Starting phenix.real_space_refine on Wed Jul 30 06:18:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqh_23486/07_2025/7lqh_23486.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqh_23486/07_2025/7lqh_23486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqh_23486/07_2025/7lqh_23486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqh_23486/07_2025/7lqh_23486.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqh_23486/07_2025/7lqh_23486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqh_23486/07_2025/7lqh_23486.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.029 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 8640 2.51 5 N 1584 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 324 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 144 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "UA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "VA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "WA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "XA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "aA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "cA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "dA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "eA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "fA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "gA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "hA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "iA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "jA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "kA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "lA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "mA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "nA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "oA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "pA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "qA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "rA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "sA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "tA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "uA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "vA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "wA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "xA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "yA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "zA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 8.41, per 1000 atoms: 0.70 Number of scatterers: 12096 At special positions: 0 Unit cell: (89.64, 89.64, 111.24, 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 1872 8.00 N 1584 7.00 C 8640 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=35, symmetry=0 Number of additional bonds: simple=35, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 665.1 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'M' and resid 1006 through 1007 Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'T' and resid 1006 through 1007 Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'j' and resid 1006 through 1007 Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'q' and resid 1006 through 1007 Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'x' and resid 1006 through 1007 Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AB3, first strand: chain '4' and resid 1006 through 1007 Processing sheet with id=AB4, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'BA' and resid 1006 through 1007 Processing sheet with id=AB6, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'IA' and resid 1006 through 1007 Processing sheet with id=AB8, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AB9, first strand: chain 'PA' and resid 1006 through 1007 Processing sheet with id=AC1, first strand: chain 'h' and resid 2 through 6 removed outlier: 3.535A pdb=" N PHEGB 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE h 5 " --> pdb=" O PHEGB 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE2A 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE f 5 " --> pdb=" O PHE2A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEoA 105 " --> pdb=" O PHE d 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE d 5 " --> pdb=" O PHEoA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEaA 105 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE b 5 " --> pdb=" O PHEaA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHETA 105 " --> pdb=" O PHE a 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE a 5 " --> pdb=" O PHETA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHEhA 105 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE c 5 " --> pdb=" O PHEhA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEvA 105 " --> pdb=" O PHE e 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE e 5 " --> pdb=" O PHEvA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE9A 105 " --> pdb=" O PHE g 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE g 5 " --> pdb=" O PHE9A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHENB 105 " --> pdb=" O PHE i 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE i 5 " --> pdb=" O PHENB 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HB' and resid 202 through 206 removed outlier: 3.521A pdb=" N LYSIB 302 " --> pdb=" O GMA3A 208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS3A 206 " --> pdb=" O GLUIB 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAIB 308 " --> pdb=" O LYS3A 202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS4A 302 " --> pdb=" O GMApA 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSpA 206 " --> pdb=" O GLU4A 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSqA 302 " --> pdb=" O GMAbA 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSbA 206 " --> pdb=" O GLUqA 304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYScA 302 " --> pdb=" O GMAUA 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSUA 206 " --> pdb=" O GLUcA 304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAcA 308 " --> pdb=" O LYSUA 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSVA 302 " --> pdb=" O GMAiA 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSiA 206 " --> pdb=" O GLUVA 304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAVA 308 " --> pdb=" O LYSiA 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSjA 302 " --> pdb=" O GMAwA 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYSwA 206 " --> pdb=" O GLUjA 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSxA 302 " --> pdb=" O GMAAB 208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSAB 206 " --> pdb=" O GLUxA 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMAxA 308 " --> pdb=" O LYSAB 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSBB 302 " --> pdb=" O GMAOB 208 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYSOB 206 " --> pdb=" O GLUBB 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'JB' and resid 1002 through 1006 removed outlier: 3.536A pdb=" N PHEKB1105 " --> pdb=" O PHEJB1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEJB1005 " --> pdb=" O PHEKB1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE6A1105 " --> pdb=" O PHE5A1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE5A1005 " --> pdb=" O PHE6A1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEsA1105 " --> pdb=" O PHErA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHErA1005 " --> pdb=" O PHEsA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEeA1105 " --> pdb=" O PHEdA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEdA1005 " --> pdb=" O PHEeA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEXA1105 " --> pdb=" O PHEWA1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEWA1005 " --> pdb=" O PHEXA1103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHElA1105 " --> pdb=" O PHEkA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEkA1005 " --> pdb=" O PHElA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEzA1105 " --> pdb=" O PHEyA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEyA1005 " --> pdb=" O PHEzA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEDB1105 " --> pdb=" O PHECB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHECB1005 " --> pdb=" O PHEDB1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHERB1105 " --> pdb=" O PHEQB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEQB1005 " --> pdb=" O PHERB1103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LB' and resid 1202 through 1206 removed outlier: 3.521A pdb=" N LYSMB1302 " --> pdb=" O GMA7A1208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS7A1206 " --> pdb=" O GLUMB1304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAMB1308 " --> pdb=" O LYS7A1202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS8A1302 " --> pdb=" O GMAtA1208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYStA1206 " --> pdb=" O GLU8A1304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSuA1302 " --> pdb=" O GMAfA1208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSfA1206 " --> pdb=" O GLUuA1304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSgA1302 " --> pdb=" O GMAYA1208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSYA1206 " --> pdb=" O GLUgA1304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAgA1308 " --> pdb=" O LYSYA1202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSZA1302 " --> pdb=" O GMAmA1208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSmA1206 " --> pdb=" O GLUZA1304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAZA1308 " --> pdb=" O LYSmA1202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSnA1302 " --> pdb=" O GMA0A1208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS0A1206 " --> pdb=" O GLUnA1304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS1A1302 " --> pdb=" O GMAEB1208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSEB1206 " --> pdb=" O GLU1A1304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMA1A1308 " --> pdb=" O LYSEB1202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSFB1302 " --> pdb=" O GMASB1208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSSB1206 " --> pdb=" O GLUFB1304 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 1489 1.26 - 1.33: 1391 1.33 - 1.41: 3600 1.41 - 1.48: 1308 1.48 - 1.56: 4740 Bond restraints: 12528 Sorted by residual: bond pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRrA1001 " pdb=" CAL 5CRrA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRyA1001 " pdb=" CAL 5CRyA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 12523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 14239 1.98 - 3.96: 1589 3.96 - 5.94: 318 5.94 - 7.92: 108 7.92 - 9.90: 18 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.81 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.80 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR5A1001 " pdb=" CAL 5CR5A1001 " pdb=" CAA 5CR5A1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " pdb=" CAA 5CR a 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CRWA1001 " pdb=" CAL 5CRWA1001 " pdb=" CAA 5CRWA1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 4844 15.26 - 30.52: 790 30.52 - 45.79: 342 45.79 - 61.05: 198 61.05 - 76.31: 18 Dihedral angle restraints: 6192 sinusoidal: 2880 harmonic: 3312 Sorted by residual: dihedral pdb=" CA LYSMA 106 " pdb=" CB LYSMA 106 " pdb=" CG LYSMA 106 " pdb=" CD LYSMA 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.26 58.74 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYSQA1106 " pdb=" CB LYSQA1106 " pdb=" CG LYSQA1106 " pdb=" CD LYSQA1106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS 1 106 " pdb=" CB LYS 1 106 " pdb=" CG LYS 1 106 " pdb=" CD LYS 1 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.018: 407 0.018 - 0.036: 334 0.036 - 0.054: 299 0.054 - 0.073: 89 0.073 - 0.091: 23 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.06e-01 chirality pdb=" CA LYS V1202 " pdb=" N LYS V1202 " pdb=" C LYS V1202 " pdb=" CB LYS V1202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.02e-01 chirality pdb=" CA LYS Y 202 " pdb=" N LYS Y 202 " pdb=" C LYS Y 202 " pdb=" CB LYS Y 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.86e-01 ... (remaining 1149 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEUA 205 " -0.008 2.00e-02 2.50e+03 7.00e-03 8.57e-01 pdb=" CG PHEUA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEUA 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEUA 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEUA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEYA1205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-01 pdb=" CG PHEYA1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEYA1205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEYA1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEYA1205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEAB 205 " -0.009 2.00e-02 2.50e+03 6.97e-03 8.51e-01 pdb=" CG PHEAB 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEAB 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 281 2.66 - 3.22: 10092 3.22 - 3.78: 19029 3.78 - 4.34: 28093 4.34 - 4.90: 46315 Nonbonded interactions: 103810 Sorted by model distance: nonbonded pdb=" CD LYS N1102 " pdb=" OE2 GMA 9 208 " model vdw 2.098 2.752 nonbonded pdb=" OE2 GMA Y 208 " pdb=" CD LYS r1102 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS U1102 " pdb=" OE2 GMA v 208 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS k1102 " pdb=" OE2 GMANA 208 " model vdw 2.117 2.752 nonbonded pdb=" CD LYS Q 102 " pdb=" OE2 GMADA1208 " model vdw 2.118 2.752 ... (remaining 103805 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 '0' selection = chain '0A' selection = chain '1' selection = chain '1A' selection = chain '2' selection = chain '2A' selection = chain '3' selection = chain '3A' selection = chain '4' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '6A' selection = chain '7' selection = chain '7A' selection = chain '8' selection = chain '8A' selection = chain '9' selection = chain '9A' selection = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'RA' selection = chain 'RB' selection = chain 'S' selection = chain 'SA' selection = chain 'SB' selection = chain 'T' selection = chain 'TA' selection = chain 'TB' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' selection = chain 'a' selection = chain 'aA' selection = chain 'b' selection = chain 'bA' selection = chain 'c' selection = chain 'cA' selection = chain 'd' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'v' selection = chain 'vA' selection = chain 'w' selection = chain 'wA' selection = chain 'x' selection = chain 'xA' selection = chain 'y' selection = chain 'yA' selection = chain 'z' selection = chain 'zA' } 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: 0.010 Normalize map: mean=0, sd=1: 4.330 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 29.880 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.220 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.034 0.786 12563 Z= 3.145 Angle : 1.417 9.902 16272 Z= 0.592 Chirality : 0.035 0.091 1152 Planarity : 0.002 0.009 2160 Dihedral : 20.718 76.311 3888 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 31.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % 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: -5.94 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEUA 205 Details of bonding type rmsd hydrogen bonds : bond 0.31155 ( 278) hydrogen bonds : angle 15.44491 ( 786) covalent geometry : bond 0.01603 (12528) covalent geometry : angle 1.41746 (16272) Misc. bond : bond 0.57724 ( 35) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 472 time to evaluate : 1.286 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: A 4 GLU cc_start: 0.7369 (mp0) cc_final: 0.6755 (pm20) REVERT: B 4 GLU cc_start: 0.7493 (mp0) cc_final: 0.6748 (pm20) REVERT: S 306 LYS cc_start: 0.8629 (tttt) cc_final: 0.8357 (mttt) REVERT: Y 206 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8180 (ttmm) REVERT: Z 306 LYS cc_start: 0.8563 (tttt) cc_final: 0.8262 (tttt) REVERT: j 1006 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8034 (mtmt) REVERT: m 1306 LYS cc_start: 0.8633 (tttt) cc_final: 0.8339 (mttt) REVERT: o 204 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7064 (mt-10) REVERT: s 1206 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8228 (ttmm) REVERT: t 1306 LYS cc_start: 0.8695 (tttt) cc_final: 0.8441 (mttt) REVERT: v 206 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8231 (ttmm) REVERT: w 304 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7091 (mm-30) REVERT: w 306 LYS cc_start: 0.8689 (tttt) cc_final: 0.8339 (mttt) REVERT: x 1004 GLU cc_start: 0.7152 (mp0) cc_final: 0.6745 (mp0) REVERT: 0 1304 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7144 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8594 (tttt) cc_final: 0.8264 (tttt) REVERT: F 4 GLU cc_start: 0.7397 (mp0) cc_final: 0.6657 (pm20) REVERT: 3 304 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7148 (mm-30) REVERT: 6 1204 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6808 (mt-10) REVERT: 6 1206 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8366 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8772 (tttt) cc_final: 0.8420 (mttt) REVERT: G 4 GLU cc_start: 0.7313 (mp0) cc_final: 0.6485 (pm20) REVERT: 9 204 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6532 (mt-10) REVERT: AA 306 LYS cc_start: 0.8673 (tttt) cc_final: 0.8387 (mttt) REVERT: DA 1204 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7037 (mt-10) REVERT: EA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8431 (mttt) REVERT: HA 306 LYS cc_start: 0.8699 (tttt) cc_final: 0.8363 (mttt) REVERT: LA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8323 (mttt) REVERT: OA 306 LYS cc_start: 0.8570 (tttt) cc_final: 0.8318 (mttt) REVERT: SA 1306 LYS cc_start: 0.8648 (tttt) cc_final: 0.8295 (tttt) REVERT: a 2 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8344 (ttpt) REVERT: TA 104 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: TA 105 PHE cc_start: 0.9072 (t80) cc_final: 0.8761 (t80) REVERT: UA 202 LYS cc_start: 0.8784 (tttm) cc_final: 0.8340 (ttmm) REVERT: VA 305 PHE cc_start: 0.8549 (t80) cc_final: 0.8266 (t80) REVERT: WA 1003 PHE cc_start: 0.9115 (t80) cc_final: 0.8755 (t80) REVERT: WA 1005 PHE cc_start: 0.8951 (t80) cc_final: 0.8609 (t80) REVERT: WA 1007 PHE cc_start: 0.9301 (t80) cc_final: 0.8997 (t80) REVERT: XA 1103 PHE cc_start: 0.8930 (t80) cc_final: 0.8678 (t80) REVERT: XA 1107 PHE cc_start: 0.8921 (t80) cc_final: 0.8714 (t80) REVERT: YA 1202 LYS cc_start: 0.8788 (tttm) cc_final: 0.8391 (tttm) REVERT: ZA 1304 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8190 (tm-30) REVERT: aA 103 PHE cc_start: 0.9101 (t80) cc_final: 0.8425 (t80) REVERT: aA 106 LYS cc_start: 0.8822 (tttp) cc_final: 0.8564 (tttp) REVERT: bA 202 LYS cc_start: 0.8841 (tttm) cc_final: 0.8397 (ttmm) REVERT: cA 303 PHE cc_start: 0.9015 (t80) cc_final: 0.8654 (t80) REVERT: cA 304 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8429 (tm-30) REVERT: fA 1202 LYS cc_start: 0.8656 (tttm) cc_final: 0.8373 (tttm) REVERT: c 5 PHE cc_start: 0.8932 (t80) cc_final: 0.8452 (t80) REVERT: c 7 PHE cc_start: 0.9209 (t80) cc_final: 0.8995 (t80) REVERT: hA 106 LYS cc_start: 0.8870 (tttp) cc_final: 0.8657 (tttp) REVERT: iA 202 LYS cc_start: 0.8878 (tttm) cc_final: 0.8562 (ttmm) REVERT: jA 306 LYS cc_start: 0.8334 (tptp) cc_final: 0.8046 (tptp) REVERT: kA 1005 PHE cc_start: 0.9077 (t80) cc_final: 0.8703 (t80) REVERT: lA 1103 PHE cc_start: 0.8901 (t80) cc_final: 0.8521 (t80) REVERT: mA 1206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8582 (tttt) REVERT: nA 1305 PHE cc_start: 0.8662 (t80) cc_final: 0.8453 (t80) REVERT: d 3 PHE cc_start: 0.9295 (t80) cc_final: 0.8996 (t80) REVERT: d 5 PHE cc_start: 0.9090 (t80) cc_final: 0.8869 (t80) REVERT: d 7 PHE cc_start: 0.9253 (t80) cc_final: 0.8845 (t80) REVERT: oA 107 PHE cc_start: 0.8813 (t80) cc_final: 0.8347 (t80) REVERT: pA 202 LYS cc_start: 0.8916 (tttm) cc_final: 0.8524 (mmmm) REVERT: pA 206 LYS cc_start: 0.8826 (tttt) cc_final: 0.8593 (tttt) REVERT: qA 305 PHE cc_start: 0.8722 (t80) cc_final: 0.8402 (t80) REVERT: rA 1005 PHE cc_start: 0.8915 (t80) cc_final: 0.8588 (t80) REVERT: sA 1103 PHE cc_start: 0.9020 (t80) cc_final: 0.8784 (t80) REVERT: tA 1206 LYS cc_start: 0.8812 (tttt) cc_final: 0.8431 (tttt) REVERT: vA 106 LYS cc_start: 0.8825 (tttp) cc_final: 0.8561 (tttp) REVERT: wA 202 LYS cc_start: 0.8733 (tttm) cc_final: 0.8401 (mmmm) REVERT: wA 206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8503 (tttt) REVERT: xA 303 PHE cc_start: 0.8927 (t80) cc_final: 0.8677 (t80) REVERT: zA 1106 LYS cc_start: 0.8767 (tttp) cc_final: 0.8557 (tttp) REVERT: 1A 1303 PHE cc_start: 0.8829 (t80) cc_final: 0.8602 (t80) REVERT: 1A 1305 PHE cc_start: 0.8465 (t80) cc_final: 0.8239 (t80) REVERT: 3A 202 LYS cc_start: 0.8922 (tttm) cc_final: 0.8551 (mmmm) REVERT: 3A 206 LYS cc_start: 0.8739 (tttt) cc_final: 0.8527 (tttt) REVERT: 4A 306 LYS cc_start: 0.8459 (tptp) cc_final: 0.8229 (tptp) REVERT: 4A 307 PHE cc_start: 0.8508 (t80) cc_final: 0.8127 (t80) REVERT: 5A 1003 PHE cc_start: 0.9169 (t80) cc_final: 0.8731 (t80) REVERT: 5A 1005 PHE cc_start: 0.9041 (t80) cc_final: 0.8732 (t80) REVERT: 5A 1007 PHE cc_start: 0.9152 (t80) cc_final: 0.8671 (t80) REVERT: 6A 1106 LYS cc_start: 0.8863 (tttp) cc_final: 0.8585 (tttp) REVERT: 7A 1205 PHE cc_start: 0.8502 (t80) cc_final: 0.8271 (t80) REVERT: 7A 1206 LYS cc_start: 0.8695 (tttt) cc_final: 0.8343 (tttm) REVERT: 9A 104 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: 9A 106 LYS cc_start: 0.8906 (tttp) cc_final: 0.8655 (tttm) REVERT: BB 305 PHE cc_start: 0.8766 (t80) cc_final: 0.8355 (t80) REVERT: BB 307 PHE cc_start: 0.8514 (t80) cc_final: 0.8208 (t80) REVERT: CB 1003 PHE cc_start: 0.9123 (t80) cc_final: 0.8740 (t80) REVERT: CB 1005 PHE cc_start: 0.9008 (t80) cc_final: 0.8652 (t80) REVERT: CB 1007 PHE cc_start: 0.9161 (t80) cc_final: 0.8929 (t80) REVERT: DB 1106 LYS cc_start: 0.8792 (tttp) cc_final: 0.8527 (tttp) REVERT: EB 1202 LYS cc_start: 0.8867 (tttm) cc_final: 0.8491 (tttm) REVERT: EB 1206 LYS cc_start: 0.8740 (tttt) cc_final: 0.8538 (tttm) REVERT: FB 1304 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8667 (tm-30) REVERT: GB 103 PHE cc_start: 0.9078 (t80) cc_final: 0.8876 (t80) REVERT: GB 106 LYS cc_start: 0.8643 (tttp) cc_final: 0.8431 (tttm) REVERT: HB 206 LYS cc_start: 0.8809 (tttt) cc_final: 0.8555 (tttm) REVERT: IB 303 PHE cc_start: 0.8906 (t80) cc_final: 0.8678 (t80) REVERT: IB 304 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8429 (tm-30) REVERT: KB 1105 PHE cc_start: 0.8731 (t80) cc_final: 0.8308 (t80) REVERT: KB 1106 LYS cc_start: 0.8655 (tttp) cc_final: 0.8378 (tttp) REVERT: MB 1303 PHE cc_start: 0.8794 (t80) cc_final: 0.8553 (t80) REVERT: i 6 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8467 (ttpt) REVERT: NB 104 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: OB 206 LYS cc_start: 0.8866 (tttt) cc_final: 0.8654 (tttt) REVERT: PB 304 GLU cc_start: 0.8840 (tm-30) cc_final: 0.6113 (pm20) REVERT: PB 305 PHE cc_start: 0.8434 (t80) cc_final: 0.7272 (t80) REVERT: TB 1305 PHE cc_start: 0.8317 (t80) cc_final: 0.8019 (t80) REVERT: TB 1307 PHE cc_start: 0.8067 (t80) cc_final: 0.7620 (t80) outliers start: 126 outliers final: 85 residues processed: 495 average time/residue: 0.4715 time to fit residues: 283.9550 Evaluate side-chains 550 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 460 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain U residue 1106 LYS Chi-restraints excluded: chain W residue 1302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain k residue 1102 LYS Chi-restraints excluded: chain k residue 1106 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain p residue 302 LYS Chi-restraints excluded: chain r residue 1102 LYS Chi-restraints excluded: chain r residue 1106 LYS Chi-restraints excluded: chain t residue 1302 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain y residue 1102 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 302 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1102 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain FA residue 102 LYS Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain JA residue 1102 LYS Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain QA residue 1102 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain yA residue 1006 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain CB residue 1006 LYS Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain JB residue 1006 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.058017 restraints weight = 33176.564| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.25 r_work: 0.2583 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.341 12563 Z= 4.883 Angle : 3.929 32.936 16272 Z= 1.769 Chirality : 0.301 1.035 1152 Planarity : 0.017 0.058 2160 Dihedral : 21.336 111.528 1779 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 100.64 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.76 % Favored : 84.90 % Rotamer: Outliers : 15.16 % Allowed : 18.06 % Favored : 66.78 % Cbeta Deviations : 13.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % 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: -6.31 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.80 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.118 0.018 PHE4A 305 Details of bonding type rmsd hydrogen bonds : bond 0.18522 ( 278) hydrogen bonds : angle 9.45492 ( 786) covalent geometry : bond 0.10982 (12528) covalent geometry : angle 3.92882 (16272) Misc. bond : bond 0.01143 ( 35) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 453 time to evaluate : 1.341 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: A 6 LYS cc_start: 0.9272 (mtmt) cc_final: 0.8909 (mtmt) REVERT: J 106 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9002 (mmmm) REVERT: M 1004 GLU cc_start: 0.8302 (mp0) cc_final: 0.7534 (mp0) REVERT: N 1104 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8232 (mm-30) REVERT: N 1106 LYS cc_start: 0.9183 (mmmm) cc_final: 0.8789 (mmmm) REVERT: B 4 GLU cc_start: 0.8317 (mp0) cc_final: 0.7685 (mp0) REVERT: Q 106 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8958 (mmmm) REVERT: T 1006 LYS cc_start: 0.9225 (mtmt) cc_final: 0.8759 (mtmt) REVERT: U 1104 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8153 (mm-30) REVERT: U 1106 LYS cc_start: 0.9020 (tptm) cc_final: 0.8691 (tptm) REVERT: W 1302 LYS cc_start: 0.9401 (ttpt) cc_final: 0.9028 (mtpp) REVERT: W 1304 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8253 (mm-30) REVERT: C 6 LYS cc_start: 0.9280 (mtmt) cc_final: 0.9057 (mtmt) REVERT: X 106 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8825 (mmmm) REVERT: Y 206 LYS cc_start: 0.9382 (ttmm) cc_final: 0.9175 (mtpp) REVERT: j 1002 LYS cc_start: 0.8704 (tttt) cc_final: 0.8491 (tttp) REVERT: j 1004 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: j 1006 LYS cc_start: 0.9247 (mtmt) cc_final: 0.8941 (mtmt) REVERT: k 1102 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8259 (ttpt) REVERT: k 1104 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8119 (mm-30) REVERT: k 1106 LYS cc_start: 0.9072 (mmmm) cc_final: 0.8812 (mmmm) REVERT: l 1206 LYS cc_start: 0.9278 (ttmm) cc_final: 0.9058 (ttmm) REVERT: D 4 GLU cc_start: 0.8358 (mp0) cc_final: 0.7791 (mp0) REVERT: n 106 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8707 (mmmm) REVERT: o 204 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8167 (mt-10) REVERT: q 1004 GLU cc_start: 0.8662 (mp0) cc_final: 0.8316 (mp0) REVERT: r 1106 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8870 (mmmm) REVERT: s 1204 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8208 (mt-10) REVERT: t 1304 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8108 (mm-30) REVERT: u 102 LYS cc_start: 0.9227 (ttpt) cc_final: 0.8836 (ttpt) REVERT: u 104 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7969 (mm-30) REVERT: u 106 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8701 (mmmm) REVERT: v 202 LYS cc_start: 0.9357 (mtpt) cc_final: 0.9064 (mmmm) REVERT: y 1102 LYS cc_start: 0.9216 (ttpt) cc_final: 0.8898 (ttpt) REVERT: y 1106 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8863 (mmmm) REVERT: F 4 GLU cc_start: 0.8388 (mp0) cc_final: 0.7468 (mp0) REVERT: 1 106 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8893 (mmmm) REVERT: 3 304 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8243 (mm-30) REVERT: 4 1004 GLU cc_start: 0.8291 (mp0) cc_final: 0.8047 (mp0) REVERT: 4 1006 LYS cc_start: 0.9223 (mtmt) cc_final: 0.9013 (ttmt) REVERT: 5 1104 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8102 (mm-30) REVERT: 6 1202 LYS cc_start: 0.9491 (mtpt) cc_final: 0.8937 (mmmm) REVERT: 6 1204 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8124 (mt-10) REVERT: 7 1304 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8077 (mm-30) REVERT: G 4 GLU cc_start: 0.8245 (mp0) cc_final: 0.7427 (mp0) REVERT: G 6 LYS cc_start: 0.9280 (mtmt) cc_final: 0.8999 (mtmt) REVERT: 8 102 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8977 (ttpt) REVERT: 8 104 GLU cc_start: 0.8690 (mm-30) cc_final: 0.7872 (mm-30) REVERT: BA 1006 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8759 (mtmt) REVERT: CA 1104 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8242 (mm-30) REVERT: CA 1106 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8766 (mmmm) REVERT: EA 1304 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8372 (mm-30) REVERT: FA 106 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8731 (mmmm) REVERT: JA 1106 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8741 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9300 (mtpt) cc_final: 0.9024 (pttm) REVERT: KA 1206 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8923 (pptt) REVERT: LA 1304 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7889 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9319 (tttt) cc_final: 0.9085 (tttt) REVERT: I 4 GLU cc_start: 0.8416 (mp0) cc_final: 0.7231 (mp0) REVERT: MA 102 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8737 (mmtm) REVERT: MA 106 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8930 (mmmt) REVERT: PA 1004 GLU cc_start: 0.8467 (mp0) cc_final: 0.7566 (mp0) REVERT: QA 1102 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8809 (mmmt) REVERT: RA 1202 LYS cc_start: 0.9386 (mtpt) cc_final: 0.9059 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8510 (mm-30) REVERT: a 2 LYS cc_start: 0.9203 (tppt) cc_final: 0.8737 (tppt) REVERT: a 4 GLU cc_start: 0.8770 (tp30) cc_final: 0.8460 (tp30) REVERT: TA 106 LYS cc_start: 0.9132 (tttp) cc_final: 0.8824 (ptmm) REVERT: UA 202 LYS cc_start: 0.9412 (tttm) cc_final: 0.9020 (ttmm) REVERT: UA 204 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7899 (tm-30) REVERT: VA 302 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9074 (tptp) REVERT: VA 306 LYS cc_start: 0.9113 (tptp) cc_final: 0.8891 (tptp) REVERT: WA 1004 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8632 (tp30) REVERT: YA 1202 LYS cc_start: 0.9312 (tttm) cc_final: 0.9044 (tttm) REVERT: YA 1204 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8087 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8459 (tm-30) REVERT: aA 106 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8710 (ptmm) REVERT: bA 202 LYS cc_start: 0.9377 (tttm) cc_final: 0.8940 (ttmm) REVERT: bA 204 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7947 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9228 (ttmt) cc_final: 0.9016 (ttmt) REVERT: dA 1004 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8108 (tp30) REVERT: iA 202 LYS cc_start: 0.9392 (tttm) cc_final: 0.9022 (tppp) REVERT: lA 1103 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.9072 (t80) REVERT: d 2 LYS cc_start: 0.9131 (tppt) cc_final: 0.8585 (tppt) REVERT: d 4 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8249 (tp30) REVERT: pA 202 LYS cc_start: 0.9410 (tttm) cc_final: 0.9188 (tttm) REVERT: pA 204 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7598 (tm-30) REVERT: qA 306 LYS cc_start: 0.9093 (tptp) cc_final: 0.8854 (tptp) REVERT: rA 1002 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9103 (ttpt) REVERT: sA 1103 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8913 (t80) REVERT: tA 1204 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7930 (tm-30) REVERT: e 4 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8464 (tp30) REVERT: vA 104 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8624 (tm-30) REVERT: wA 202 LYS cc_start: 0.9338 (tttm) cc_final: 0.8867 (tppp) REVERT: wA 204 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8191 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8999 (tppt) REVERT: yA 1004 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8397 (tp30) REVERT: 1A 1304 GLU cc_start: 0.9335 (tm-30) cc_final: 0.7885 (tm-30) REVERT: f 2 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8873 (ttmt) REVERT: f 4 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8491 (tp30) REVERT: 3A 202 LYS cc_start: 0.9405 (tttm) cc_final: 0.9058 (ttmm) REVERT: 3A 204 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7842 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8798 (tptp) REVERT: 4A 304 GLU cc_start: 0.9326 (tm-30) cc_final: 0.8267 (tm-30) REVERT: 4A 306 LYS cc_start: 0.9043 (tptp) cc_final: 0.8833 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9244 (ptpt) cc_final: 0.9014 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7885 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8799 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8237 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.8801 (tptp) cc_final: 0.8491 (tptp) REVERT: g 2 LYS cc_start: 0.9185 (tppt) cc_final: 0.8677 (tppt) REVERT: g 4 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8460 (tp30) REVERT: 9A 105 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.9105 (t80) REVERT: AB 202 LYS cc_start: 0.9343 (tttm) cc_final: 0.8960 (ttmm) REVERT: AB 204 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8064 (tm-30) REVERT: BB 302 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8962 (tptp) REVERT: BB 306 LYS cc_start: 0.9063 (tptp) cc_final: 0.8859 (tptp) REVERT: CB 1004 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8441 (tp30) REVERT: DB 1102 LYS cc_start: 0.9259 (tptm) cc_final: 0.9044 (tptm) REVERT: EB 1204 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7485 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9010 (tptp) cc_final: 0.8779 (tptp) REVERT: FB 1303 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8361 (t80) REVERT: FB 1306 LYS cc_start: 0.9001 (tptp) cc_final: 0.8793 (tptp) REVERT: HB 202 LYS cc_start: 0.9408 (tttm) cc_final: 0.8963 (pttm) REVERT: IB 306 LYS cc_start: 0.9035 (tptp) cc_final: 0.8790 (tptp) REVERT: IB 307 PHE cc_start: 0.9381 (t80) cc_final: 0.9147 (t80) REVERT: JB 1004 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8189 (tp30) REVERT: LB 1202 LYS cc_start: 0.9330 (tttm) cc_final: 0.9019 (pptt) REVERT: i 4 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8373 (tp30) REVERT: NB 102 LYS cc_start: 0.9346 (tptm) cc_final: 0.9119 (pttt) REVERT: NB 103 PHE cc_start: 0.9116 (t80) cc_final: 0.8777 (t80) REVERT: NB 104 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: OB 202 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9132 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8232 (tp30) REVERT: QB 1006 LYS cc_start: 0.9263 (ttpt) cc_final: 0.8945 (ttpt) REVERT: SB 1204 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8272 (tm-30) outliers start: 131 outliers final: 67 residues processed: 497 average time/residue: 0.6488 time to fit residues: 398.3254 Evaluate side-chains 549 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 453 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain MA residue 102 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.059107 restraints weight = 33940.695| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.25 r_work: 0.2614 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.338 12563 Z= 4.888 Angle : 4.002 34.612 16272 Z= 1.803 Chirality : 0.299 1.003 1152 Planarity : 0.017 0.057 2160 Dihedral : 20.681 89.761 1519 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 106.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 18.06 % Favored : 81.77 % Rotamer: Outliers : 20.95 % Allowed : 21.88 % Favored : 57.18 % Cbeta Deviations : 14.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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: -5.73 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.123 0.017 PHE 2 205 Details of bonding type rmsd hydrogen bonds : bond 0.18772 ( 278) hydrogen bonds : angle 9.39435 ( 786) covalent geometry : bond 0.11005 (12528) covalent geometry : angle 4.00180 (16272) Misc. bond : bond 0.01217 ( 35) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 438 time to evaluate : 1.791 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: A 6 LYS cc_start: 0.9261 (mtmt) cc_final: 0.9009 (mtmt) REVERT: K 206 LYS cc_start: 0.9299 (ttmm) cc_final: 0.9093 (ttmm) REVERT: M 1004 GLU cc_start: 0.8368 (mp0) cc_final: 0.7579 (mp0) REVERT: N 1104 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8342 (mm-30) REVERT: N 1106 LYS cc_start: 0.9167 (mmmm) cc_final: 0.8793 (mmmm) REVERT: P 1304 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8742 (mm-30) REVERT: B 4 GLU cc_start: 0.8397 (mp0) cc_final: 0.7916 (mp0) REVERT: Q 106 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8935 (mmmm) REVERT: S 307 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9065 (m-80) REVERT: T 1004 GLU cc_start: 0.8703 (mp0) cc_final: 0.8029 (mp0) REVERT: T 1006 LYS cc_start: 0.9323 (mtmt) cc_final: 0.9044 (mtmt) REVERT: U 1104 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8087 (mm-30) REVERT: U 1106 LYS cc_start: 0.9096 (tptm) cc_final: 0.8616 (tptm) REVERT: C 4 GLU cc_start: 0.8459 (mp0) cc_final: 0.7948 (mp0) REVERT: X 106 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8869 (mmmm) REVERT: Z 304 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8796 (mm-30) REVERT: j 1002 LYS cc_start: 0.8707 (tttt) cc_final: 0.8431 (tttp) REVERT: j 1004 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: j 1006 LYS cc_start: 0.9259 (mtmt) cc_final: 0.8948 (mtmt) REVERT: k 1102 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8197 (ttpt) REVERT: k 1104 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8273 (mm-30) REVERT: k 1106 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8724 (mmmm) REVERT: l 1202 LYS cc_start: 0.9363 (mtpt) cc_final: 0.9138 (mtpp) REVERT: l 1204 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8712 (mm-30) REVERT: l 1206 LYS cc_start: 0.9336 (ttmm) cc_final: 0.9103 (ttmm) REVERT: D 4 GLU cc_start: 0.8385 (mp0) cc_final: 0.7847 (mp0) REVERT: n 106 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8754 (mmmm) REVERT: o 202 LYS cc_start: 0.9397 (ttpt) cc_final: 0.9188 (ttpt) REVERT: o 204 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8410 (mt-10) REVERT: q 1004 GLU cc_start: 0.8604 (mp0) cc_final: 0.8230 (mp0) REVERT: r 1104 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8005 (mm-30) REVERT: r 1106 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8850 (mmmm) REVERT: s 1204 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8471 (mt-10) REVERT: t 1304 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8266 (mm-30) REVERT: E 6 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8960 (mtmt) REVERT: u 106 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8687 (mmmm) REVERT: v 206 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9216 (ttmm) REVERT: w 307 PHE cc_start: 0.9535 (OUTLIER) cc_final: 0.9056 (m-80) REVERT: x 1003 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: y 1102 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8880 (ttpt) REVERT: y 1106 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8901 (mmmm) REVERT: 1 106 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8653 (mmmm) REVERT: 3 304 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8542 (mm-30) REVERT: 4 1004 GLU cc_start: 0.8371 (mp0) cc_final: 0.8095 (mp0) REVERT: 6 1202 LYS cc_start: 0.9502 (mtpt) cc_final: 0.9085 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8440 (mm-30) REVERT: G 4 GLU cc_start: 0.8315 (mp0) cc_final: 0.7749 (mp0) REVERT: G 6 LYS cc_start: 0.9279 (mtmt) cc_final: 0.9061 (mtmt) REVERT: 8 106 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8699 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8361 (mp0) cc_final: 0.8109 (mp0) REVERT: FA 104 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8033 (mm-30) REVERT: FA 106 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8832 (mmmm) REVERT: HA 302 LYS cc_start: 0.9360 (mtpt) cc_final: 0.9042 (mtpp) REVERT: JA 1106 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8705 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9275 (mtpt) cc_final: 0.9020 (pttm) REVERT: I 4 GLU cc_start: 0.8249 (mp0) cc_final: 0.7861 (mp0) REVERT: I 6 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9034 (ttmt) REVERT: MA 102 LYS cc_start: 0.9065 (ttpt) cc_final: 0.8846 (mmtt) REVERT: PA 1004 GLU cc_start: 0.8344 (mp0) cc_final: 0.7550 (mp0) REVERT: QA 1106 LYS cc_start: 0.6294 (tptt) cc_final: 0.5577 (tptp) REVERT: RA 1202 LYS cc_start: 0.9326 (mtpt) cc_final: 0.9033 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8653 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: a 2 LYS cc_start: 0.9214 (tppt) cc_final: 0.8836 (tppt) REVERT: a 4 GLU cc_start: 0.8815 (tp30) cc_final: 0.8506 (tp30) REVERT: TA 106 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8837 (ptmm) REVERT: VA 302 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8914 (tptp) REVERT: VA 306 LYS cc_start: 0.9090 (tptp) cc_final: 0.8820 (tptp) REVERT: WA 1002 LYS cc_start: 0.9250 (tppt) cc_final: 0.8877 (tppt) REVERT: WA 1004 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8629 (tp30) REVERT: XA 1105 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8775 (p90) REVERT: YA 1202 LYS cc_start: 0.9372 (tttm) cc_final: 0.9138 (tttm) REVERT: YA 1204 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7845 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8761 (t80) REVERT: ZA 1304 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8485 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8865 (tptp) cc_final: 0.8625 (tptp) REVERT: bA 202 LYS cc_start: 0.9344 (tttm) cc_final: 0.8971 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9243 (ttmt) cc_final: 0.9026 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9201 (tm-30) cc_final: 0.7948 (tm-30) REVERT: iA 202 LYS cc_start: 0.9427 (tttm) cc_final: 0.9003 (tppp) REVERT: iA 204 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7966 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.9091 (t80) REVERT: nA 1306 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8853 (tptp) REVERT: d 4 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: oA 102 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9042 (tptm) REVERT: pA 204 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7618 (tm-30) REVERT: qA 306 LYS cc_start: 0.9072 (tptp) cc_final: 0.8797 (tptp) REVERT: rA 1006 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8835 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7785 (tm-30) REVERT: e 4 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8381 (tp30) REVERT: e 6 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8757 (ttpt) REVERT: wA 202 LYS cc_start: 0.9328 (tttm) cc_final: 0.8832 (tppp) REVERT: wA 204 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8158 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8851 (tppt) REVERT: yA 1004 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8326 (tp30) REVERT: zA 1102 LYS cc_start: 0.9389 (tptm) cc_final: 0.9164 (tptm) REVERT: 1A 1304 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8172 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8951 (t80) REVERT: f 2 LYS cc_start: 0.9224 (ttmt) cc_final: 0.8863 (ttmt) REVERT: f 4 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8489 (tp30) REVERT: 3A 202 LYS cc_start: 0.9367 (tttm) cc_final: 0.9011 (ttmm) REVERT: 3A 204 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7945 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8838 (tptp) REVERT: 4A 304 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8317 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7966 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8865 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8162 (tm-30) REVERT: g 2 LYS cc_start: 0.9139 (tppt) cc_final: 0.8625 (tppt) REVERT: g 4 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: 9A 105 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.9159 (t80) REVERT: AB 202 LYS cc_start: 0.9389 (tttm) cc_final: 0.8995 (ttmm) REVERT: AB 204 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7983 (tm-30) REVERT: BB 302 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8991 (tptp) REVERT: CB 1004 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8496 (tp30) REVERT: EB 1204 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7422 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8657 (tptp) REVERT: FB 1306 LYS cc_start: 0.8976 (tptp) cc_final: 0.8727 (tptp) REVERT: h 4 GLU cc_start: 0.8725 (tp30) cc_final: 0.7888 (pm20) REVERT: HB 202 LYS cc_start: 0.9360 (tttm) cc_final: 0.8957 (pttt) REVERT: JB 1004 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: i 4 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8462 (tp30) REVERT: NB 102 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9098 (pttt) REVERT: NB 104 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: NB 105 PHE cc_start: 0.9092 (t80) cc_final: 0.8890 (t80) REVERT: NB 106 LYS cc_start: 0.9242 (tttp) cc_final: 0.8715 (pptt) REVERT: OB 202 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9172 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: RB 1103 PHE cc_start: 0.9029 (t80) cc_final: 0.8607 (t80) REVERT: SB 1204 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8315 (tm-30) outliers start: 181 outliers final: 111 residues processed: 509 average time/residue: 0.5366 time to fit residues: 329.2313 Evaluate side-chains 586 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 437 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1003 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.059815 restraints weight = 33517.576| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.21 r_work: 0.2636 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.377 12563 Z= 4.891 Angle : 4.041 32.449 16272 Z= 1.829 Chirality : 0.299 0.973 1152 Planarity : 0.017 0.057 2160 Dihedral : 20.745 81.958 1507 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 107.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 18.40 % Favored : 81.42 % Rotamer: Outliers : 24.19 % Allowed : 21.64 % Favored : 54.17 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.39 % 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: -5.90 (0.23), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.49 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 Details of bonding type rmsd hydrogen bonds : bond 0.18918 ( 278) hydrogen bonds : angle 9.37472 ( 786) covalent geometry : bond 0.11018 (12528) covalent geometry : angle 4.04110 (16272) Misc. bond : bond 0.01196 ( 35) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 433 time to evaluate : 1.380 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: A 4 GLU cc_start: 0.7999 (mp0) cc_final: 0.7358 (mp0) REVERT: M 1004 GLU cc_start: 0.8411 (mp0) cc_final: 0.7599 (mp0) REVERT: N 1104 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8410 (mm-30) REVERT: N 1106 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8657 (mmmm) REVERT: B 4 GLU cc_start: 0.8381 (mp0) cc_final: 0.7928 (mp0) REVERT: S 307 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.9040 (m-80) REVERT: T 1004 GLU cc_start: 0.8677 (mp0) cc_final: 0.7975 (mp0) REVERT: T 1006 LYS cc_start: 0.9306 (mtmt) cc_final: 0.9042 (mtmt) REVERT: U 1104 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8135 (mm-30) REVERT: U 1106 LYS cc_start: 0.9088 (tptm) cc_final: 0.8677 (tptm) REVERT: W 1302 LYS cc_start: 0.9402 (mtpt) cc_final: 0.9060 (mtpp) REVERT: W 1304 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8532 (mm-30) REVERT: C 4 GLU cc_start: 0.8473 (mp0) cc_final: 0.8066 (mp0) REVERT: X 106 LYS cc_start: 0.9305 (mmmm) cc_final: 0.8964 (mmmm) REVERT: Z 304 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8755 (mm-30) REVERT: j 1004 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: j 1006 LYS cc_start: 0.9259 (mtmt) cc_final: 0.8841 (mtmt) REVERT: k 1102 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8501 (ttpt) REVERT: k 1104 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8263 (mm-30) REVERT: k 1106 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8751 (mmmm) REVERT: l 1202 LYS cc_start: 0.9375 (mtpt) cc_final: 0.9083 (mtpp) REVERT: l 1204 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8730 (mm-30) REVERT: D 4 GLU cc_start: 0.8362 (mp0) cc_final: 0.7713 (mp0) REVERT: D 6 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8703 (mtmt) REVERT: D 7 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8691 (t80) REVERT: n 106 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8711 (mmmm) REVERT: o 202 LYS cc_start: 0.9419 (ttpt) cc_final: 0.9152 (ttpt) REVERT: q 1004 GLU cc_start: 0.8500 (mp0) cc_final: 0.8124 (mp0) REVERT: r 1104 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7966 (mm-30) REVERT: r 1106 LYS cc_start: 0.9161 (mmmm) cc_final: 0.8829 (mmmm) REVERT: s 1204 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8500 (mt-10) REVERT: E 6 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8907 (mtmt) REVERT: u 106 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8555 (mmmm) REVERT: v 206 LYS cc_start: 0.9437 (ttmm) cc_final: 0.9213 (ttmm) REVERT: x 1003 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: x 1006 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8668 (mtmt) REVERT: y 1102 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8831 (ttpt) REVERT: y 1106 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8865 (mmmm) REVERT: 1 104 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8006 (mm-30) REVERT: 1 106 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8647 (mmmm) REVERT: 3 302 LYS cc_start: 0.9440 (ttpt) cc_final: 0.9032 (ttmm) REVERT: 4 1006 LYS cc_start: 0.9216 (ttmt) cc_final: 0.8942 (ttmt) REVERT: 5 1104 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8036 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8888 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9484 (mtpt) cc_final: 0.9075 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8379 (mm-30) REVERT: G 3 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: G 4 GLU cc_start: 0.8349 (mp0) cc_final: 0.7978 (mp0) REVERT: G 6 LYS cc_start: 0.9276 (mtmt) cc_final: 0.9057 (mtmt) REVERT: 8 104 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7901 (mm-30) REVERT: 8 106 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8531 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8566 (mp0) cc_final: 0.8119 (mp0) REVERT: CA 1106 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8781 (mmmm) REVERT: FA 104 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8134 (mm-30) REVERT: FA 106 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8885 (mmmm) REVERT: GA 207 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8939 (t80) REVERT: HA 302 LYS cc_start: 0.9350 (mtpt) cc_final: 0.9013 (mtpp) REVERT: HA 304 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8550 (mm-30) REVERT: IA 1004 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8709 (pm20) REVERT: JA 1106 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8761 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9266 (mtpt) cc_final: 0.8999 (pttm) REVERT: KA 1204 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5983 (pm20) REVERT: I 4 GLU cc_start: 0.8236 (mp0) cc_final: 0.7290 (mp0) REVERT: I 6 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8981 (mtmt) REVERT: MA 106 LYS cc_start: 0.5193 (OUTLIER) cc_final: 0.4738 (tptp) REVERT: NA 202 LYS cc_start: 0.9427 (mtpt) cc_final: 0.8968 (mptt) REVERT: PA 1004 GLU cc_start: 0.8452 (mp0) cc_final: 0.8187 (mp0) REVERT: QA 1106 LYS cc_start: 0.5014 (OUTLIER) cc_final: 0.2061 (mmmt) REVERT: RA 1202 LYS cc_start: 0.9322 (mtpt) cc_final: 0.9070 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8637 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.8759 (m-80) REVERT: a 2 LYS cc_start: 0.9238 (tppt) cc_final: 0.8940 (tppt) REVERT: a 4 GLU cc_start: 0.8824 (tp30) cc_final: 0.8525 (tp30) REVERT: TA 106 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8870 (ptmm) REVERT: UA 204 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7787 (tm-30) REVERT: VA 302 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9064 (tptp) REVERT: WA 1002 LYS cc_start: 0.9244 (tppt) cc_final: 0.8877 (tppt) REVERT: WA 1004 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8669 (tp30) REVERT: XA 1105 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8787 (p90) REVERT: YA 1204 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7842 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8834 (t80) REVERT: ZA 1304 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8533 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8929 (tptp) cc_final: 0.8679 (tptp) REVERT: bA 202 LYS cc_start: 0.9352 (tttm) cc_final: 0.9007 (ttmm) REVERT: bA 204 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8141 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9247 (ttmt) cc_final: 0.9018 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9232 (tm-30) cc_final: 0.7886 (tm-30) REVERT: c 4 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: iA 202 LYS cc_start: 0.9451 (tttm) cc_final: 0.9024 (tppp) REVERT: iA 204 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7936 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.9104 (t80) REVERT: nA 1306 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8906 (tptp) REVERT: d 4 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8094 (tp30) REVERT: oA 102 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9067 (tptm) REVERT: pA 204 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7554 (tm-30) REVERT: qA 306 LYS cc_start: 0.9069 (tptp) cc_final: 0.8799 (tptp) REVERT: rA 1006 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8823 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8645 (tm-30) cc_final: 0.7906 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9178 (tttt) cc_final: 0.8970 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.9058 (t80) REVERT: e 4 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8384 (tp30) REVERT: e 6 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8806 (ttpt) REVERT: vA 104 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8570 (tm-30) REVERT: wA 202 LYS cc_start: 0.9326 (tttm) cc_final: 0.8964 (ttmm) REVERT: wA 204 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8206 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8342 (tp30) REVERT: zA 1102 LYS cc_start: 0.9392 (tptm) cc_final: 0.9178 (tptm) REVERT: 1A 1304 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8478 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8986 (t80) REVERT: f 2 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8846 (ttmt) REVERT: f 4 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8481 (tp30) REVERT: 3A 202 LYS cc_start: 0.9356 (tttm) cc_final: 0.9048 (mmmm) REVERT: 4A 304 GLU cc_start: 0.9289 (tm-30) cc_final: 0.8300 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7969 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8906 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8259 (tm-30) REVERT: g 2 LYS cc_start: 0.9167 (tppt) cc_final: 0.8632 (tppt) REVERT: g 4 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8330 (tp30) REVERT: 9A 105 PHE cc_start: 0.9444 (OUTLIER) cc_final: 0.9193 (t80) REVERT: AB 202 LYS cc_start: 0.9426 (tttm) cc_final: 0.9054 (ttmm) REVERT: AB 204 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7989 (tm-30) REVERT: BB 302 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.9028 (tptp) REVERT: BB 305 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9163 (t80) REVERT: CB 1004 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: DB 1102 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9079 (tptm) REVERT: EB 1204 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7441 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8691 (tptp) REVERT: h 4 GLU cc_start: 0.8769 (tp30) cc_final: 0.8088 (pm20) REVERT: GB 103 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.9113 (t80) REVERT: HB 202 LYS cc_start: 0.9399 (tttm) cc_final: 0.9031 (pttt) REVERT: IB 306 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8871 (tptp) REVERT: JB 1004 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8240 (tp30) REVERT: LB 1202 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9105 (pptt) REVERT: MB 1306 LYS cc_start: 0.9031 (tptp) cc_final: 0.8796 (tptp) REVERT: i 4 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8425 (tp30) REVERT: NB 102 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9096 (pttt) REVERT: NB 104 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8287 (pm20) REVERT: NB 106 LYS cc_start: 0.9218 (tttp) cc_final: 0.8694 (pptt) REVERT: OB 202 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9177 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8015 (tp30) REVERT: QB 1005 PHE cc_start: 0.9276 (t80) cc_final: 0.8645 (t80) outliers start: 209 outliers final: 129 residues processed: 515 average time/residue: 0.5785 time to fit residues: 365.5999 Evaluate side-chains 610 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 432 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 4 residue 1002 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain QA residue 1104 GLU Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.060169 restraints weight = 34277.925| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.19 r_work: 0.2651 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.346 12563 Z= 4.895 Angle : 4.051 30.120 16272 Z= 1.833 Chirality : 0.299 0.971 1152 Planarity : 0.017 0.057 2160 Dihedral : 20.621 82.042 1496 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 108.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.79 % Favored : 80.03 % Rotamer: Outliers : 25.35 % Allowed : 22.92 % Favored : 51.74 % Cbeta Deviations : 14.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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: -5.95 (0.23), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 Details of bonding type rmsd hydrogen bonds : bond 0.19060 ( 278) hydrogen bonds : angle 9.44582 ( 786) covalent geometry : bond 0.11025 (12528) covalent geometry : angle 4.05140 (16272) Misc. bond : bond 0.01127 ( 35) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 431 time to evaluate : 2.063 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: A 6 LYS cc_start: 0.9297 (mtmt) cc_final: 0.9011 (mtmt) REVERT: M 1004 GLU cc_start: 0.8493 (mp0) cc_final: 0.7710 (mp0) REVERT: N 1104 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8565 (mm-30) REVERT: N 1106 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8671 (mmmm) REVERT: O 1206 LYS cc_start: 0.9258 (ttmm) cc_final: 0.9044 (ttmm) REVERT: B 4 GLU cc_start: 0.8406 (mp0) cc_final: 0.8064 (mp0) REVERT: B 5 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.9188 (m-80) REVERT: Q 104 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8122 (mm-30) REVERT: Q 106 LYS cc_start: 0.9282 (mmmm) cc_final: 0.8947 (mmmm) REVERT: S 307 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.9109 (m-80) REVERT: T 1004 GLU cc_start: 0.8688 (mp0) cc_final: 0.7948 (mp0) REVERT: T 1006 LYS cc_start: 0.9337 (mtmt) cc_final: 0.9055 (mtmt) REVERT: U 1104 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8214 (mm-30) REVERT: U 1106 LYS cc_start: 0.9051 (tptm) cc_final: 0.8704 (tptm) REVERT: C 4 GLU cc_start: 0.8538 (mp0) cc_final: 0.8175 (mp0) REVERT: X 106 LYS cc_start: 0.9306 (mmmm) cc_final: 0.8986 (mmmm) REVERT: j 1004 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: j 1006 LYS cc_start: 0.9276 (mtmt) cc_final: 0.8903 (mtmt) REVERT: k 1102 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8459 (ttpt) REVERT: k 1104 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8297 (mm-30) REVERT: k 1106 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8803 (mmmm) REVERT: l 1202 LYS cc_start: 0.9386 (mtpt) cc_final: 0.9115 (mtpp) REVERT: D 4 GLU cc_start: 0.8379 (mp0) cc_final: 0.7596 (mp0) REVERT: D 6 LYS cc_start: 0.9290 (mtmt) cc_final: 0.8837 (mtmt) REVERT: D 7 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8783 (t80) REVERT: n 106 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8756 (mmmm) REVERT: q 1004 GLU cc_start: 0.8553 (mp0) cc_final: 0.8274 (mp0) REVERT: r 1104 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8004 (mm-30) REVERT: r 1106 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8824 (mmmm) REVERT: t 1302 LYS cc_start: 0.9393 (tttt) cc_final: 0.9173 (tttp) REVERT: E 6 LYS cc_start: 0.9218 (mtmt) cc_final: 0.8938 (mtmt) REVERT: u 106 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8588 (mmmm) REVERT: v 206 LYS cc_start: 0.9433 (ttmm) cc_final: 0.9180 (ttmm) REVERT: w 307 PHE cc_start: 0.9546 (OUTLIER) cc_final: 0.8797 (m-80) REVERT: x 1003 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: x 1006 LYS cc_start: 0.9157 (mtmt) cc_final: 0.8748 (mtmt) REVERT: y 1106 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8953 (mmmm) REVERT: F 6 LYS cc_start: 0.9257 (mtmt) cc_final: 0.8932 (mtmt) REVERT: 1 104 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8098 (mm-30) REVERT: 1 106 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8721 (mmmm) REVERT: 5 1104 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8228 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8768 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9437 (mtpt) cc_final: 0.9071 (mtpp) REVERT: G 3 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: G 4 GLU cc_start: 0.8333 (mp0) cc_final: 0.7929 (mp0) REVERT: 8 104 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7898 (mm-30) REVERT: 8 106 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8650 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8464 (mp0) cc_final: 0.7903 (mp0) REVERT: CA 1104 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8198 (mm-30) REVERT: H 4 GLU cc_start: 0.4238 (OUTLIER) cc_final: 0.2936 (pm20) REVERT: FA 106 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8945 (mmmm) REVERT: HA 302 LYS cc_start: 0.9351 (mtpt) cc_final: 0.9033 (mmmm) REVERT: HA 304 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8596 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8961 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9249 (mtpt) cc_final: 0.9035 (pttm) REVERT: I 4 GLU cc_start: 0.8249 (mp0) cc_final: 0.7356 (mp0) REVERT: PA 1004 GLU cc_start: 0.8437 (mp0) cc_final: 0.7831 (mp0) REVERT: PA 1006 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9025 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9128 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8566 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9267 (tttt) cc_final: 0.8863 (tttt) REVERT: SA 1307 PHE cc_start: 0.9462 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: a 2 LYS cc_start: 0.9298 (tppt) cc_final: 0.9037 (tppt) REVERT: a 4 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8439 (tp30) REVERT: TA 106 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8898 (ptmm) REVERT: UA 204 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7847 (tm-30) REVERT: VA 302 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9092 (tptp) REVERT: WA 1002 LYS cc_start: 0.9280 (tppt) cc_final: 0.8905 (tppt) REVERT: WA 1004 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8629 (tp30) REVERT: YA 1204 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7909 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8821 (t80) REVERT: ZA 1304 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8596 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8978 (tptp) cc_final: 0.8758 (tptp) REVERT: aA 104 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8033 (tm-30) REVERT: bA 202 LYS cc_start: 0.9370 (tttm) cc_final: 0.9016 (ttmm) REVERT: bA 204 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8117 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8958 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9243 (tm-30) cc_final: 0.7968 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9327 (t80) cc_final: 0.8943 (t80) REVERT: iA 204 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8098 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.9112 (t80) REVERT: nA 1306 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8923 (tptp) REVERT: d 4 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: oA 102 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9073 (tptm) REVERT: pA 204 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7659 (tm-30) REVERT: qA 306 LYS cc_start: 0.9130 (tptp) cc_final: 0.8857 (tptp) REVERT: tA 1204 GLU cc_start: 0.8691 (tm-30) cc_final: 0.7925 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9210 (tttt) cc_final: 0.9008 (tmtt) REVERT: e 4 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8427 (tp30) REVERT: e 6 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8809 (ttpt) REVERT: vA 104 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8597 (tm-30) REVERT: wA 202 LYS cc_start: 0.9333 (tttm) cc_final: 0.8954 (ttmm) REVERT: wA 204 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8275 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: zA 1102 LYS cc_start: 0.9373 (tptm) cc_final: 0.9168 (tptm) REVERT: 1A 1304 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8523 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.9080 (t80) REVERT: f 2 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8910 (ttmt) REVERT: f 4 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8569 (tp30) REVERT: 3A 202 LYS cc_start: 0.9372 (tttm) cc_final: 0.9097 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8196 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8888 (tptp) REVERT: 4A 304 GLU cc_start: 0.9337 (tm-30) cc_final: 0.8425 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8058 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8947 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8327 (tm-30) REVERT: g 2 LYS cc_start: 0.9186 (tppt) cc_final: 0.8681 (tppt) REVERT: g 4 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8384 (tp30) REVERT: AB 202 LYS cc_start: 0.9453 (tttm) cc_final: 0.9103 (ttmm) REVERT: AB 204 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8051 (tm-30) REVERT: BB 302 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9059 (tptp) REVERT: CB 1004 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8448 (tp30) REVERT: DB 1102 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9073 (tptm) REVERT: EB 1204 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7558 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8738 (tptp) REVERT: h 4 GLU cc_start: 0.8825 (tp30) cc_final: 0.8052 (pm20) REVERT: GB 103 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.9144 (t80) REVERT: HB 202 LYS cc_start: 0.9409 (tttm) cc_final: 0.9051 (pttt) REVERT: IB 306 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8943 (tptp) REVERT: JB 1004 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8298 (tp30) REVERT: i 4 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8498 (tp30) REVERT: NB 102 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9130 (pttt) REVERT: NB 104 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8259 (pm20) REVERT: NB 106 LYS cc_start: 0.9235 (tttp) cc_final: 0.8720 (pptt) REVERT: OB 202 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9221 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: QB 1005 PHE cc_start: 0.9300 (t80) cc_final: 0.8672 (t80) outliers start: 219 outliers final: 153 residues processed: 524 average time/residue: 0.4817 time to fit residues: 310.1603 Evaluate side-chains 626 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 432 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060088 restraints weight = 34878.985| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.21 r_work: 0.2647 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.7563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.350 12563 Z= 4.892 Angle : 4.050 30.015 16272 Z= 1.832 Chirality : 0.299 0.970 1152 Planarity : 0.017 0.061 2160 Dihedral : 20.584 82.781 1496 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 108.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.97 % Favored : 79.86 % Rotamer: Outliers : 26.39 % Allowed : 23.50 % Favored : 50.12 % Cbeta Deviations : 15.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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: -5.94 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 Details of bonding type rmsd hydrogen bonds : bond 0.19112 ( 278) hydrogen bonds : angle 9.46860 ( 786) covalent geometry : bond 0.11017 (12528) covalent geometry : angle 4.05032 (16272) Misc. bond : bond 0.01067 ( 35) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 431 time to evaluate : 1.198 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: A 4 GLU cc_start: 0.8278 (mp0) cc_final: 0.7368 (mp0) REVERT: A 6 LYS cc_start: 0.9315 (mtmt) cc_final: 0.9047 (mtmt) REVERT: J 104 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8172 (mm-30) REVERT: M 1004 GLU cc_start: 0.8435 (mp0) cc_final: 0.7611 (mp0) REVERT: N 1104 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8497 (mm-30) REVERT: N 1106 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8664 (mmmm) REVERT: O 1206 LYS cc_start: 0.9266 (ttmm) cc_final: 0.9052 (ttmm) REVERT: P 1304 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8537 (mm-30) REVERT: B 4 GLU cc_start: 0.8401 (mp0) cc_final: 0.8022 (mp0) REVERT: Q 106 LYS cc_start: 0.9286 (mmmm) cc_final: 0.8956 (mmmm) REVERT: T 1004 GLU cc_start: 0.8695 (mp0) cc_final: 0.7954 (mp0) REVERT: T 1006 LYS cc_start: 0.9330 (mtmt) cc_final: 0.9028 (mtmt) REVERT: U 1104 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8196 (mm-30) REVERT: U 1106 LYS cc_start: 0.9036 (tptm) cc_final: 0.8656 (tptm) REVERT: W 1302 LYS cc_start: 0.9411 (mtpt) cc_final: 0.9060 (mtpp) REVERT: W 1304 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8520 (mm-30) REVERT: C 4 GLU cc_start: 0.8555 (mp0) cc_final: 0.7641 (mp0) REVERT: X 106 LYS cc_start: 0.9339 (mmmm) cc_final: 0.8999 (mmmm) REVERT: j 1002 LYS cc_start: 0.8742 (tttt) cc_final: 0.8462 (tttp) REVERT: j 1004 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: j 1006 LYS cc_start: 0.9292 (mtmt) cc_final: 0.8939 (mtmt) REVERT: k 1102 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8238 (ttpt) REVERT: k 1104 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8238 (mm-30) REVERT: k 1106 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8817 (mmmm) REVERT: l 1202 LYS cc_start: 0.9385 (mtpt) cc_final: 0.9173 (mtpp) REVERT: l 1204 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8782 (mm-30) REVERT: D 4 GLU cc_start: 0.8394 (mp0) cc_final: 0.7672 (mp0) REVERT: D 6 LYS cc_start: 0.9292 (mtmt) cc_final: 0.8838 (mtmt) REVERT: D 7 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.8712 (t80) REVERT: n 106 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8764 (mmmm) REVERT: q 1004 GLU cc_start: 0.8540 (mp0) cc_final: 0.8284 (mp0) REVERT: r 1104 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8072 (mm-30) REVERT: r 1106 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8804 (mmmm) REVERT: E 6 LYS cc_start: 0.9206 (mtmt) cc_final: 0.8938 (mtmt) REVERT: u 106 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8586 (mmmm) REVERT: v 206 LYS cc_start: 0.9440 (ttmm) cc_final: 0.9189 (ttmm) REVERT: w 307 PHE cc_start: 0.9567 (OUTLIER) cc_final: 0.8846 (m-80) REVERT: x 1006 LYS cc_start: 0.9154 (mtmt) cc_final: 0.8732 (mtmt) REVERT: y 1106 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8945 (mmmm) REVERT: F 6 LYS cc_start: 0.9256 (mtmt) cc_final: 0.8958 (mtmt) REVERT: 1 104 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8171 (mm-30) REVERT: 1 106 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8726 (mmmm) REVERT: 3 302 LYS cc_start: 0.9472 (ttpt) cc_final: 0.9105 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8809 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9436 (mtpt) cc_final: 0.9070 (mtpp) REVERT: G 3 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: G 4 GLU cc_start: 0.8368 (mp0) cc_final: 0.7950 (mp0) REVERT: G 6 LYS cc_start: 0.9347 (mtmt) cc_final: 0.9015 (mtmt) REVERT: 8 104 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7936 (mm-30) REVERT: 8 106 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8680 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8507 (mp0) cc_final: 0.8157 (mp0) REVERT: CA 1104 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8224 (mm-30) REVERT: H 4 GLU cc_start: 0.4204 (OUTLIER) cc_final: 0.3066 (pm20) REVERT: FA 106 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8966 (mmmm) REVERT: HA 302 LYS cc_start: 0.9339 (mtpt) cc_final: 0.9040 (mmmm) REVERT: HA 304 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8605 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8516 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8810 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9249 (mtpt) cc_final: 0.9036 (pttm) REVERT: I 4 GLU cc_start: 0.8263 (mp0) cc_final: 0.7367 (mp0) REVERT: MA 106 LYS cc_start: 0.4905 (OUTLIER) cc_final: 0.3802 (tptt) REVERT: PA 1004 GLU cc_start: 0.8467 (mp0) cc_final: 0.7815 (mp0) REVERT: PA 1006 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9019 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9361 (mtpt) cc_final: 0.9125 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8567 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9270 (tttt) cc_final: 0.8864 (tttt) REVERT: SA 1307 PHE cc_start: 0.9458 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: a 2 LYS cc_start: 0.9259 (tppt) cc_final: 0.9008 (tppt) REVERT: a 4 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8483 (tp30) REVERT: TA 104 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8483 (tm-30) REVERT: TA 106 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8856 (ptmm) REVERT: UA 202 LYS cc_start: 0.9440 (tttm) cc_final: 0.9028 (ttmm) REVERT: UA 204 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7875 (tm-30) REVERT: VA 302 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9089 (tptp) REVERT: WA 1002 LYS cc_start: 0.9281 (tppt) cc_final: 0.8900 (tppt) REVERT: WA 1004 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8621 (tp30) REVERT: YA 1204 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7900 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8820 (t80) REVERT: ZA 1304 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8610 (tm-30) REVERT: b 6 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9032 (ttpt) REVERT: aA 104 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8024 (tm-30) REVERT: bA 202 LYS cc_start: 0.9369 (tttm) cc_final: 0.9009 (ttmm) REVERT: bA 204 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8127 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9197 (ttmt) cc_final: 0.8961 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9227 (tm-30) cc_final: 0.7927 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9319 (t80) cc_final: 0.8949 (t80) REVERT: iA 204 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8175 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.9109 (t80) REVERT: nA 1306 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8933 (tptp) REVERT: d 4 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8087 (tp30) REVERT: oA 102 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9073 (tptm) REVERT: pA 204 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7668 (tm-30) REVERT: qA 306 LYS cc_start: 0.9129 (tptp) cc_final: 0.8861 (tptp) REVERT: tA 1204 GLU cc_start: 0.8721 (tm-30) cc_final: 0.7933 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9222 (tttt) cc_final: 0.9014 (tmtt) REVERT: e 4 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8412 (tp30) REVERT: e 6 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8831 (ttpt) REVERT: vA 104 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8571 (tm-30) REVERT: wA 202 LYS cc_start: 0.9347 (tttm) cc_final: 0.8982 (ttmm) REVERT: wA 204 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8297 (tm-30) REVERT: wA 206 LYS cc_start: 0.9199 (pttt) cc_final: 0.8869 (pptt) REVERT: yA 1004 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8342 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8598 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.9078 (t80) REVERT: f 2 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8901 (ttmt) REVERT: f 4 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8568 (tp30) REVERT: 3A 202 LYS cc_start: 0.9390 (tttm) cc_final: 0.9123 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8243 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8878 (tptp) REVERT: 4A 304 GLU cc_start: 0.9337 (tm-30) cc_final: 0.8436 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8060 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8938 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8325 (tm-30) REVERT: g 2 LYS cc_start: 0.9169 (tppt) cc_final: 0.8668 (tppt) REVERT: g 4 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8386 (tp30) REVERT: 9A 105 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9220 (t80) REVERT: AB 202 LYS cc_start: 0.9452 (tttm) cc_final: 0.9111 (ttmm) REVERT: AB 204 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8058 (tm-30) REVERT: BB 302 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9052 (tptp) REVERT: BB 305 PHE cc_start: 0.9496 (OUTLIER) cc_final: 0.9263 (t80) REVERT: CB 1004 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8449 (tp30) REVERT: DB 1102 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9089 (tptm) REVERT: EB 1204 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7565 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8687 (tptp) REVERT: h 4 GLU cc_start: 0.8810 (tp30) cc_final: 0.8212 (pm20) REVERT: GB 103 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9140 (t80) REVERT: HB 202 LYS cc_start: 0.9434 (tttm) cc_final: 0.9046 (pttt) REVERT: IB 306 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8974 (tptp) REVERT: JB 1004 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: i 4 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8505 (tp30) REVERT: NB 102 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9140 (pttt) REVERT: NB 104 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8269 (pm20) REVERT: NB 106 LYS cc_start: 0.9229 (tttp) cc_final: 0.8703 (pptt) REVERT: OB 202 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9204 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8084 (tp30) REVERT: QB 1005 PHE cc_start: 0.9306 (t80) cc_final: 0.8721 (t80) outliers start: 228 outliers final: 164 residues processed: 528 average time/residue: 0.4556 time to fit residues: 293.5299 Evaluate side-chains 639 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 431 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.060093 restraints weight = 34700.629| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.18 r_work: 0.2649 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.7605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.352 12563 Z= 4.897 Angle : 4.067 30.143 16272 Z= 1.841 Chirality : 0.300 0.963 1152 Planarity : 0.017 0.062 2160 Dihedral : 20.602 83.079 1496 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 108.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.62 % Favored : 80.21 % Rotamer: Outliers : 27.31 % Allowed : 22.80 % Favored : 49.88 % Cbeta Deviations : 15.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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: -5.93 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 Details of bonding type rmsd hydrogen bonds : bond 0.19072 ( 278) hydrogen bonds : angle 9.45715 ( 786) covalent geometry : bond 0.11029 (12528) covalent geometry : angle 4.06700 (16272) Misc. bond : bond 0.01090 ( 35) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 429 time to evaluate : 1.531 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: A 6 LYS cc_start: 0.9313 (mtmt) cc_final: 0.8964 (mtmt) REVERT: J 104 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8169 (mm-30) REVERT: J 106 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8844 (tmmm) REVERT: M 1004 GLU cc_start: 0.8451 (mp0) cc_final: 0.7520 (mp0) REVERT: N 1104 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8488 (mm-30) REVERT: N 1106 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8651 (mmmm) REVERT: O 1206 LYS cc_start: 0.9265 (ttmm) cc_final: 0.9055 (ttmm) REVERT: P 1304 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8519 (mm-30) REVERT: B 4 GLU cc_start: 0.8409 (mp0) cc_final: 0.8063 (mp0) REVERT: Q 104 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8342 (mm-30) REVERT: Q 106 LYS cc_start: 0.9276 (mmmm) cc_final: 0.8974 (mmmm) REVERT: T 1004 GLU cc_start: 0.8689 (mp0) cc_final: 0.7957 (mp0) REVERT: T 1006 LYS cc_start: 0.9334 (mtmt) cc_final: 0.9026 (mtmt) REVERT: U 1104 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8190 (mm-30) REVERT: U 1106 LYS cc_start: 0.9040 (tptm) cc_final: 0.8666 (tptm) REVERT: W 1302 LYS cc_start: 0.9421 (mtpt) cc_final: 0.9047 (mtpp) REVERT: W 1304 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8480 (mm-30) REVERT: C 4 GLU cc_start: 0.8568 (mp0) cc_final: 0.7649 (mp0) REVERT: X 106 LYS cc_start: 0.9348 (mmmm) cc_final: 0.9010 (mmmm) REVERT: j 1002 LYS cc_start: 0.8737 (tttt) cc_final: 0.8456 (tttp) REVERT: j 1004 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: j 1006 LYS cc_start: 0.9293 (mtmt) cc_final: 0.8946 (mtmt) REVERT: k 1102 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8218 (ttpt) REVERT: k 1104 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8226 (mm-30) REVERT: k 1106 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8823 (mmmm) REVERT: l 1202 LYS cc_start: 0.9377 (mtpt) cc_final: 0.9139 (mtpp) REVERT: l 1204 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8719 (mm-30) REVERT: D 4 GLU cc_start: 0.8394 (mp0) cc_final: 0.7675 (mp0) REVERT: D 6 LYS cc_start: 0.9298 (mtmt) cc_final: 0.8845 (mtmt) REVERT: D 7 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8698 (t80) REVERT: n 106 LYS cc_start: 0.9210 (mmmm) cc_final: 0.8773 (mmmm) REVERT: r 1104 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: r 1106 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8827 (mmmm) REVERT: E 6 LYS cc_start: 0.9204 (mtmt) cc_final: 0.8939 (mtmt) REVERT: u 106 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8597 (mmmm) REVERT: v 206 LYS cc_start: 0.9445 (ttmm) cc_final: 0.9188 (ttmm) REVERT: w 307 PHE cc_start: 0.9547 (OUTLIER) cc_final: 0.9023 (m-80) REVERT: x 1006 LYS cc_start: 0.9142 (mtmt) cc_final: 0.8763 (mtmt) REVERT: y 1106 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8957 (mmmm) REVERT: F 6 LYS cc_start: 0.9275 (mtmt) cc_final: 0.8982 (mtmt) REVERT: 1 104 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8176 (mm-30) REVERT: 1 106 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8730 (mmmm) REVERT: 3 302 LYS cc_start: 0.9483 (ttpt) cc_final: 0.9115 (ttmm) REVERT: 5 1104 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8275 (mp0) REVERT: 5 1106 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8811 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9432 (mtpt) cc_final: 0.9061 (mtpp) REVERT: G 3 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: G 4 GLU cc_start: 0.8380 (mp0) cc_final: 0.7995 (mp0) REVERT: G 6 LYS cc_start: 0.9353 (mtmt) cc_final: 0.9028 (mtmt) REVERT: 8 104 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7952 (mm-30) REVERT: 8 106 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8669 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8461 (mp0) cc_final: 0.8079 (mp0) REVERT: CA 1104 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8228 (mm-30) REVERT: H 4 GLU cc_start: 0.4213 (OUTLIER) cc_final: 0.2952 (pm20) REVERT: FA 106 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8988 (mmmm) REVERT: HA 302 LYS cc_start: 0.9340 (mtpt) cc_final: 0.9034 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8464 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8798 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9253 (mtpt) cc_final: 0.9029 (pttp) REVERT: I 4 GLU cc_start: 0.8258 (mp0) cc_final: 0.7396 (mp0) REVERT: MA 106 LYS cc_start: 0.5308 (OUTLIER) cc_final: 0.5020 (tptt) REVERT: PA 1004 GLU cc_start: 0.8471 (mp0) cc_final: 0.7820 (mp0) REVERT: PA 1006 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.9039 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9375 (mtpt) cc_final: 0.9144 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8568 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9277 (tttt) cc_final: 0.8873 (tttt) REVERT: SA 1307 PHE cc_start: 0.9461 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: a 2 LYS cc_start: 0.9272 (tppt) cc_final: 0.9027 (tppt) REVERT: a 4 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8491 (tp30) REVERT: TA 106 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8835 (ptmm) REVERT: UA 202 LYS cc_start: 0.9444 (tttm) cc_final: 0.9034 (ttmm) REVERT: UA 204 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7859 (tm-30) REVERT: VA 302 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9087 (tptp) REVERT: WA 1002 LYS cc_start: 0.9265 (tppt) cc_final: 0.8895 (tppt) REVERT: WA 1004 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8641 (tp30) REVERT: YA 1204 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7941 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8818 (t80) REVERT: ZA 1304 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8590 (tm-30) REVERT: aA 104 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8006 (tm-30) REVERT: bA 202 LYS cc_start: 0.9377 (tttm) cc_final: 0.9047 (ttmm) REVERT: bA 204 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8117 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8971 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9234 (tm-30) cc_final: 0.7934 (tm-30) REVERT: c 4 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: iA 204 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8220 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.9117 (t80) REVERT: nA 1306 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8935 (tptp) REVERT: d 2 LYS cc_start: 0.9202 (tppt) cc_final: 0.8894 (tppt) REVERT: d 4 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: oA 102 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9085 (tptm) REVERT: pA 204 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7646 (tm-30) REVERT: qA 306 LYS cc_start: 0.9133 (tptp) cc_final: 0.8866 (tptp) REVERT: rA 1006 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8957 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8716 (tm-30) cc_final: 0.7915 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9227 (tttt) cc_final: 0.9005 (tmtt) REVERT: e 4 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8380 (tp30) REVERT: e 6 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8840 (ttpt) REVERT: vA 104 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8567 (tm-30) REVERT: wA 202 LYS cc_start: 0.9345 (tttm) cc_final: 0.8977 (ttmm) REVERT: wA 204 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8302 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8345 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8608 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.9086 (t80) REVERT: f 2 LYS cc_start: 0.9252 (ttmt) cc_final: 0.8904 (ttmt) REVERT: f 4 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8566 (tp30) REVERT: 3A 202 LYS cc_start: 0.9375 (tttm) cc_final: 0.9116 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8187 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8885 (tptp) REVERT: 4A 304 GLU cc_start: 0.9351 (tm-30) cc_final: 0.8415 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8068 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8950 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8318 (tm-30) REVERT: g 2 LYS cc_start: 0.9165 (tppt) cc_final: 0.8674 (tppt) REVERT: g 4 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8384 (tp30) REVERT: 9A 105 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.9181 (t80) REVERT: AB 202 LYS cc_start: 0.9454 (tttm) cc_final: 0.9116 (ttmm) REVERT: AB 204 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8063 (tm-30) REVERT: BB 302 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9052 (tptp) REVERT: BB 305 PHE cc_start: 0.9500 (OUTLIER) cc_final: 0.9272 (t80) REVERT: CB 1004 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8462 (tp30) REVERT: DB 1102 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9101 (tptm) REVERT: EB 1204 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7577 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8730 (tptp) REVERT: h 4 GLU cc_start: 0.8789 (tp30) cc_final: 0.8175 (pm20) REVERT: GB 103 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9140 (t80) REVERT: HB 202 LYS cc_start: 0.9430 (tttm) cc_final: 0.9049 (pttt) REVERT: IB 306 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8955 (tptp) REVERT: JB 1004 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: i 4 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8533 (tp30) REVERT: NB 102 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9144 (pttt) REVERT: NB 104 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8302 (pm20) REVERT: NB 106 LYS cc_start: 0.9230 (tttp) cc_final: 0.8717 (pptt) REVERT: QB 1004 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: QB 1005 PHE cc_start: 0.9312 (t80) cc_final: 0.8732 (t80) REVERT: QB 1006 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9046 (ttpt) outliers start: 236 outliers final: 171 residues processed: 533 average time/residue: 0.4810 time to fit residues: 312.5175 Evaluate side-chains 645 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 429 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060051 restraints weight = 34799.350| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.16 r_work: 0.2650 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.7628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.346 12563 Z= 4.893 Angle : 4.087 31.172 16272 Z= 1.846 Chirality : 0.300 0.967 1152 Planarity : 0.017 0.063 2160 Dihedral : 20.560 83.309 1496 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 108.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.97 % Favored : 80.03 % Rotamer: Outliers : 27.66 % Allowed : 22.92 % Favored : 49.42 % Cbeta Deviations : 15.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.69 % 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: -5.94 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 Details of bonding type rmsd hydrogen bonds : bond 0.19106 ( 278) hydrogen bonds : angle 9.47358 ( 786) covalent geometry : bond 0.11023 (12528) covalent geometry : angle 4.08710 (16272) Misc. bond : bond 0.01112 ( 35) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 432 time to evaluate : 2.522 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: A 4 GLU cc_start: 0.8279 (mp0) cc_final: 0.7551 (mp0) REVERT: A 6 LYS cc_start: 0.9306 (mtmt) cc_final: 0.8947 (mtmt) REVERT: J 104 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8209 (mm-30) REVERT: J 106 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.8798 (tmmm) REVERT: M 1004 GLU cc_start: 0.8478 (mp0) cc_final: 0.7549 (mp0) REVERT: N 1104 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8492 (mm-30) REVERT: N 1106 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8634 (mmmm) REVERT: O 1206 LYS cc_start: 0.9265 (ttmm) cc_final: 0.9056 (ttmm) REVERT: B 4 GLU cc_start: 0.8399 (mp0) cc_final: 0.8149 (mp0) REVERT: Q 104 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7975 (mm-30) REVERT: Q 106 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8974 (mmmm) REVERT: T 1004 GLU cc_start: 0.8690 (mp0) cc_final: 0.7970 (mp0) REVERT: T 1006 LYS cc_start: 0.9324 (mtmt) cc_final: 0.8968 (mtmt) REVERT: U 1104 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8195 (mm-30) REVERT: U 1106 LYS cc_start: 0.9046 (tptm) cc_final: 0.8674 (tptm) REVERT: W 1302 LYS cc_start: 0.9413 (mtpt) cc_final: 0.9042 (mtpp) REVERT: W 1304 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8455 (mm-30) REVERT: C 4 GLU cc_start: 0.8564 (mp0) cc_final: 0.7632 (mp0) REVERT: X 106 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9010 (mmmm) REVERT: j 1002 LYS cc_start: 0.8738 (tttt) cc_final: 0.8455 (tttp) REVERT: j 1004 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: j 1006 LYS cc_start: 0.9292 (mtmt) cc_final: 0.8880 (mtmt) REVERT: k 1102 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8217 (ttpt) REVERT: k 1104 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8180 (mm-30) REVERT: k 1106 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8829 (mmmm) REVERT: l 1202 LYS cc_start: 0.9367 (mtpt) cc_final: 0.9132 (mtpp) REVERT: l 1204 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8746 (mm-30) REVERT: D 4 GLU cc_start: 0.8393 (mp0) cc_final: 0.7701 (mp0) REVERT: D 6 LYS cc_start: 0.9299 (mtmt) cc_final: 0.8850 (mtmt) REVERT: D 7 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8707 (t80) REVERT: n 106 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8760 (mmmm) REVERT: o 202 LYS cc_start: 0.9385 (ttpt) cc_final: 0.9085 (ttpt) REVERT: r 1104 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7955 (mm-30) REVERT: r 1106 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8755 (mmmm) REVERT: E 6 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8949 (mtmt) REVERT: u 106 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8585 (mmmm) REVERT: v 206 LYS cc_start: 0.9446 (ttmm) cc_final: 0.9190 (ttmm) REVERT: w 302 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8978 (mmmm) REVERT: w 307 PHE cc_start: 0.9577 (OUTLIER) cc_final: 0.9006 (m-80) REVERT: x 1003 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8819 (m-80) REVERT: x 1006 LYS cc_start: 0.9142 (mtmt) cc_final: 0.8725 (mtmt) REVERT: y 1106 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8964 (mmmm) REVERT: F 6 LYS cc_start: 0.9275 (mtmt) cc_final: 0.8991 (mtmt) REVERT: 1 104 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8195 (mm-30) REVERT: 1 106 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8726 (mmmm) REVERT: 3 302 LYS cc_start: 0.9446 (ttpt) cc_final: 0.9132 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8803 (mmmm) REVERT: G 3 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: G 4 GLU cc_start: 0.8366 (mp0) cc_final: 0.7990 (mp0) REVERT: G 6 LYS cc_start: 0.9344 (mtmt) cc_final: 0.9020 (mtmt) REVERT: 8 104 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7950 (mm-30) REVERT: 8 106 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8669 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8474 (mp0) cc_final: 0.8132 (mp0) REVERT: CA 1104 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8122 (mm-30) REVERT: H 4 GLU cc_start: 0.4208 (OUTLIER) cc_final: 0.2996 (pm20) REVERT: FA 106 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8991 (mmmm) REVERT: HA 302 LYS cc_start: 0.9352 (mtpt) cc_final: 0.9044 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8466 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8806 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9251 (mtpt) cc_final: 0.9023 (pttp) REVERT: I 4 GLU cc_start: 0.8241 (mp0) cc_final: 0.7402 (mp0) REVERT: MA 106 LYS cc_start: 0.5042 (OUTLIER) cc_final: 0.4130 (tptt) REVERT: PA 1004 GLU cc_start: 0.8464 (mp0) cc_final: 0.7779 (mp0) REVERT: PA 1006 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.9026 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9515 (OUTLIER) cc_final: 0.8921 (m-80) REVERT: RA 1202 LYS cc_start: 0.9373 (mtpt) cc_final: 0.9140 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8555 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9261 (tttt) cc_final: 0.8860 (tttt) REVERT: SA 1307 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.8629 (m-80) REVERT: a 2 LYS cc_start: 0.9270 (tppt) cc_final: 0.9031 (tppt) REVERT: a 4 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8488 (tp30) REVERT: TA 106 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8893 (ptmm) REVERT: UA 202 LYS cc_start: 0.9438 (tttm) cc_final: 0.9028 (ttmm) REVERT: UA 204 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7861 (tm-30) REVERT: VA 302 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9091 (tptp) REVERT: WA 1002 LYS cc_start: 0.9276 (tppt) cc_final: 0.8900 (tppt) REVERT: WA 1004 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8634 (tp30) REVERT: YA 1204 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7894 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8823 (t80) REVERT: ZA 1304 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8604 (tm-30) REVERT: aA 104 GLU cc_start: 0.8885 (tm-30) cc_final: 0.7993 (tm-30) REVERT: bA 202 LYS cc_start: 0.9370 (tttm) cc_final: 0.9038 (ttmm) REVERT: bA 204 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8110 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8953 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9231 (tm-30) cc_final: 0.7903 (tm-30) REVERT: iA 202 LYS cc_start: 0.9439 (tttm) cc_final: 0.9137 (mmmm) REVERT: iA 204 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8215 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.9113 (t80) REVERT: nA 1306 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8932 (tptp) REVERT: d 2 LYS cc_start: 0.9194 (tppt) cc_final: 0.8894 (tppt) REVERT: d 4 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8100 (tp30) REVERT: oA 102 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9085 (tptm) REVERT: pA 204 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7637 (tm-30) REVERT: qA 306 LYS cc_start: 0.9128 (tptp) cc_final: 0.8856 (tptp) REVERT: tA 1204 GLU cc_start: 0.8713 (tm-30) cc_final: 0.7903 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.9018 (tmtt) REVERT: e 4 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: e 6 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8836 (ttpt) REVERT: vA 104 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8566 (tm-30) REVERT: wA 202 LYS cc_start: 0.9348 (tttm) cc_final: 0.8979 (ttmm) REVERT: wA 204 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8327 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8342 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8352 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8619 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9089 (t80) REVERT: f 2 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8890 (ttmt) REVERT: f 4 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: 3A 202 LYS cc_start: 0.9364 (tttm) cc_final: 0.9109 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8163 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8880 (tptp) REVERT: 4A 304 GLU cc_start: 0.9351 (tm-30) cc_final: 0.8431 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8058 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8946 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8317 (tm-30) REVERT: g 2 LYS cc_start: 0.9166 (tppt) cc_final: 0.8675 (tppt) REVERT: g 4 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8389 (tp30) REVERT: 9A 105 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9164 (t80) REVERT: AB 202 LYS cc_start: 0.9457 (tttm) cc_final: 0.9118 (ttmm) REVERT: AB 204 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8051 (tm-30) REVERT: BB 302 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9048 (tptp) REVERT: BB 305 PHE cc_start: 0.9501 (OUTLIER) cc_final: 0.9272 (t80) REVERT: CB 1004 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: DB 1102 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9101 (tptm) REVERT: EB 1204 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7567 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8735 (tptp) REVERT: h 4 GLU cc_start: 0.8785 (tp30) cc_final: 0.8175 (pm20) REVERT: GB 103 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9137 (t80) REVERT: HB 202 LYS cc_start: 0.9424 (tttm) cc_final: 0.9044 (pttt) REVERT: IB 306 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8952 (tptp) REVERT: JB 1004 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: i 4 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8534 (tp30) REVERT: NB 102 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9148 (pttt) REVERT: NB 104 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8304 (pm20) REVERT: NB 106 LYS cc_start: 0.9230 (tttp) cc_final: 0.8721 (pptt) REVERT: QB 1004 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: QB 1005 PHE cc_start: 0.9311 (t80) cc_final: 0.8725 (t80) REVERT: QB 1006 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9030 (ttpt) outliers start: 239 outliers final: 174 residues processed: 535 average time/residue: 0.5814 time to fit residues: 390.1401 Evaluate side-chains 653 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 432 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060081 restraints weight = 34400.485| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.15 r_work: 0.2654 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.7651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.345 12563 Z= 4.895 Angle : 4.075 30.427 16272 Z= 1.843 Chirality : 0.300 0.964 1152 Planarity : 0.017 0.064 2160 Dihedral : 20.512 83.432 1496 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 109.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.14 % Favored : 79.86 % Rotamer: Outliers : 27.89 % Allowed : 23.15 % Favored : 48.96 % Cbeta Deviations : 15.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.69 % 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: -5.89 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 Details of bonding type rmsd hydrogen bonds : bond 0.19115 ( 278) hydrogen bonds : angle 9.46933 ( 786) covalent geometry : bond 0.11026 (12528) covalent geometry : angle 4.07473 (16272) Misc. bond : bond 0.01094 ( 35) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 431 time to evaluate : 1.982 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: A 4 GLU cc_start: 0.8336 (mp0) cc_final: 0.7497 (mp0) REVERT: A 6 LYS cc_start: 0.9305 (mtmt) cc_final: 0.8969 (mtmt) REVERT: J 104 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8208 (mm-30) REVERT: J 106 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8804 (tmmm) REVERT: M 1004 GLU cc_start: 0.8469 (mp0) cc_final: 0.7625 (mp0) REVERT: N 1104 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8508 (mm-30) REVERT: N 1106 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8650 (mmmm) REVERT: O 1206 LYS cc_start: 0.9259 (ttmm) cc_final: 0.9052 (ttmm) REVERT: B 4 GLU cc_start: 0.8378 (mp0) cc_final: 0.8136 (mp0) REVERT: Q 104 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7791 (mm-30) REVERT: Q 106 LYS cc_start: 0.9288 (mmmm) cc_final: 0.8983 (mmmm) REVERT: T 1004 GLU cc_start: 0.8706 (mp0) cc_final: 0.7981 (mp0) REVERT: T 1006 LYS cc_start: 0.9323 (mtmt) cc_final: 0.8946 (mtmt) REVERT: U 1104 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8201 (mm-30) REVERT: U 1106 LYS cc_start: 0.9050 (tptm) cc_final: 0.8679 (tptm) REVERT: W 1302 LYS cc_start: 0.9424 (mtpt) cc_final: 0.9053 (mtpp) REVERT: W 1304 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8463 (mm-30) REVERT: C 4 GLU cc_start: 0.8568 (mp0) cc_final: 0.7644 (mp0) REVERT: X 106 LYS cc_start: 0.9357 (mmmm) cc_final: 0.9022 (mmmm) REVERT: j 1002 LYS cc_start: 0.8717 (tttt) cc_final: 0.8446 (tttp) REVERT: j 1004 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: j 1006 LYS cc_start: 0.9284 (mtmt) cc_final: 0.8934 (mtmt) REVERT: k 1102 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8200 (ttpt) REVERT: k 1104 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8182 (mm-30) REVERT: k 1106 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8836 (mmmm) REVERT: l 1202 LYS cc_start: 0.9368 (mtpt) cc_final: 0.9027 (mtpp) REVERT: l 1204 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8769 (mm-30) REVERT: D 4 GLU cc_start: 0.8400 (mp0) cc_final: 0.7726 (mp0) REVERT: D 6 LYS cc_start: 0.9299 (mtmt) cc_final: 0.8851 (mtmt) REVERT: D 7 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.8708 (t80) REVERT: n 106 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8754 (mmmm) REVERT: o 202 LYS cc_start: 0.9380 (ttpt) cc_final: 0.9064 (ttpt) REVERT: r 1104 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: r 1106 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8743 (mmmm) REVERT: E 6 LYS cc_start: 0.9203 (mtmt) cc_final: 0.8956 (mtmt) REVERT: u 106 LYS cc_start: 0.9034 (mmmm) cc_final: 0.8586 (mmmm) REVERT: v 206 LYS cc_start: 0.9442 (ttmm) cc_final: 0.9180 (ttmm) REVERT: w 307 PHE cc_start: 0.9538 (OUTLIER) cc_final: 0.9089 (m-80) REVERT: x 1003 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: x 1006 LYS cc_start: 0.9121 (mtmt) cc_final: 0.8721 (mtmt) REVERT: y 1106 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8951 (mmmm) REVERT: F 6 LYS cc_start: 0.9282 (mtmt) cc_final: 0.9011 (mtmt) REVERT: 1 104 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8204 (mm-30) REVERT: 1 106 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8794 (mmmm) REVERT: 3 302 LYS cc_start: 0.9448 (ttpt) cc_final: 0.9149 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8819 (mmmm) REVERT: G 3 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: G 4 GLU cc_start: 0.8379 (mp0) cc_final: 0.8008 (mp0) REVERT: G 6 LYS cc_start: 0.9347 (mtmt) cc_final: 0.9031 (mtmt) REVERT: 8 104 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7962 (mm-30) REVERT: 8 106 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8674 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8451 (mp0) cc_final: 0.8113 (mp0) REVERT: CA 1104 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8116 (mm-30) REVERT: H 4 GLU cc_start: 0.4199 (OUTLIER) cc_final: 0.2951 (pm20) REVERT: FA 106 LYS cc_start: 0.9250 (mmmm) cc_final: 0.9012 (mmmm) REVERT: HA 302 LYS cc_start: 0.9352 (mtpt) cc_final: 0.9057 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8401 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8811 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9252 (mtpt) cc_final: 0.9023 (pttp) REVERT: I 4 GLU cc_start: 0.8237 (mp0) cc_final: 0.7406 (mp0) REVERT: MA 106 LYS cc_start: 0.4931 (OUTLIER) cc_final: 0.4241 (tptt) REVERT: PA 1004 GLU cc_start: 0.8457 (mp0) cc_final: 0.7774 (mp0) REVERT: PA 1006 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9026 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9518 (OUTLIER) cc_final: 0.8928 (m-80) REVERT: RA 1202 LYS cc_start: 0.9374 (mtpt) cc_final: 0.9135 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8559 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9272 (tttt) cc_final: 0.8870 (tttt) REVERT: SA 1307 PHE cc_start: 0.9472 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: a 2 LYS cc_start: 0.9258 (tppt) cc_final: 0.9024 (tppt) REVERT: a 4 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8500 (tp30) REVERT: TA 106 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8885 (ptmm) REVERT: UA 202 LYS cc_start: 0.9445 (tttm) cc_final: 0.9041 (ttmm) REVERT: UA 204 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7846 (tm-30) REVERT: VA 302 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9090 (tptp) REVERT: WA 1002 LYS cc_start: 0.9268 (tppt) cc_final: 0.8879 (tppt) REVERT: WA 1004 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8636 (tp30) REVERT: YA 1204 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7879 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8824 (t80) REVERT: ZA 1304 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8608 (tm-30) REVERT: aA 104 GLU cc_start: 0.8872 (tm-30) cc_final: 0.7977 (tm-30) REVERT: bA 202 LYS cc_start: 0.9381 (tttm) cc_final: 0.9051 (ttmm) REVERT: bA 204 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8070 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8949 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9227 (tm-30) cc_final: 0.7906 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9264 (t80) cc_final: 0.8910 (t80) REVERT: c 4 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: iA 202 LYS cc_start: 0.9429 (tttm) cc_final: 0.9128 (mmmm) REVERT: iA 204 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8229 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.9112 (t80) REVERT: d 2 LYS cc_start: 0.9197 (tppt) cc_final: 0.8894 (tppt) REVERT: d 4 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: oA 102 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9097 (tptm) REVERT: pA 204 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7644 (tm-30) REVERT: qA 306 LYS cc_start: 0.9126 (tptp) cc_final: 0.8859 (tptp) REVERT: tA 1204 GLU cc_start: 0.8719 (tm-30) cc_final: 0.7902 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.9013 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.9188 (t80) REVERT: e 4 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8390 (tp30) REVERT: e 6 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8834 (ttpt) REVERT: vA 104 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8559 (tm-30) REVERT: wA 202 LYS cc_start: 0.9341 (tttm) cc_final: 0.8969 (ttmm) REVERT: wA 204 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8317 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8342 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8337 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8632 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.9083 (t80) REVERT: f 2 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8893 (ttmt) REVERT: f 4 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8561 (tp30) REVERT: 3A 202 LYS cc_start: 0.9360 (tttm) cc_final: 0.9102 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8164 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8893 (tptp) REVERT: 4A 304 GLU cc_start: 0.9348 (tm-30) cc_final: 0.8426 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8069 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8945 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8307 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.8878 (tptp) cc_final: 0.8631 (tptp) REVERT: g 2 LYS cc_start: 0.9162 (tppt) cc_final: 0.8673 (tppt) REVERT: g 4 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: 9A 105 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.9173 (t80) REVERT: AB 202 LYS cc_start: 0.9455 (tttm) cc_final: 0.9121 (ttmm) REVERT: AB 204 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8072 (tm-30) REVERT: BB 302 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9046 (tptp) REVERT: BB 305 PHE cc_start: 0.9506 (OUTLIER) cc_final: 0.9280 (t80) REVERT: CB 1004 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8466 (tp30) REVERT: DB 1102 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9089 (tptm) REVERT: EB 1204 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7574 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8731 (tptp) REVERT: h 4 GLU cc_start: 0.8781 (tp30) cc_final: 0.8170 (pm20) REVERT: GB 103 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.9140 (t80) REVERT: HB 202 LYS cc_start: 0.9408 (tttm) cc_final: 0.9041 (pttt) REVERT: IB 306 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8934 (tptp) REVERT: JB 1004 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8287 (tp30) REVERT: i 4 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8536 (tp30) REVERT: NB 102 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9148 (pttt) REVERT: NB 104 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8288 (pm20) REVERT: NB 106 LYS cc_start: 0.9230 (tttp) cc_final: 0.8733 (pptt) REVERT: QB 1004 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: QB 1005 PHE cc_start: 0.9310 (t80) cc_final: 0.8725 (t80) REVERT: QB 1006 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9028 (ttpt) outliers start: 241 outliers final: 177 residues processed: 536 average time/residue: 0.5682 time to fit residues: 372.1578 Evaluate side-chains 655 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 431 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060116 restraints weight = 34352.059| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.18 r_work: 0.2651 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.7668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.339 12563 Z= 4.893 Angle : 4.074 30.564 16272 Z= 1.841 Chirality : 0.300 0.964 1152 Planarity : 0.017 0.064 2160 Dihedral : 20.524 83.443 1496 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 109.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.49 % Favored : 79.51 % Rotamer: Outliers : 27.66 % Allowed : 23.50 % Favored : 48.84 % Cbeta Deviations : 15.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % 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: -5.88 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.017 PHE 2 205 Details of bonding type rmsd hydrogen bonds : bond 0.19218 ( 278) hydrogen bonds : angle 9.47257 ( 786) covalent geometry : bond 0.11024 (12528) covalent geometry : angle 4.07362 (16272) Misc. bond : bond 0.01132 ( 35) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 430 time to evaluate : 1.344 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: A 6 LYS cc_start: 0.9304 (mtmt) cc_final: 0.8957 (mtmt) REVERT: J 104 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8207 (mm-30) REVERT: J 106 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8768 (tmmm) REVERT: M 1004 GLU cc_start: 0.8278 (mp0) cc_final: 0.7481 (mp0) REVERT: N 1104 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8487 (mm-30) REVERT: N 1106 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8646 (mmmm) REVERT: O 1206 LYS cc_start: 0.9261 (ttmm) cc_final: 0.9056 (ttmm) REVERT: Q 104 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8071 (mm-30) REVERT: Q 106 LYS cc_start: 0.9284 (mmmm) cc_final: 0.8977 (mmmm) REVERT: T 1004 GLU cc_start: 0.8703 (mp0) cc_final: 0.7981 (mp0) REVERT: T 1006 LYS cc_start: 0.9320 (mtmt) cc_final: 0.8918 (mtmt) REVERT: U 1104 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8192 (mm-30) REVERT: U 1106 LYS cc_start: 0.9052 (tptm) cc_final: 0.8679 (tptm) REVERT: W 1302 LYS cc_start: 0.9410 (mtpt) cc_final: 0.9035 (mtpp) REVERT: W 1304 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8437 (mm-30) REVERT: C 4 GLU cc_start: 0.8577 (mp0) cc_final: 0.7640 (mp0) REVERT: X 106 LYS cc_start: 0.9358 (mmmm) cc_final: 0.9019 (mmmm) REVERT: j 1002 LYS cc_start: 0.8732 (tttt) cc_final: 0.8446 (tttp) REVERT: j 1004 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: j 1006 LYS cc_start: 0.9301 (mtmt) cc_final: 0.8928 (mtmt) REVERT: k 1102 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8208 (ttpt) REVERT: k 1104 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8182 (mm-30) REVERT: k 1106 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8838 (mmmm) REVERT: l 1202 LYS cc_start: 0.9366 (mtpt) cc_final: 0.9042 (mtpp) REVERT: l 1204 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8727 (mm-30) REVERT: D 4 GLU cc_start: 0.8395 (mp0) cc_final: 0.7721 (mp0) REVERT: D 6 LYS cc_start: 0.9294 (mtmt) cc_final: 0.8853 (mtmt) REVERT: D 7 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8708 (t80) REVERT: n 106 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8716 (mmmm) REVERT: o 202 LYS cc_start: 0.9387 (ttpt) cc_final: 0.9104 (ttpt) REVERT: r 1104 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: r 1106 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8736 (mmmm) REVERT: E 6 LYS cc_start: 0.9208 (mtmt) cc_final: 0.8965 (mtmt) REVERT: u 106 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8606 (mmmm) REVERT: v 206 LYS cc_start: 0.9447 (ttmm) cc_final: 0.9178 (ttmm) REVERT: w 302 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.8964 (mmmm) REVERT: w 307 PHE cc_start: 0.9577 (OUTLIER) cc_final: 0.9005 (m-80) REVERT: x 1003 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8850 (m-80) REVERT: x 1006 LYS cc_start: 0.9136 (mtmt) cc_final: 0.8767 (mtmt) REVERT: y 1106 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8946 (mmmm) REVERT: F 6 LYS cc_start: 0.9269 (mtmt) cc_final: 0.8995 (mtmt) REVERT: 1 104 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8211 (mm-30) REVERT: 1 106 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8796 (mmmm) REVERT: 3 302 LYS cc_start: 0.9433 (ttpt) cc_final: 0.9133 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8809 (mmmm) REVERT: G 3 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: G 4 GLU cc_start: 0.8382 (mp0) cc_final: 0.8006 (mp0) REVERT: G 6 LYS cc_start: 0.9356 (mtmt) cc_final: 0.9057 (mtmt) REVERT: 8 104 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7959 (mm-30) REVERT: 8 106 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8677 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8456 (mp0) cc_final: 0.8118 (mp0) REVERT: CA 1104 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8114 (mm-30) REVERT: H 4 GLU cc_start: 0.4189 (OUTLIER) cc_final: 0.2980 (pm20) REVERT: FA 106 LYS cc_start: 0.9249 (mmmm) cc_final: 0.9007 (mmmm) REVERT: HA 302 LYS cc_start: 0.9350 (mtpt) cc_final: 0.9054 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8335 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8811 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9251 (mtpt) cc_final: 0.9018 (pttp) REVERT: I 4 GLU cc_start: 0.8253 (mp0) cc_final: 0.7426 (mp0) REVERT: MA 106 LYS cc_start: 0.4935 (OUTLIER) cc_final: 0.4177 (tptt) REVERT: PA 1004 GLU cc_start: 0.8440 (mp0) cc_final: 0.7772 (mp0) REVERT: PA 1006 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.9049 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9536 (OUTLIER) cc_final: 0.8955 (m-80) REVERT: RA 1202 LYS cc_start: 0.9370 (mtpt) cc_final: 0.9128 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8556 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9268 (tttt) cc_final: 0.8862 (tttt) REVERT: SA 1307 PHE cc_start: 0.9491 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: a 2 LYS cc_start: 0.9261 (tppt) cc_final: 0.9032 (tppt) REVERT: a 4 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8496 (tp30) REVERT: TA 106 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8897 (ptmm) REVERT: UA 202 LYS cc_start: 0.9445 (tttm) cc_final: 0.9043 (ttmm) REVERT: UA 204 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7858 (tm-30) REVERT: VA 302 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9092 (tptp) REVERT: WA 1002 LYS cc_start: 0.9271 (tppt) cc_final: 0.8882 (tppt) REVERT: WA 1004 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8634 (tp30) REVERT: YA 1204 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7879 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8826 (t80) REVERT: ZA 1304 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8610 (tm-30) REVERT: aA 104 GLU cc_start: 0.8854 (tm-30) cc_final: 0.7991 (tm-30) REVERT: bA 202 LYS cc_start: 0.9382 (tttm) cc_final: 0.9052 (ttmm) REVERT: bA 204 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8076 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8955 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9220 (tm-30) cc_final: 0.7890 (tm-30) REVERT: c 2 LYS cc_start: 0.9365 (tppt) cc_final: 0.9120 (tppt) REVERT: c 4 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: iA 202 LYS cc_start: 0.9432 (tttm) cc_final: 0.9122 (mmmm) REVERT: iA 204 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8221 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.9114 (t80) REVERT: d 2 LYS cc_start: 0.9208 (tppt) cc_final: 0.8906 (tppt) REVERT: d 4 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8092 (tp30) REVERT: oA 102 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9085 (tptm) REVERT: pA 204 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7644 (tm-30) REVERT: qA 306 LYS cc_start: 0.9132 (tptp) cc_final: 0.8864 (tptp) REVERT: tA 1204 GLU cc_start: 0.8728 (tm-30) cc_final: 0.7908 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.9005 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9473 (OUTLIER) cc_final: 0.9186 (t80) REVERT: e 4 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8386 (tp30) REVERT: e 6 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8835 (ttpt) REVERT: vA 104 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8567 (tm-30) REVERT: wA 202 LYS cc_start: 0.9345 (tttm) cc_final: 0.8977 (ttmm) REVERT: wA 204 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8307 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8349 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8629 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.9083 (t80) REVERT: f 2 LYS cc_start: 0.9243 (ttmt) cc_final: 0.8893 (ttmt) REVERT: f 4 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8569 (tp30) REVERT: 3A 202 LYS cc_start: 0.9364 (tttm) cc_final: 0.9062 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8163 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8887 (tptp) REVERT: 4A 304 GLU cc_start: 0.9350 (tm-30) cc_final: 0.8442 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8053 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8939 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8318 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.8877 (tptp) cc_final: 0.8627 (tptp) REVERT: g 2 LYS cc_start: 0.9172 (tppt) cc_final: 0.8684 (tppt) REVERT: g 4 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: 9A 105 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9169 (t80) REVERT: AB 202 LYS cc_start: 0.9452 (tttm) cc_final: 0.9151 (ttmm) REVERT: AB 204 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8071 (tm-30) REVERT: BB 302 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9044 (tptp) REVERT: BB 305 PHE cc_start: 0.9500 (OUTLIER) cc_final: 0.9274 (t80) REVERT: CB 1004 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8464 (tp30) REVERT: DB 1102 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9091 (tptm) REVERT: EB 1204 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7566 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8728 (tptp) REVERT: h 4 GLU cc_start: 0.8776 (tp30) cc_final: 0.8170 (pm20) REVERT: GB 103 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9137 (t80) REVERT: HB 202 LYS cc_start: 0.9411 (tttm) cc_final: 0.9039 (pttt) REVERT: IB 306 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8894 (tptp) REVERT: JB 1004 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8287 (tp30) REVERT: i 4 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8503 (tp30) REVERT: NB 102 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9146 (pttt) REVERT: NB 104 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8294 (pm20) REVERT: NB 106 LYS cc_start: 0.9235 (tttp) cc_final: 0.8733 (pptt) REVERT: QB 1004 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: QB 1005 PHE cc_start: 0.9307 (t80) cc_final: 0.8717 (t80) REVERT: QB 1006 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9015 (ttpt) outliers start: 239 outliers final: 181 residues processed: 534 average time/residue: 0.4679 time to fit residues: 305.5681 Evaluate side-chains 659 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 430 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.070415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060062 restraints weight = 34415.779| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.17 r_work: 0.2650 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.7677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.338 12563 Z= 4.893 Angle : 4.075 30.606 16272 Z= 1.841 Chirality : 0.300 0.965 1152 Planarity : 0.017 0.064 2160 Dihedral : 20.519 83.605 1496 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 110.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.49 % Favored : 79.51 % Rotamer: Outliers : 27.31 % Allowed : 24.31 % Favored : 48.38 % Cbeta Deviations : 15.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % 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: -5.89 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 Details of bonding type rmsd hydrogen bonds : bond 0.19232 ( 278) hydrogen bonds : angle 9.47236 ( 786) covalent geometry : bond 0.11022 (12528) covalent geometry : angle 4.07520 (16272) Misc. bond : bond 0.01110 ( 35) =============================================================================== Job complete usr+sys time: 7233.30 seconds wall clock time: 130 minutes 36.81 seconds (7836.81 seconds total)