0.8409 (p) REVERT: L 50 ASP cc_start: 0.8723 (m-30) cc_final: 0.8283 (m-30) REVERT: M 7 SER cc_start: 0.8772 (m) cc_final: 0.8384 (p) REVERT: N 7 SER cc_start: 0.8751 (m) cc_final: 0.8384 (p) outliers start: 55 outliers final: 43 residues processed: 334 average time/residue: 0.3614 time to fit residues: 181.0259 Evaluate side-chains 348 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 114 GLN Chi-restraints excluded: chain A residue 127 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 273 ARG 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 51 THR 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 201 ILE Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 457 ASP 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 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 I residue 112 SER 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 14 SER 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 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 47 optimal weight: 0.1980 chunk 129 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 115 optimal weight: 0.0470 chunk 41 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 231 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103449 restraints weight = 26623.612| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.17 r_work: 0.2991 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2596 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= 0.115 Angle : 0.647 16.225 29475 Z= 0.298 Chirality : 0.047 0.665 3577 Planarity : 0.004 0.049 3543 Dihedral : 7.300 58.090 5090 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.46 % Allowed : 17.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2421 helix: 1.82 (0.27), residues: 390 sheet: -1.25 (0.19), residues: 696 loop : -0.72 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 69 HIS 0.005 0.001 HIS H 50 PHE 0.017 0.001 PHE M 21 TYR 0.016 0.001 TYR F 638 ARG 0.007 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 54) link_NAG-ASN : angle 3.47994 ( 162) link_ALPHA1-6 : bond 0.00831 ( 6) link_ALPHA1-6 : angle 1.30791 ( 18) link_BETA1-4 : bond 0.00463 ( 54) link_BETA1-4 : angle 1.68416 ( 162) link_ALPHA1-3 : bond 0.01188 ( 5) link_ALPHA1-3 : angle 1.52944 ( 15) hydrogen bonds : bond 0.03649 ( 603) hydrogen bonds : angle 5.27962 ( 1629) SS BOND : bond 0.00171 ( 33) SS BOND : angle 0.43668 ( 66) covalent geometry : bond 0.00253 (21397) covalent geometry : angle 0.58163 (29052) ********************** 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 339 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8746 (m100) cc_final: 0.8443 (m100) REVERT: A 66 HIS cc_start: 0.8095 (m90) cc_final: 0.7711 (m90) REVERT: A 207 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8410 (mmtm) REVERT: A 264 SER cc_start: 0.9179 (t) cc_final: 0.8759 (p) REVERT: A 273 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7682 (ptp-110) REVERT: A 502 LYS cc_start: 0.8106 (tptt) cc_final: 0.7714 (tptt) REVERT: C 65 LYS cc_start: 0.8879 (mmtt) cc_final: 0.7922 (tttt) REVERT: C 66 HIS cc_start: 0.8200 (m90) cc_final: 0.7842 (m90) REVERT: C 151 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7602 (ttt180) REVERT: D 634 GLU cc_start: 0.7845 (tt0) cc_final: 0.7597 (mt-10) REVERT: E 457 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: H 35 ARG cc_start: 0.8867 (mtp85) cc_final: 0.8597 (mtp85) REVERT: I 100 ASP cc_start: 0.8721 (t70) cc_final: 0.8510 (t0) REVERT: L 7 SER cc_start: 0.8833 (m) cc_final: 0.8516 (p) REVERT: L 50 ASP cc_start: 0.8623 (m-30) cc_final: 0.8251 (m-30) REVERT: M 7 SER cc_start: 0.8887 (m) cc_final: 0.8561 (p) REVERT: N 7 SER cc_start: 0.8790 (m) cc_final: 0.8501 (p) REVERT: N 50 ASP cc_start: 0.8728 (m-30) cc_final: 0.8396 (m-30) outliers start: 31 outliers final: 27 residues processed: 328 average time/residue: 0.3721 time to fit residues: 181.4065 Evaluate side-chains 330 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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 114 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 201 ILE 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 68 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 457 ASP 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 I residue 93 VAL Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 95 optimal weight: 0.0670 chunk 218 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 234 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3427 r_free = 0.3427 target = 0.125797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103475 restraints weight = 26700.875| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.17 r_work: 0.2873 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 21549 Z= 0.162 Angle : 0.809 59.200 29475 Z= 0.408 Chirality : 0.052 1.336 3577 Planarity : 0.004 0.049 3543 Dihedral : 7.302 58.093 5090 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.60 % Allowed : 17.66 % Favored : 80.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2421 helix: 1.83 (0.27), residues: 390 sheet: -1.23 (0.19), residues: 696 loop : -0.71 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 100H HIS 0.005 0.001 HIS H 50 PHE 0.016 0.001 PHE M 21 TYR 0.015 0.001 TYR D 638 ARG 0.020 0.001 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 54) link_NAG-ASN : angle 3.43682 ( 162) link_ALPHA1-6 : bond 0.00829 ( 6) link_ALPHA1-6 : angle 1.31411 ( 18) link_BETA1-4 : bond 0.00446 ( 54) link_BETA1-4 : angle 1.68024 ( 162) link_ALPHA1-3 : bond 0.00948 ( 5) link_ALPHA1-3 : angle 1.42873 ( 15) hydrogen bonds : bond 0.03664 ( 603) hydrogen bonds : angle 5.27756 ( 1629) SS BOND : bond 0.00177 ( 33) SS BOND : angle 0.42483 ( 66) covalent geometry : bond 0.00358 (21397) covalent geometry : angle 0.76136 (29052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11495.30 seconds wall clock time: 198 minutes 13.32 seconds (11893.32 seconds total)