Starting phenix.real_space_refine on Tue Jan 21 10:16:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bqw_16189/01_2025/8bqw_16189.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bqw_16189/01_2025/8bqw_16189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bqw_16189/01_2025/8bqw_16189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bqw_16189/01_2025/8bqw_16189.map" model { file = "/net/cci-nas-00/data/ceres_data/8bqw_16189/01_2025/8bqw_16189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bqw_16189/01_2025/8bqw_16189.cif" } resolution = 2.3 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= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 10740 2.51 5 N 3060 2.21 5 O 3585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17385 Number of models: 1 Model: "" Number of chains: 90 Chain: "M" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "N" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "O" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "R" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "V" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "Z" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "1" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "Y" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "2" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "3" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "4" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "2" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "3" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "7" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "8" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "9" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "F" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "J" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "b" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "c" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "b" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "e" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "f" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "g" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "h" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "j" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "k" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "l" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "i" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "m" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "n" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "o" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "p" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "q" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "r" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "s" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "t" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "r" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "u" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "v" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "w" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "x" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "u" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "v" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 10.05, per 1000 atoms: 0.58 Number of scatterers: 17385 At special positions: 0 Unit cell: (141.765, 90.148, 57.433, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3585 8.00 N 3060 7.00 C 10740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 TRANS " UNK 0 6 " - " UNK G 5 " " UNK 0 9 " - " UNK G 8 " " UNK 1 6 " - " UNK H 5 " " UNK 1 7 " - " UNK H 6 " " UNK 1 9 " - " UNK H 8 " " VAL 2 16 " - " VAL M 15 " " ALA 2 18 " - " ALA M 17 " " GLU 2 20 " - " ALA M 19 " " LYS 2 21 " - " GLU M 20 " " THR 2 22 " - " LYS M 21 " " LYS 2 23 " - " THR M 22 " " GLN 2 24 " - " LYS M 23 " " GLY 2 25 " - " GLN M 24 " " VAL 2 37 " - " GLY M 36 " " LEU 2 38 " - " VAL M 37 " " TYR 2 39 " - " LEU M 38 " " VAL 2 40 " - " TYR M 39 " " GLY 2 41 " - " VAL M 40 " " SER 2 42 " - " GLY M 41 " " LYS 2 43 " - " SER M 42 " " THR 2 44 " - " LYS M 43 " " LYS 2 45 " - " THR M 44 " " GLU 2 46 " - " LYS M 45 " " GLY 2 47 " - " GLU M 46 " " VAL 2 48 " - " GLY M 47 " " VAL 2 49 " - " VAL M 48 " " HIS 2 50 " - " VAL M 49 " " GLY 2 51 " - " HIS M 50 " " VAL 2 52 " - " GLY M 51 " " ALA 2 53 " - " VAL M 52 " " THR 2 54 " - " ALA M 53 " " VAL 2 55 " - " THR M 54 " " ALA 2 56 " - " VAL M 55 " " GLU 2 57 " - " ALA M 56 " " LYS 2 58 " - " GLU M 57 " " LYS 2 60 " - " THR M 59 " " GLN 2 62 " - " GLU M 61 " " GLY 2 68 " - " GLY M 67 " " ALA 2 69 " - " GLY M 68 " " VAL 2 70 " - " ALA M 69 " " VAL 2 71 " - " VAL M 70 " " THR 2 72 " - " VAL M 71 " " GLY 2 73 " - " THR M 72 " " THR 2 81 " - " LYS M 80 " " VAL 2 82 " - " THR M 81 " " GLU 2 83 " - " VAL M 82 " " GLY 2 84 " - " GLU M 83 " " ALA 2 85 " - " GLY M 84 " " GLY 2 86 " - " ALA M 85 " " SER 2 87 " - " GLY M 86 " " ILE 2 88 " - " SER M 87 " " ALA 2 90 " - " ALA M 89 " " ALA 2 91 " - " ALA M 90 " " THR 2 92 " - " ALA M 91 " " GLY 2 93 " - " THR M 92 " " VAL 2 95 " - " PHE M 94 " " LYS 2 97 " - " LYS M 96 " " VAL 3 16 " - " VAL N 15 " " ALA 3 18 " - " ALA N 17 " " GLU 3 20 " - " ALA N 19 " " LYS 3 21 " - " GLU N 20 " " THR 3 22 " - " LYS N 21 " " LYS 3 23 " - " THR N 22 " " GLN 3 24 " - " LYS N 23 " " GLY 3 25 " - " GLN N 24 " " VAL 3 37 " - " GLY N 36 " " LEU 3 38 " - " VAL N 37 " " TYR 3 39 " - " LEU N 38 " " VAL 3 40 " - " TYR N 39 " " GLY 3 41 " - " VAL N 40 " " SER 3 42 " - " GLY N 41 " " LYS 3 43 " - " SER N 42 " " THR 3 44 " - " LYS N 43 " " LYS 3 45 " - " THR N 44 " " GLU 3 46 " - " LYS N 45 " " GLY 3 47 " - " GLU N 46 " " VAL 3 48 " - " GLY N 47 " " VAL 3 49 " - " VAL N 48 " " HIS 3 50 " - " VAL N 49 " " GLY 3 51 " - " HIS N 50 " " VAL 3 52 " - " GLY N 51 " " ALA 3 53 " - " VAL N 52 " " THR 3 54 " - " ALA N 53 " " VAL 3 55 " - " THR N 54 " " ALA 3 56 " - " VAL N 55 " " GLU 3 57 " - " ALA N 56 " " LYS 3 58 " - " GLU N 57 " " LYS 3 60 " - " THR N 59 " " GLN 3 62 " - " GLU N 61 " " GLY 3 68 " - " GLY N 67 " " ALA 3 69 " - " GLY N 68 " " VAL 3 70 " - " ALA N 69 " " VAL 3 71 " - " VAL N 70 " " THR 3 72 " - " VAL N 71 " " GLY 3 73 " - " THR N 72 " " THR 3 81 " - " LYS N 80 " " VAL 3 82 " - " THR N 81 " " GLU 3 83 " - " VAL N 82 " " GLY 3 84 " - " GLU N 83 " " ALA 3 85 " - " GLY N 84 " " GLY 3 86 " - " ALA N 85 " " SER 3 87 " - " GLY N 86 " " ILE 3 88 " - " SER N 87 " " ALA 3 90 " - " ALA N 89 " " ALA 3 91 " - " ALA N 90 " " THR 3 92 " - " ALA N 91 " " GLY 3 93 " - " THR N 92 " " VAL 3 95 " - " PHE N 94 " " LYS 3 97 " - " LYS N 96 " " UNK 4 6 " - " UNK O 5 " " UNK 5 6 " - " UNK P 5 " " VAL 6 15 " - " GLY e 14 " " VAL 6 16 " - " VAL e 15 " " ALA 6 17 " - " VAL e 16 " " ALA 6 18 " - " ALA e 17 " " ALA 6 19 " - " ALA e 18 " " LYS 6 21 " - " GLU e 20 " " LYS 6 23 " - " THR e 22 " " GLY 6 25 " - " GLN e 24 " " SER 6 42 " - " GLY e 41 " " VAL 6 48 " - " GLY A 47 " " HIS 6 50 " - " VAL e 49 " " THR 6 59 " - " LYS e 58 " " LYS 6 60 " - " THR e 59 " " GLU 6 61 " - " LYS e 60 " " GLN 6 62 " - " GLU e 61 " " VAL 6 63 " - " GLN e 62 " " THR 6 64 " - " VAL e 63 " " ASN 6 65 " - " THR e 64 " " VAL 6 66 " - " ASN e 65 " " GLY 6 67 " - " VAL e 66 " " ALA 6 69 " - " GLY e 68 " " VAL 6 71 " - " VAL e 70 " " GLY 6 73 " - " THR e 72 " " VAL 6 74 " - " GLY e 73 " " THR 6 75 " - " VAL e 74 " " ALA 6 76 " - " THR e 75 " " VAL 6 77 " - " ALA e 76 " " ALA 6 78 " - " VAL e 77 " " GLN 6 79 " - " ALA e 78 " " LYS 6 80 " - " GLN e 79 " " GLU 6 83 " - " VAL e 82 " " ALA 6 85 " - " GLY A 84 " " SER 6 87 " - " GLY e 86 " " ALA 6 89 " - " ILE e 88 " " PHE 6 94 " - " GLY A 93 " " VAL 6 95 " - " PHE A 94 " " LYS 6 96 " - " VAL e 95 " " LYS 6 97 " - " LYS A 96 " " ASP 6 98 " - " LYS e 97 " " GLN 6 99 " - " ASP e 98 " " LEU 6 100 " - " GLN e 99 " " VAL 7 15 " - " GLY f 14 " " VAL 7 16 " - " VAL f 15 " " ALA 7 17 " - " VAL f 16 " " ALA 7 18 " - " ALA f 17 " " ALA 7 19 " - " ALA f 18 " " LYS 7 21 " - " GLU f 20 " " LYS 7 23 " - " THR f 22 " " GLY 7 25 " - " GLN f 24 " " SER 7 42 " - " GLY f 41 " " VAL 7 48 " - " GLY C 47 " " HIS 7 50 " - " VAL f 49 " " THR 7 59 " - " LYS f 58 " " LYS 7 60 " - " THR f 59 " " GLU 7 61 " - " LYS f 60 " " GLN 7 62 " - " GLU f 61 " " VAL 7 63 " - " GLN f 62 " " THR 7 64 " - " VAL f 63 " " ASN 7 65 " - " THR f 64 " " VAL 7 66 " - " ASN f 65 " " GLY 7 67 " - " VAL f 66 " " ALA 7 69 " - " GLY f 68 " " VAL 7 71 " - " VAL f 70 " " GLY 7 73 " - " THR f 72 " " VAL 7 74 " - " GLY f 73 " " THR 7 75 " - " VAL f 74 " " ALA 7 76 " - " THR f 75 " " VAL 7 77 " - " ALA f 76 " " ALA 7 78 " - " VAL f 77 " " GLN 7 79 " - " ALA f 78 " " LYS 7 80 " - " GLN f 79 " " GLU 7 83 " - " VAL f 82 " " ALA 7 85 " - " GLY C 84 " " SER 7 87 " - " GLY f 86 " " ALA 7 89 " - " ILE f 88 " " PHE 7 94 " - " GLY C 93 " " VAL 7 95 " - " PHE C 94 " " LYS 7 96 " - " VAL f 95 " " LYS 7 97 " - " LYS C 96 " " ASP 7 98 " - " LYS f 97 " " GLN 7 99 " - " ASP f 98 " " LEU 7 100 " - " GLN f 99 " " UNK 8 2 " - " UNK g 1 " " UNK 8 3 " - " UNK g 2 " " UNK 8 4 " - " UNK g 3 " " UNK 8 5 " - " UNK g 4 " " UNK 8 6 " - " UNK B 5 " " UNK 8 7 " - " UNK g 6 " " UNK 8 8 " - " UNK g 7 " " UNK 8 9 " - " UNK B 8 " " UNK 9 2 " - " UNK h 1 " " UNK 9 3 " - " UNK h 2 " " UNK 9 4 " - " UNK h 3 " " UNK 9 5 " - " UNK h 4 " " UNK 9 6 " - " UNK D 5 " " UNK 9 7 " - " UNK D 6 " " UNK 9 8 " - " UNK h 7 " " UNK 9 9 " - " UNK D 8 " " GLU A 20 " - " ALA 6 19 " " THR A 22 " - " LYS e 21 " " GLN A 24 " - " LYS e 23 " " LYS A 43 " - " SER e 42 " " VAL A 48 " - " GLY e 47 " " GLY A 68 " - " GLY e 67 " " THR A 81 " - " LYS e 80 " " VAL A 82 " - " THR 6 81 " " ALA A 85 " - " GLY e 84 " " PHE A 94 " - " GLY e 93 " " VAL A 95 " - " PHE e 94 " " LYS A 97 " - " LYS e 96 " " UNK B 6 " - " UNK g 5 " " UNK B 9 " - " UNK g 8 " " GLU C 20 " - " ALA 7 19 " " THR C 22 " - " LYS f 21 " " GLN C 24 " - " LYS f 23 " " LYS C 43 " - " SER f 42 " " VAL C 48 " - " GLY f 47 " " GLY C 68 " - " GLY f 67 " " THR C 81 " - " LYS f 80 " " VAL C 82 " - " THR 7 81 " " ALA C 85 " - " GLY f 84 " " PHE C 94 " - " GLY f 93 " " VAL C 95 " - " PHE f 94 " " LYS C 97 " - " LYS f 96 " " UNK D 6 " - " UNK h 5 " " UNK D 7 " - " UNK h 6 " " UNK D 9 " - " UNK h 8 " " GLU E 20 " - " ALA Y 19 " " THR E 22 " - " LYS U 21 " " LYS E 23 " - " THR Y 22 " " GLN E 24 " - " LYS U 23 " " GLY E 25 " - " GLN Y 24 " " VAL E 37 " - " GLY Y 36 " " LEU E 38 " - " VAL U 37 " " TYR E 39 " - " LEU U 38 " " VAL E 40 " - " TYR U 39 " " GLY E 41 " - " VAL U 40 " " SER E 42 " - " GLY Y 41 " " LYS E 43 " - " SER U 42 " " THR E 44 " - " LYS U 43 " " LYS E 45 " - " THR U 44 " " GLU E 46 " - " LYS U 45 " " GLY E 47 " - " GLU U 46 " " VAL E 49 " - " VAL U 48 " " HIS E 50 " - " VAL Y 49 " " GLY E 51 " - " HIS U 50 " " VAL E 52 " - " GLY U 51 " " ALA E 53 " - " VAL U 52 " " THR E 54 " - " ALA U 53 " " VAL E 55 " - " THR U 54 " " ALA E 56 " - " VAL U 55 " " GLU E 57 " - " ALA U 56 " " LYS E 58 " - " GLU U 57 " " LYS E 60 " - " THR Y 59 " " GLN E 62 " - " GLU Y 61 " " ALA E 69 " - " GLY Y 68 " " VAL E 70 " - " ALA U 69 " " VAL E 71 " - " VAL Y 70 " " THR E 72 " - " VAL U 71 " " GLY E 73 " - " THR Y 72 " " THR E 81 " - " LYS U 80 " " VAL E 82 " - " THR Y 81 " " GLY E 84 " - " GLU Y 83 " " GLY E 86 " - " ALA U 85 " " SER E 87 " - " GLY Y 86 " " ILE E 88 " - " SER U 87 " " ALA E 90 " - " ALA U 89 " " ALA E 91 " - " ALA U 90 " " THR E 92 " - " ALA U 91 " " GLY E 93 " - " THR U 92 " " GLU F 20 " - " ALA Z 19 " " THR F 22 " - " LYS V 21 " " LYS F 23 " - " THR Z 22 " " GLN F 24 " - " LYS V 23 " " GLY F 25 " - " GLN Z 24 " " VAL F 37 " - " GLY Z 36 " " LEU F 38 " - " VAL V 37 " " TYR F 39 " - " LEU V 38 " " VAL F 40 " - " TYR V 39 " " GLY F 41 " - " VAL V 40 " " SER F 42 " - " GLY Z 41 " " LYS F 43 " - " SER V 42 " " THR F 44 " - " LYS V 43 " " LYS F 45 " - " THR V 44 " " GLU F 46 " - " LYS V 45 " " GLY F 47 " - " GLU V 46 " " VAL F 49 " - " VAL V 48 " " HIS F 50 " - " VAL Z 49 " " GLY F 51 " - " HIS V 50 " " VAL F 52 " - " GLY V 51 " " ALA F 53 " - " VAL V 52 " " THR F 54 " - " ALA V 53 " " VAL F 55 " - " THR V 54 " " ALA F 56 " - " VAL V 55 " " GLU F 57 " - " ALA V 56 " " LYS F 58 " - " GLU V 57 " " LYS F 60 " - " THR Z 59 " " GLN F 62 " - " GLU Z 61 " " ALA F 69 " - " GLY Z 68 " " VAL F 70 " - " ALA V 69 " " VAL F 71 " - " VAL Z 70 " " THR F 72 " - " VAL V 71 " " GLY F 73 " - " THR Z 72 " " THR F 81 " - " LYS V 80 " " VAL F 82 " - " THR Z 81 " " GLY F 84 " - " GLU Z 83 " " GLY F 86 " - " ALA V 85 " " SER F 87 " - " GLY Z 86 " " ILE F 88 " - " SER V 87 " " ALA F 90 " - " ALA V 89 " " ALA F 91 " - " ALA V 90 " " THR F 92 " - " ALA V 91 " " GLY F 93 " - " THR V 92 " " VAL I 15 " - " GLY q 14 " " VAL I 16 " - " VAL q 15 " " ALA I 17 " - " VAL q 16 " " ALA I 18 " - " ALA q 17 " " ALA I 19 " - " ALA q 18 " " LYS I 21 " - " GLU q 20 " " LYS I 23 " - " THR q 22 " " GLY I 25 " - " GLN q 24 " " SER I 42 " - " GLY q 41 " " VAL I 48 " - " GLY a 47 " " HIS I 50 " - " VAL q 49 " " THR I 59 " - " LYS q 58 " " LYS I 60 " - " THR q 59 " " GLU I 61 " - " LYS q 60 " " GLN I 62 " - " GLU q 61 " " VAL I 63 " - " GLN q 62 " " THR I 64 " - " VAL q 63 " " ASN I 65 " - " THR q 64 " " VAL I 66 " - " ASN q 65 " " GLY I 67 " - " VAL q 66 " " ALA I 69 " - " GLY q 68 " " VAL I 71 " - " VAL q 70 " " GLY I 73 " - " THR q 72 " " VAL I 74 " - " GLY q 73 " " THR I 75 " - " VAL q 74 " " ALA I 76 " - " THR q 75 " " VAL I 77 " - " ALA q 76 " " ALA I 78 " - " VAL q 77 " " GLN I 79 " - " ALA q 78 " " LYS I 80 " - " GLN q 79 " " GLU I 83 " - " VAL q 82 " " ALA I 85 " - " GLY a 84 " " SER I 87 " - " GLY q 86 " " ALA I 89 " - " ILE q 88 " " PHE I 94 " - " GLY a 93 " " VAL I 95 " - " PHE a 94 " " LYS I 96 " - " VAL q 95 " " LYS I 97 " - " LYS a 96 " " ASP I 98 " - " LYS q 97 " " GLN I 99 " - " ASP q 98 " " LEU I 100 " - " GLN q 99 " " VAL J 15 " - " GLY r 14 " " VAL J 16 " - " VAL r 15 " " ALA J 17 " - " VAL r 16 " " ALA J 18 " - " ALA r 17 " " ALA J 19 " - " ALA r 18 " " LYS J 21 " - " GLU r 20 " " LYS J 23 " - " THR r 22 " " GLY J 25 " - " GLN r 24 " " SER J 42 " - " GLY r 41 " " VAL J 48 " - " GLY b 47 " " HIS J 50 " - " VAL r 49 " " THR J 59 " - " LYS r 58 " " LYS J 60 " - " THR r 59 " " GLU J 61 " - " LYS r 60 " " GLN J 62 " - " GLU r 61 " " VAL J 63 " - " GLN r 62 " " THR J 64 " - " VAL r 63 " " ASN J 65 " - " THR r 64 " " VAL J 66 " - " ASN r 65 " " GLY J 67 " - " VAL r 66 " " ALA J 69 " - " GLY r 68 " " VAL J 71 " - " VAL r 70 " " GLY J 73 " - " THR r 72 " " VAL J 74 " - " GLY r 73 " " THR J 75 " - " VAL r 74 " " ALA J 76 " - " THR r 75 " " VAL J 77 " - " ALA r 76 " " ALA J 78 " - " VAL r 77 " " GLN J 79 " - " ALA r 78 " " LYS J 80 " - " GLN r 79 " " GLU J 83 " - " VAL r 82 " " ALA J 85 " - " GLY b 84 " " SER J 87 " - " GLY r 86 " " ALA J 89 " - " ILE r 88 " " PHE J 94 " - " GLY b 93 " " VAL J 95 " - " PHE b 94 " " LYS J 96 " - " VAL r 95 " " LYS J 97 " - " LYS b 96 " " ASP J 98 " - " LYS r 97 " " GLN J 99 " - " ASP r 98 " " LEU J 100 " - " GLN r 99 " " UNK K 2 " - " UNK s 1 " " UNK K 3 " - " UNK s 2 " " UNK K 4 " - " UNK s 3 " " UNK K 5 " - " UNK s 4 " " UNK K 6 " - " UNK c 5 " " UNK K 7 " - " UNK s 6 " " UNK K 8 " - " UNK s 7 " " UNK K 9 " - " UNK c 8 " " UNK L 2 " - " UNK t 1 " " UNK L 3 " - " UNK t 2 " " UNK L 4 " - " UNK t 3 " " UNK L 5 " - " UNK t 4 " " UNK L 6 " - " UNK d 5 " " UNK L 7 " - " UNK d 6 " " UNK L 8 " - " UNK t 7 " " UNK L 9 " - " UNK d 8 " " VAL M 15 " - " GLY 2 14 " " VAL M 16 " - " VAL 2 15 " " ALA M 17 " - " VAL 2 16 " " ALA M 18 " - " ALA 2 17 " " ALA M 19 " - " ALA 2 18 " " GLU M 20 " - " ALA 2 19 " " LYS M 21 " - " GLU 2 20 " " THR M 22 " - " LYS 2 21 " " LYS M 23 " - " THR 2 22 " " GLN M 24 " - " LYS 2 23 " " GLY M 25 " - " GLN 2 24 " " SER M 42 " - " GLY 2 41 " " LYS M 43 " - " SER 2 42 " " VAL M 48 " - " GLY 2 47 " " HIS M 50 " - " VAL 2 49 " " THR M 59 " - " LYS 2 58 " " LYS M 60 " - " THR 2 59 " " GLU M 61 " - " LYS 2 60 " " GLN M 62 " - " GLU 2 61 " " VAL M 63 " - " GLN 2 62 " " THR M 64 " - " VAL 2 63 " " ASN M 65 " - " THR 2 64 " " VAL M 66 " - " ASN 2 65 " " GLY M 67 " - " VAL 2 66 " " GLY M 68 " - " GLY 2 67 " " ALA M 69 " - " GLY 2 68 " " VAL M 71 " - " VAL 2 70 " " GLY M 73 " - " THR 2 72 " " VAL M 74 " - " GLY 2 73 " " THR M 75 " - " VAL 2 74 " " ALA M 76 " - " THR 2 75 " " VAL M 77 " - " ALA 2 76 " " ALA M 78 " - " VAL 2 77 " " GLN M 79 " - " ALA 2 78 " " LYS M 80 " - " GLN 2 79 " " THR M 81 " - " LYS 2 80 " " GLU M 83 " - " VAL 2 82 " " ALA M 85 " - " GLY 2 84 " " SER M 87 " - " GLY 2 86 " " ALA M 89 " - " ILE 2 88 " " PHE M 94 " - " GLY 2 93 " " VAL M 95 " - " PHE 2 94 " " LYS M 96 " - " VAL 2 95 " " LYS M 97 " - " LYS 2 96 " " ASP M 98 " - " LYS 2 97 " " GLN M 99 " - " ASP 2 98 " " LEU M 100 " - " GLN 2 99 " " VAL N 15 " - " GLY 3 14 " " VAL N 16 " - " VAL 3 15 " " ALA N 17 " - " VAL 3 16 " " ALA N 18 " - " ALA 3 17 " " ALA N 19 " - " ALA 3 18 " " GLU N 20 " - " ALA 3 19 " " LYS N 21 " - " GLU 3 20 " " THR N 22 " - " LYS 3 21 " " LYS N 23 " - " THR 3 22 " " GLN N 24 " - " LYS 3 23 " " GLY N 25 " - " GLN 3 24 " " SER N 42 " - " GLY 3 41 " " LYS N 43 " - " SER 3 42 " " VAL N 48 " - " GLY 3 47 " " HIS N 50 " - " VAL 3 49 " " THR N 59 " - " LYS 3 58 " " LYS N 60 " - " THR 3 59 " " GLU N 61 " - " LYS 3 60 " " GLN N 62 " - " GLU 3 61 " " VAL N 63 " - " GLN 3 62 " " THR N 64 " - " VAL 3 63 " " ASN N 65 " - " THR 3 64 " " VAL N 66 " - " ASN 3 65 " " GLY N 67 " - " VAL 3 66 " " GLY N 68 " - " GLY 3 67 " " ALA N 69 " - " GLY 3 68 " " VAL N 71 " - " VAL 3 70 " " GLY N 73 " - " THR 3 72 " " VAL N 74 " - " GLY 3 73 " " THR N 75 " - " VAL 3 74 " " ALA N 76 " - " THR 3 75 " " VAL N 77 " - " ALA 3 76 " " ALA N 78 " - " VAL 3 77 " " GLN N 79 " - " ALA 3 78 " " LYS N 80 " - " GLN 3 79 " " THR N 81 " - " LYS 3 80 " " GLU N 83 " - " VAL 3 82 " " ALA N 85 " - " GLY 3 84 " " SER N 87 " - " GLY 3 86 " " ALA N 89 " - " ILE 3 88 " " PHE N 94 " - " GLY 3 93 " " VAL N 95 " - " PHE 3 94 " " LYS N 96 " - " VAL 3 95 " " LYS N 97 " - " LYS 3 96 " " ASP N 98 " - " LYS 3 97 " " GLN N 99 " - " ASP 3 98 " " LEU N 100 " - " GLN 3 99 " " UNK O 2 " - " UNK 4 1 " " UNK O 3 " - " UNK 4 2 " " UNK O 4 " - " UNK 4 3 " " UNK O 5 " - " UNK 4 4 " " UNK O 6 " - " UNK 4 5 " " UNK O 7 " - " UNK 4 6 " " UNK O 8 " - " UNK 4 7 " " UNK O 9 " - " UNK 4 8 " " UNK P 2 " - " UNK 5 1 " " UNK P 3 " - " UNK 5 2 " " UNK P 4 " - " UNK 5 3 " " UNK P 5 " - " UNK 5 4 " " UNK P 6 " - " UNK 5 5 " " UNK P 7 " - " UNK 5 6 " " UNK P 8 " - " UNK 5 7 " " UNK P 9 " - " UNK 5 8 " " VAL U 15 " - " GLY E 14 " " VAL U 16 " - " VAL E 15 " " ALA U 17 " - " VAL E 16 " " ALA U 18 " - " ALA E 17 " " ALA U 19 " - " ALA E 18 " " LYS U 21 " - " GLU E 20 " " LYS U 23 " - " THR E 22 " " GLY U 25 " - " GLN E 24 " " SER U 42 " - " GLY E 41 " " VAL U 48 " - " GLY Y 47 " " HIS U 50 " - " VAL E 49 " " THR U 59 " - " LYS E 58 " " LYS U 60 " - " THR E 59 " " GLU U 61 " - " LYS E 60 " " GLN U 62 " - " GLU E 61 " " VAL U 63 " - " GLN E 62 " " THR U 64 " - " VAL E 63 " " ASN U 65 " - " THR E 64 " " VAL U 66 " - " ASN E 65 " " GLY U 67 " - " VAL E 66 " " ALA U 69 " - " GLY E 68 " " VAL U 71 " - " VAL E 70 " " GLY U 73 " - " THR E 72 " " VAL U 74 " - " GLY E 73 " " THR U 75 " - " VAL E 74 " " ALA U 76 " - " THR E 75 " " VAL U 77 " - " ALA E 76 " " ALA U 78 " - " VAL E 77 " " GLN U 79 " - " ALA E 78 " " LYS U 80 " - " GLN E 79 " " GLU U 83 " - " VAL E 82 " " ALA U 85 " - " GLY Y 84 " " SER U 87 " - " GLY E 86 " " ALA U 89 " - " ILE E 88 " " PHE U 94 " - " GLY Y 93 " " VAL U 95 " - " PHE Y 94 " " LYS U 96 " - " VAL E 95 " " LYS U 97 " - " LYS Y 96 " " ASP U 98 " - " LYS E 97 " " GLN U 99 " - " ASP E 98 " " LEU U 100 " - " GLN E 99 " " VAL V 15 " - " GLY F 14 " " VAL V 16 " - " VAL F 15 " " ALA V 17 " - " VAL F 16 " " ALA V 18 " - " ALA F 17 " " ALA V 19 " - " ALA F 18 " " LYS V 21 " - " GLU F 20 " " LYS V 23 " - " THR F 22 " " GLY V 25 " - " GLN F 24 " " SER V 42 " - " GLY F 41 " " VAL V 48 " - " GLY Z 47 " " HIS V 50 " - " VAL F 49 " " THR V 59 " - " LYS F 58 " " LYS V 60 " - " THR F 59 " " GLU V 61 " - " LYS F 60 " " GLN V 62 " - " GLU F 61 " " VAL V 63 " - " GLN F 62 " " THR V 64 " - " VAL F 63 " " ASN V 65 " - " THR F 64 " " VAL V 66 " - " ASN F 65 " " GLY V 67 " - " VAL F 66 " " ALA V 69 " - " GLY F 68 " " VAL V 71 " - " VAL F 70 " " GLY V 73 " - " THR F 72 " " VAL V 74 " - " GLY Z 73 " " THR V 75 " - " VAL F 74 " " ALA V 76 " - " THR F 75 " " VAL V 77 " - " ALA F 76 " " ALA V 78 " - " VAL F 77 " " GLN V 79 " - " ALA F 78 " " LYS V 80 " - " GLN F 79 " " GLU V 83 " - " VAL F 82 " " ALA V 85 " - " GLY Z 84 " " SER V 87 " - " GLY F 86 " " ALA V 89 " - " ILE F 88 " " PHE V 94 " - " GLY Z 93 " " VAL V 95 " - " PHE Z 94 " " LYS V 96 " - " VAL F 95 " " LYS V 97 " - " LYS Z 96 " " ASP V 98 " - " LYS F 97 " " GLN V 99 " - " ASP F 98 " " LEU V 100 " - " GLN F 99 " " UNK W 2 " - " UNK G 1 " " UNK W 3 " - " UNK G 2 " " UNK W 4 " - " UNK G 3 " " UNK W 5 " - " UNK G 4 " " UNK W 6 " - " UNK 0 5 " " UNK W 7 " - " UNK G 6 " " UNK W 8 " - " UNK G 7 " " UNK W 9 " - " UNK 0 8 " " UNK X 2 " - " UNK H 1 " " UNK X 3 " - " UNK H 2 " " UNK X 4 " - " UNK H 3 " " UNK X 5 " - " UNK H 4 " " UNK X 6 " - " UNK 1 5 " " UNK X 7 " - " UNK 1 6 " " UNK X 8 " - " UNK H 7 " " UNK X 9 " - " UNK 1 8 " " GLU Y 20 " - " ALA U 19 " " THR Y 22 " - " LYS E 21 " " GLN Y 24 " - " LYS E 23 " " LYS Y 43 " - " SER E 42 " " VAL Y 48 " - " GLY E 47 " " GLY Y 68 " - " GLY E 67 " " THR Y 81 " - " LYS E 80 " " VAL Y 82 " - " THR U 81 " " ALA Y 85 " - " GLY E 84 " " PHE Y 94 " - " GLY E 93 " " VAL Y 95 " - " PHE E 94 " " LYS Y 97 " - " LYS E 96 " " GLU Z 20 " - " ALA V 19 " " THR Z 22 " - " LYS F 21 " " GLN Z 24 " - " LYS F 23 " " LYS Z 43 " - " SER F 42 " " VAL Z 48 " - " GLY F 47 " " GLY Z 68 " - " GLY F 67 " " VAL Z 74 " - " GLY F 73 " " THR Z 81 " - " LYS F 80 " " VAL Z 82 " - " THR V 81 " " ALA Z 85 " - " GLY F 84 " " PHE Z 94 " - " GLY F 93 " " VAL Z 95 " - " PHE F 94 " " LYS Z 97 " - " LYS F 96 " " GLU a 20 " - " ALA I 19 " " THR a 22 " - " LYS q 21 " " GLN a 24 " - " LYS q 23 " " LYS a 43 " - " SER q 42 " " VAL a 48 " - " GLY q 47 " " GLY a 68 " - " GLY q 67 " " THR a 81 " - " LYS q 80 " " VAL a 82 " - " THR I 81 " " ALA a 85 " - " GLY q 84 " " PHE a 94 " - " GLY q 93 " " VAL a 95 " - " PHE q 94 " " LYS a 97 " - " LYS q 96 " " GLU b 20 " - " ALA J 19 " " THR b 22 " - " LYS r 21 " " GLN b 24 " - " LYS r 23 " " LYS b 43 " - " SER r 42 " " VAL b 48 " - " GLY r 47 " " GLY b 68 " - " GLY r 67 " " THR b 81 " - " LYS r 80 " " VAL b 82 " - " THR J 81 " " ALA b 85 " - " GLY r 84 " " PHE b 94 " - " GLY r 93 " " VAL b 95 " - " PHE r 94 " " LYS b 97 " - " LYS r 96 " " UNK c 6 " - " UNK s 5 " " UNK c 9 " - " UNK s 8 " " UNK d 6 " - " UNK t 5 " " UNK d 7 " - " UNK t 6 " " UNK d 9 " - " UNK t 8 " " GLU e 20 " - " ALA A 19 " " THR e 22 " - " LYS 6 21 " " LYS e 23 " - " THR A 22 " " GLN e 24 " - " LYS 6 23 " " GLY e 25 " - " GLN A 24 " " VAL e 37 " - " GLY A 36 " " LEU e 38 " - " VAL 6 37 " " TYR e 39 " - " LEU 6 38 " " VAL e 40 " - " TYR 6 39 " " GLY e 41 " - " VAL 6 40 " " SER e 42 " - " GLY A 41 " " LYS e 43 " - " SER 6 42 " " THR e 44 " - " LYS 6 43 " " LYS e 45 " - " THR 6 44 " " GLU e 46 " - " LYS 6 45 " " GLY e 47 " - " GLU 6 46 " " VAL e 49 " - " VAL 6 48 " " HIS e 50 " - " VAL A 49 " " GLY e 51 " - " HIS 6 50 " " VAL e 52 " - " GLY 6 51 " " ALA e 53 " - " VAL 6 52 " " THR e 54 " - " ALA 6 53 " " VAL e 55 " - " THR 6 54 " " ALA e 56 " - " VAL 6 55 " " GLU e 57 " - " ALA 6 56 " " LYS e 58 " - " GLU 6 57 " " LYS e 60 " - " THR A 59 " " GLN e 62 " - " GLU A 61 " " ALA e 69 " - " GLY A 68 " " VAL e 70 " - " ALA 6 69 " " VAL e 71 " - " VAL A 70 " " THR e 72 " - " VAL 6 71 " " GLY e 73 " - " THR A 72 " " THR e 81 " - " LYS 6 80 " " VAL e 82 " - " THR A 81 " " GLY e 84 " - " GLU A 83 " " GLY e 86 " - " ALA 6 85 " " SER e 87 " - " GLY A 86 " " ILE e 88 " - " SER 6 87 " " ALA e 90 " - " ALA 6 89 " " ALA e 91 " - " ALA 6 90 " " THR e 92 " - " ALA 6 91 " " GLY e 93 " - " THR 6 92 " " GLU f 20 " - " ALA C 19 " " THR f 22 " - " LYS 7 21 " " LYS f 23 " - " THR C 22 " " GLN f 24 " - " LYS 7 23 " " GLY f 25 " - " GLN C 24 " " VAL f 37 " - " GLY C 36 " " LEU f 38 " - " VAL 7 37 " " TYR f 39 " - " LEU 7 38 " " VAL f 40 " - " TYR 7 39 " " GLY f 41 " - " VAL 7 40 " " SER f 42 " - " GLY C 41 " " LYS f 43 " - " SER 7 42 " " THR f 44 " - " LYS 7 43 " " LYS f 45 " - " THR 7 44 " " GLU f 46 " - " LYS 7 45 " " GLY f 47 " - " GLU 7 46 " " VAL f 49 " - " VAL 7 48 " " HIS f 50 " - " VAL C 49 " " GLY f 51 " - " HIS 7 50 " " VAL f 52 " - " GLY 7 51 " " ALA f 53 " - " VAL 7 52 " " THR f 54 " - " ALA 7 53 " " VAL f 55 " - " THR 7 54 " " ALA f 56 " - " VAL 7 55 " " GLU f 57 " - " ALA 7 56 " " LYS f 58 " - " GLU 7 57 " " LYS f 60 " - " THR C 59 " " GLN f 62 " - " GLU C 61 " " ALA f 69 " - " GLY C 68 " " VAL f 70 " - " ALA 7 69 " " VAL f 71 " - " VAL C 70 " " THR f 72 " - " VAL 7 71 " " GLY f 73 " - " THR C 72 " " THR f 81 " - " LYS 7 80 " " VAL f 82 " - " THR C 81 " " GLY f 84 " - " GLU C 83 " " GLY f 86 " - " ALA 7 85 " " SER f 87 " - " GLY C 86 " " ILE f 88 " - " SER 7 87 " " ALA f 90 " - " ALA 7 89 " " ALA f 91 " - " ALA 7 90 " " THR f 92 " - " ALA 7 91 " " GLY f 93 " - " THR 7 92 " " VAL i 15 " - " GLY m 14 " " VAL i 16 " - " VAL m 15 " " ALA i 17 " - " VAL m 16 " " ALA i 18 " - " ALA m 17 " " ALA i 19 " - " ALA m 18 " " GLU i 20 " - " ALA m 19 " " LYS i 21 " - " GLU m 20 " " THR i 22 " - " LYS m 21 " " LYS i 23 " - " THR m 22 " " GLN i 24 " - " LYS m 23 " " GLY i 25 " - " GLN m 24 " " SER i 42 " - " GLY m 41 " " LYS i 43 " - " SER m 42 " " VAL i 48 " - " GLY m 47 " " HIS i 50 " - " VAL m 49 " " THR i 59 " - " LYS m 58 " " LYS i 60 " - " THR m 59 " " GLU i 61 " - " LYS m 60 " " GLN i 62 " - " GLU m 61 " " VAL i 63 " - " GLN m 62 " " THR i 64 " - " VAL m 63 " " ASN i 65 " - " THR m 64 " " VAL i 66 " - " ASN m 65 " " GLY i 67 " - " VAL m 66 " " GLY i 68 " - " GLY m 67 " " ALA i 69 " - " GLY m 68 " " VAL i 71 " - " VAL m 70 " " GLY i 73 " - " THR m 72 " " VAL i 74 " - " GLY m 73 " " THR i 75 " - " VAL m 74 " " ALA i 76 " - " THR m 75 " " VAL i 77 " - " ALA m 76 " " ALA i 78 " - " VAL m 77 " " GLN i 79 " - " ALA m 78 " " LYS i 80 " - " GLN m 79 " " THR i 81 " - " LYS m 80 " " GLU i 83 " - " VAL m 82 " " ALA i 85 " - " GLY m 84 " " SER i 87 " - " GLY m 86 " " ALA i 89 " - " ILE m 88 " " PHE i 94 " - " GLY m 93 " " VAL i 95 " - " PHE m 94 " " LYS i 96 " - " VAL m 95 " " LYS i 97 " - " LYS m 96 " " ASP i 98 " - " LYS m 97 " " GLN i 99 " - " ASP m 98 " " LEU i 100 " - " GLN m 99 " " VAL j 15 " - " GLY n 14 " " VAL j 16 " - " VAL n 15 " " ALA j 17 " - " VAL n 16 " " ALA j 18 " - " ALA n 17 " " ALA j 19 " - " ALA n 18 " " GLU j 20 " - " ALA n 19 " " LYS j 21 " - " GLU n 20 " " THR j 22 " - " LYS n 21 " " LYS j 23 " - " THR n 22 " " GLN j 24 " - " LYS n 23 " " GLY j 25 " - " GLN n 24 " " SER j 42 " - " GLY n 41 " " LYS j 43 " - " SER n 42 " " VAL j 48 " - " GLY n 47 " " HIS j 50 " - " VAL n 49 " " THR j 59 " - " LYS n 58 " " LYS j 60 " - " THR n 59 " " GLU j 61 " - " LYS n 60 " " GLN j 62 " - " GLU n 61 " " VAL j 63 " - " GLN n 62 " " THR j 64 " - " VAL n 63 " " ASN j 65 " - " THR n 64 " " VAL j 66 " - " ASN n 65 " " GLY j 67 " - " VAL n 66 " " GLY j 68 " - " GLY n 67 " " ALA j 69 " - " GLY n 68 " " VAL j 71 " - " VAL n 70 " " GLY j 73 " - " THR n 72 " " VAL j 74 " - " GLY n 73 " " THR j 75 " - " VAL n 74 " " ALA j 76 " - " THR n 75 " " VAL j 77 " - " ALA n 76 " " ALA j 78 " - " VAL n 77 " " GLN j 79 " - " ALA n 78 " " LYS j 80 " - " GLN n 79 " " THR j 81 " - " LYS n 80 " " GLU j 83 " - " VAL n 82 " " ALA j 85 " - " GLY n 84 " " SER j 87 " - " GLY n 86 " " ALA j 89 " - " ILE n 88 " " PHE j 94 " - " GLY n 93 " " VAL j 95 " - " PHE n 94 " " LYS j 96 " - " VAL n 95 " " LYS j 97 " - " LYS n 96 " " ASP j 98 " - " LYS n 97 " " GLN j 99 " - " ASP n 98 " " LEU j 100 " - " GLN n 99 " " UNK k 2 " - " UNK o 1 " " UNK k 3 " - " UNK o 2 " " UNK k 4 " - " UNK o 3 " " UNK k 5 " - " UNK o 4 " " UNK k 6 " - " UNK o 5 " " UNK k 7 " - " UNK o 6 " " UNK k 8 " - " UNK o 7 " " UNK k 9 " - " UNK o 8 " " UNK l 2 " - " UNK p 1 " " UNK l 3 " - " UNK p 2 " " UNK l 4 " - " UNK p 3 " " UNK l 5 " - " UNK p 4 " " UNK l 6 " - " UNK p 5 " " UNK l 7 " - " UNK p 6 " " UNK l 8 " - " UNK p 7 " " UNK l 9 " - " UNK p 8 " " VAL m 16 " - " VAL i 15 " " ALA m 18 " - " ALA i 17 " " GLU m 20 " - " ALA i 19 " " LYS m 21 " - " GLU i 20 " " THR m 22 " - " LYS i 21 " " LYS m 23 " - " THR i 22 " " GLN m 24 " - " LYS i 23 " " GLY m 25 " - " GLN i 24 " " VAL m 37 " - " GLY i 36 " " LEU m 38 " - " VAL i 37 " " TYR m 39 " - " LEU i 38 " " VAL m 40 " - " TYR i 39 " " GLY m 41 " - " VAL i 40 " " SER m 42 " - " GLY i 41 " " LYS m 43 " - " SER i 42 " " THR m 44 " - " LYS i 43 " " LYS m 45 " - " THR i 44 " " GLU m 46 " - " LYS i 45 " " GLY m 47 " - " GLU i 46 " " VAL m 48 " - " GLY i 47 " " VAL m 49 " - " VAL i 48 " " HIS m 50 " - " VAL i 49 " " GLY m 51 " - " HIS i 50 " " VAL m 52 " - " GLY i 51 " " ALA m 53 " - " VAL i 52 " " THR m 54 " - " ALA i 53 " " VAL m 55 " - " THR i 54 " " ALA m 56 " - " VAL i 55 " " GLU m 57 " - " ALA i 56 " " LYS m 58 " - " GLU i 57 " " LYS m 60 " - " THR i 59 " " GLN m 62 " - " GLU i 61 " " GLY m 68 " - " GLY i 67 " " ALA m 69 " - " GLY i 68 " " VAL m 70 " - " ALA i 69 " " VAL m 71 " - " VAL i 70 " " THR m 72 " - " VAL i 71 " " GLY m 73 " - " THR i 72 " " THR m 81 " - " LYS i 80 " " VAL m 82 " - " THR i 81 " " GLU m 83 " - " VAL i 82 " " GLY m 84 " - " GLU i 83 " " ALA m 85 " - " GLY i 84 " " GLY m 86 " - " ALA i 85 " " SER m 87 " - " GLY i 86 " " ILE m 88 " - " SER i 87 " " ALA m 90 " - " ALA i 89 " " ALA m 91 " - " ALA i 90 " " THR m 92 " - " ALA i 91 " " GLY m 93 " - " THR i 92 " " VAL m 95 " - " PHE i 94 " " LYS m 97 " - " LYS i 96 " " VAL n 16 " - " VAL j 15 " " ALA n 18 " - " ALA j 17 " " GLU n 20 " - " ALA j 19 " " LYS n 21 " - " GLU j 20 " " THR n 22 " - " LYS j 21 " " LYS n 23 " - " THR j 22 " " GLN n 24 " - " LYS j 23 " " GLY n 25 " - " GLN j 24 " " VAL n 37 " - " GLY j 36 " " LEU n 38 " - " VAL j 37 " " TYR n 39 " - " LEU j 38 " " VAL n 40 " - " TYR j 39 " " GLY n 41 " - " VAL j 40 " " SER n 42 " - " GLY j 41 " " LYS n 43 " - " SER j 42 " " THR n 44 " - " LYS j 43 " " LYS n 45 " - " THR j 44 " " GLU n 46 " - " LYS j 45 " " GLY n 47 " - " GLU j 46 " " VAL n 48 " - " GLY j 47 " " VAL n 49 " - " VAL j 48 " " HIS n 50 " - " VAL j 49 " " GLY n 51 " - " HIS j 50 " " VAL n 52 " - " GLY j 51 " " ALA n 53 " - " VAL j 52 " " THR n 54 " - " ALA j 53 " " VAL n 55 " - " THR j 54 " " ALA n 56 " - " VAL j 55 " " GLU n 57 " - " ALA j 56 " " LYS n 58 " - " GLU j 57 " " LYS n 60 " - " THR j 59 " " GLN n 62 " - " GLU j 61 " " GLY n 68 " - " GLY j 67 " " ALA n 69 " - " GLY j 68 " " VAL n 70 " - " ALA j 69 " " VAL n 71 " - " VAL j 70 " " THR n 72 " - " VAL j 71 " " GLY n 73 " - " THR j 72 " " THR n 81 " - " LYS j 80 " " VAL n 82 " - " THR j 81 " " GLU n 83 " - " VAL j 82 " " GLY n 84 " - " GLU j 83 " " ALA n 85 " - " GLY j 84 " " GLY n 86 " - " ALA j 85 " " SER n 87 " - " GLY j 86 " " ILE n 88 " - " SER j 87 " " ALA n 90 " - " ALA j 89 " " ALA n 91 " - " ALA j 90 " " THR n 92 " - " ALA j 91 " " GLY n 93 " - " THR j 92 " " VAL n 95 " - " PHE j 94 " " LYS n 97 " - " LYS j 96 " " UNK o 6 " - " UNK k 5 " " UNK p 6 " - " UNK l 5 " " GLU q 20 " - " ALA a 19 " " THR q 22 " - " LYS I 21 " " LYS q 23 " - " THR a 22 " " GLN q 24 " - " LYS I 23 " " GLY q 25 " - " GLN a 24 " " VAL q 37 " - " GLY a 36 " " LEU q 38 " - " VAL I 37 " " TYR q 39 " - " LEU I 38 " " VAL q 40 " - " TYR I 39 " " GLY q 41 " - " VAL I 40 " " SER q 42 " - " GLY a 41 " " LYS q 43 " - " SER I 42 " " THR q 44 " - " LYS I 43 " " LYS q 45 " - " THR I 44 " " GLU q 46 " - " LYS I 45 " " GLY q 47 " - " GLU I 46 " " VAL q 49 " - " VAL I 48 " " HIS q 50 " - " VAL a 49 " " GLY q 51 " - " HIS I 50 " " VAL q 52 " - " GLY I 51 " " ALA q 53 " - " VAL I 52 " " THR q 54 " - " ALA I 53 " " VAL q 55 " - " THR I 54 " " ALA q 56 " - " VAL I 55 " " GLU q 57 " - " ALA I 56 " " LYS q 58 " - " GLU I 57 " " LYS q 60 " - " THR a 59 " " GLN q 62 " - " GLU a 61 " " ALA q 69 " - " GLY a 68 " " VAL q 70 " - " ALA I 69 " " VAL q 71 " - " VAL a 70 " " THR q 72 " - " VAL I 71 " " GLY q 73 " - " THR a 72 " " THR q 81 " - " LYS I 80 " " VAL q 82 " - " THR a 81 " " GLY q 84 " - " GLU a 83 " " GLY q 86 " - " ALA I 85 " " SER q 87 " - " GLY a 86 " " ILE q 88 " - " SER I 87 " " ALA q 90 " - " ALA I 89 " " ALA q 91 " - " ALA I 90 " " THR q 92 " - " ALA I 91 " " GLY q 93 " - " THR I 92 " " GLU r 20 " - " ALA b 19 " " THR r 22 " - " LYS J 21 " " LYS r 23 " - " THR b 22 " " GLN r 24 " - " LYS J 23 " " GLY r 25 " - " GLN b 24 " " VAL r 37 " - " GLY b 36 " " LEU r 38 " - " VAL J 37 " " TYR r 39 " - " LEU J 38 " " VAL r 40 " - " TYR J 39 " " GLY r 41 " - " VAL J 40 " " SER r 42 " - " GLY b 41 " " LYS r 43 " - " SER J 42 " " THR r 44 " - " LYS J 43 " " LYS r 45 " - " THR J 44 " " GLU r 46 " - " LYS J 45 " " GLY r 47 " - " GLU J 46 " " VAL r 49 " - " VAL J 48 " " HIS r 50 " - " VAL b 49 " " GLY r 51 " - " HIS J 50 " " VAL r 52 " - " GLY J 51 " " ALA r 53 " - " VAL J 52 " " THR r 54 " - " ALA J 53 " " VAL r 55 " - " THR J 54 " " ALA r 56 " - " VAL J 55 " " GLU r 57 " - " ALA J 56 " " LYS r 58 " - " GLU J 57 " " LYS r 60 " - " THR b 59 " " GLN r 62 " - " GLU b 61 " " ALA r 69 " - " GLY b 68 " " VAL r 70 " - " ALA J 69 " " VAL r 71 " - " VAL b 70 " " THR r 72 " - " VAL J 71 " " GLY r 73 " - " THR b 72 " " THR r 81 " - " LYS J 80 " " VAL r 82 " - " THR b 81 " " GLY r 84 " - " GLU b 83 " " GLY r 86 " - " ALA J 85 " " SER r 87 " - " GLY b 86 " " ILE r 88 " - " SER J 87 " " ALA r 90 " - " ALA J 89 " " ALA r 91 " - " ALA J 90 " " THR r 92 " - " ALA J 91 " " GLY r 93 " - " THR J 92 " Time building additional restraints: 20.05 Conformation dependent library (CDL) restraints added in 2.2 seconds 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 20.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 3090 1.29 - 1.35: 2730 1.35 - 1.42: 450 1.42 - 1.48: 3088 1.48 - 1.55: 7892 Bond restraints: 17250 Sorted by residual: bond pdb=" CA ALA q 89 " pdb=" CB ALA q 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.50e+00 bond pdb=" CA ALA U 89 " pdb=" CB ALA U 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.48e+00 bond pdb=" CA ALA m 89 " pdb=" CB ALA m 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.46e+00 bond pdb=" CA ALA Y 89 " pdb=" CB ALA Y 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.43e+00 bond pdb=" CA ALA u 89 " pdb=" CB ALA u 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.42e+00 ... (remaining 17245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 18500 1.30 - 2.59: 4042 2.59 - 3.89: 521 3.89 - 5.18: 127 5.18 - 6.48: 60 Bond angle restraints: 23250 Sorted by residual: angle pdb=" C HIS m 50 " pdb=" CA HIS m 50 " pdb=" CB HIS m 50 " ideal model delta sigma weight residual 109.65 116.13 -6.48 1.75e+00 3.27e-01 1.37e+01 angle pdb=" C HIS E 50 " pdb=" CA HIS E 50 " pdb=" CB HIS E 50 " ideal model delta sigma weight residual 109.65 116.12 -6.47 1.75e+00 3.27e-01 1.37e+01 angle pdb=" C HIS 2 50 " pdb=" CA HIS 2 50 " pdb=" CB HIS 2 50 " ideal model delta sigma weight residual 109.65 116.11 -6.46 1.75e+00 3.27e-01 1.36e+01 angle pdb=" C HIS I 50 " pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " ideal model delta sigma weight residual 109.65 116.11 -6.46 1.75e+00 3.27e-01 1.36e+01 angle pdb=" C HIS a 50 " pdb=" CA HIS a 50 " pdb=" CB HIS a 50 " ideal model delta sigma weight residual 109.65 116.11 -6.46 1.75e+00 3.27e-01 1.36e+01 ... (remaining 23245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11254 18.00 - 36.00: 833 36.00 - 53.99: 813 53.99 - 71.99: 342 71.99 - 89.99: 114 Dihedral angle restraints: 13356 sinusoidal: 5324 harmonic: 8032 Sorted by residual: dihedral pdb=" CA THR U 64 " pdb=" N THR U 64 " pdb=" C VAL E 63 " pdb=" CA VAL E 63 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA THR 6 64 " pdb=" N THR 6 64 " pdb=" C VAL e 63 " pdb=" CA VAL e 63 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA THR I 64 " pdb=" N THR I 64 " pdb=" C VAL q 63 " pdb=" CA VAL q 63 " ideal model delta harmonic sigma weight residual 180.00 163.27 16.73 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 13353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 964 0.028 - 0.056: 457 0.056 - 0.084: 421 0.084 - 0.112: 929 0.112 - 0.140: 289 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA ILE 7 88 " pdb=" N ILE 7 88 " pdb=" C ILE 7 88 " pdb=" CB ILE 7 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE N 88 " pdb=" N ILE N 88 " pdb=" C ILE N 88 " pdb=" CB ILE N 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE f 88 " pdb=" N ILE f 88 " pdb=" C ILE f 88 " pdb=" CB ILE f 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 3057 not shown) Planarity restraints: 3982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N GLN I 99 " -0.041 2.00e-02 2.50e+03 6.46e-02 4.18e+01 pdb=" CA ASP q 98 " -0.034 2.00e-02 2.50e+03 pdb=" C ASP q 98 " 0.112 2.00e-02 2.50e+03 pdb=" O ASP q 98 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N GLN 6 99 " -0.041 2.00e-02 2.50e+03 6.44e-02 4.14e+01 pdb=" CA ASP e 98 " -0.034 2.00e-02 2.50e+03 pdb=" C ASP e 98 " 0.111 2.00e-02 2.50e+03 pdb=" O ASP e 98 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N GLN U 99 " -0.041 2.00e-02 2.50e+03 6.43e-02 4.14e+01 pdb=" CA ASP E 98 " -0.034 2.00e-02 2.50e+03 pdb=" C ASP E 98 " 0.111 2.00e-02 2.50e+03 pdb=" O ASP E 98 " -0.037 2.00e-02 2.50e+03 ... (remaining 3979 not shown) Histogram of nonbonded interaction distances: 0.05 - 1.02: 10975 1.02 - 1.99: 24124 1.99 - 2.96: 51151 2.96 - 3.93: 110724 3.93 - 4.90: 242382 Warning: very small nonbonded interaction distances. Nonbonded interactions: 439356 Sorted by model distance: nonbonded pdb=" OE1 GLN V 24 " pdb=" OE1 GLN Z 24 " model vdw 0.052 3.040 nonbonded pdb=" OE1 GLN b 24 " pdb=" OE1 GLN r 24 " model vdw 0.052 3.040 nonbonded pdb=" OE1 GLN j 24 " pdb=" OE1 GLN n 24 " model vdw 0.053 3.040 nonbonded pdb=" OE1 GLN Z 24 " pdb=" OE1 GLN F 24 " model vdw 0.053 3.040 nonbonded pdb=" OE1 GLN N 24 " pdb=" OE1 GLN 3 24 " model vdw 0.053 3.040 ... (remaining 439351 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '4' selection = chain '5' selection = chain '8' selection = chain '9' selection = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'c' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain '3' selection = chain '6' selection = chain '7' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 'u' selection = chain 'v' } 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: 1.080 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 51.410 Find NCS groups from input model: 0.970 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:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.008 0.034 17250 Z= 0.553 Angle : 1.138 6.480 23250 Z= 0.687 Chirality : 0.074 0.140 3060 Planarity : 0.003 0.011 2910 Dihedral : 8.963 47.901 5700 Min Nonbonded Distance : 0.052 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.78 (0.14), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.11), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS U 50 PHE 0.010 0.003 PHE v 94 TYR 0.005 0.002 TYR v 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 58 LYS cc_start: 0.8296 (mttt) cc_final: 0.8067 (mttp) REVERT: Q 97 LYS cc_start: 0.7843 (mttt) cc_final: 0.7605 (mttm) REVERT: R 21 LYS cc_start: 0.8251 (tttt) cc_final: 0.7780 (ttpm) REVERT: R 97 LYS cc_start: 0.7937 (mttt) cc_final: 0.7670 (mttm) REVERT: u 21 LYS cc_start: 0.8089 (tttt) cc_final: 0.7500 (ttpt) REVERT: u 80 LYS cc_start: 0.8505 (tttt) cc_final: 0.6872 (mptt) REVERT: v 80 LYS cc_start: 0.8462 (tttt) cc_final: 0.6818 (mptt) REVERT: v 97 LYS cc_start: 0.7835 (mttt) cc_final: 0.7522 (mttm) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 1.5374 time to fit residues: 878.1693 Evaluate side-chains 509 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2462 > 50: distance: 216 - 341: 30.628 distance: 222 - 350: 35.626 distance: 231 - 357: 35.617 distance: 238 - 366: 34.437 distance: 247 - 375: 35.318 distance: 256 - 379: 33.707 distance: 258 - 377: 34.143 distance: 260 - 386: 34.826 distance: 267 - 393: 34.106 distance: 272 - 388: 35.399 distance: 274 - 403: 34.986 distance: 284 - 407: 34.528 distance: 337 - 341: 30.658 distance: 341 - 342: 56.628 distance: 342 - 343: 39.563 distance: 342 - 345: 69.353 distance: 343 - 344: 56.457 distance: 343 - 350: 39.760 distance: 345 - 346: 68.602 distance: 346 - 347: 70.409 distance: 347 - 348: 54.880 distance: 348 - 349: 70.747 distance: 350 - 351: 40.810 distance: 351 - 352: 40.269 distance: 351 - 354: 67.796 distance: 352 - 353: 70.195 distance: 352 - 357: 55.653 distance: 354 - 355: 56.045 distance: 354 - 356: 41.433 distance: 357 - 358: 57.481 distance: 358 - 359: 40.279 distance: 358 - 361: 47.968 distance: 359 - 360: 68.027 distance: 359 - 366: 40.441 distance: 361 - 362: 47.022 distance: 362 - 363: 55.581 distance: 363 - 364: 58.126 distance: 364 - 365: 47.167 distance: 366 - 367: 55.531 distance: 367 - 370: 38.442 distance: 368 - 369: 39.137 distance: 368 - 375: 55.731 distance: 370 - 371: 40.123 distance: 371 - 372: 57.568 distance: 372 - 373: 40.377 distance: 372 - 374: 39.929 distance: 375 - 376: 68.958 distance: 377 - 378: 55.834 distance: 377 - 379: 40.691 distance: 379 - 380: 57.389 distance: 380 - 381: 40.527 distance: 380 - 383: 57.122 distance: 381 - 382: 68.445 distance: 381 - 386: 40.800 distance: 383 - 384: 57.627 distance: 383 - 385: 33.231 distance: 386 - 387: 39.731 distance: 387 - 388: 38.580 distance: 387 - 390: 39.205 distance: 388 - 389: 39.772 distance: 388 - 393: 56.973 distance: 390 - 391: 56.818 distance: 390 - 392: 55.242 distance: 393 - 394: 56.394 distance: 394 - 395: 57.548 distance: 394 - 397: 68.916 distance: 395 - 403: 40.774 distance: 397 - 398: 42.689 distance: 398 - 399: 43.129 distance: 398 - 400: 26.543 distance: 399 - 401: 38.971 distance: 400 - 402: 57.224 distance: 401 - 402: 39.171 distance: 403 - 404: 38.824 distance: 404 - 405: 39.647 distance: 405 - 406: 69.982 distance: 405 - 407: 39.363 distance: 408 - 409: 56.766 distance: 408 - 411: 54.993 distance: 409 - 410: 40.184 distance: 409 - 414: 35.943 distance: 411 - 412: 70.093 distance: 411 - 413: 57.931