Starting phenix.real_space_refine on Sat Oct 24 02:50:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lqh_23486/10_2026/7lqh_23486.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqh_23486/10_2026/7lqh_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lqh_23486/10_2026/7lqh_23486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqh_23486/10_2026/7lqh_23486.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lqh_23486/10_2026/7lqh_23486.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lqh_23486/10_2026/7lqh_23486.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lqh_23486/10_2026/7lqh_23486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqh_23486/10_2026/7lqh_23486.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/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: 2.54, per 1000 atoms: 0.21 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: 0.92 Conformation dependent library (CDL) restraints added in 194.8 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: 0.23 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: 1.39 Time building geometry restraints manager: 1.19 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: 0.000 Normalize map: mean=0, sd=1: 3.300 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.930 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 31.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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/Z covalent geometry : bond 0.01603 / 0.78 (12528) covalent geometry : angle 1.41746 / 0.59 (16272) hydrogen bonds : bond 0.31155 / 16.93 ( 278) hydrogen bonds : angle 15.44491 / 8.75 ( 786) Misc. bond : bond 0.57724 / 30.34 ( 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 : 0.438 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: 0.7492 (mp0) cc_final: 0.6748 (pm20) REVERT: S 306 LYS cc_start: 0.8628 (tttt) cc_final: 0.8357 (mttt) REVERT: Y 206 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8179 (ttmm) REVERT: Z 306 LYS cc_start: 0.8563 (tttt) cc_final: 0.8261 (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: 0.8340 (mttt) REVERT: o 204 GLU cc_start: 0.7422 (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: 0.7749 (mm-30) cc_final: 0.7091 (mm-30) REVERT: w 306 LYS cc_start: 0.8690 (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: 0.7621 (mm-30) cc_final: 0.7144 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8595 (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: 0.7149 (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: 0.6533 (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: 0.7038 (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: 0.8343 (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: 0.8547 (t80) cc_final: 0.8265 (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: 0.8996 (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: 0.8426 (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: 0.8657 (tttm) cc_final: 0.8373 (tttm) REVERT: c 5 PHE cc_start: 0.8933 (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: 0.8869 (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: 0.8704 (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: 0.8846 (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: 0.8827 (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: 0.8738 (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: 0.9168 (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: 0.9153 (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: 0.9122 (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: 0.8928 (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: 0.9079 (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: 0.1937 time to fit residues: 118.6084 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 : 0.433 ------------------------------------------------------------------------------- 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: [0] chunk 0 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076669 restraints weight = 24104.301| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.34 r_work: 0.3100 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12563 Z= 0.127 Angle : 0.659 8.672 16272 Z= 0.303 Chirality : 0.032 0.083 1152 Planarity : 0.002 0.013 2160 Dihedral : 16.167 80.025 1779 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 20.95 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.61 (0.17), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.13), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.002 PHEnA1303 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (12528) covalent geometry : angle 0.65935 / 0.30 (16272) hydrogen bonds : bond 0.02719 / 1.48 ( 278) hydrogen bonds : angle 7.96744 / 4.58 ( 786) Misc. bond : bond 0.00140 / 0.08 ( 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 471 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 462 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 304 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8402 (mm-30) REVERT: N 1106 LYS cc_start: 0.8720 (tptm) cc_final: 0.8158 (tptm) REVERT: O 1206 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8468 (ttmm) REVERT: S 306 LYS cc_start: 0.8915 (tttt) cc_final: 0.8684 (mttt) REVERT: X 102 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8500 (ttpt) REVERT: Y 206 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8357 (ttmm) REVERT: Z 306 LYS cc_start: 0.8855 (tttt) cc_final: 0.8585 (tttt) REVERT: j 1002 LYS cc_start: 0.8130 (tttt) cc_final: 0.7918 (tttt) REVERT: j 1004 GLU cc_start: 0.8226 (mp0) cc_final: 0.7390 (mp0) REVERT: j 1006 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8190 (mtmt) REVERT: l 1206 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8607 (ttmm) REVERT: m 1306 LYS cc_start: 0.8909 (tttt) cc_final: 0.8608 (mttt) REVERT: D 6 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8175 (mtmt) REVERT: n 106 LYS cc_start: 0.8675 (tptm) cc_final: 0.8114 (tptm) REVERT: p 306 LYS cc_start: 0.8986 (tttt) cc_final: 0.8751 (mttt) REVERT: r 1103 PHE cc_start: 0.8765 (m-80) cc_final: 0.8502 (m-80) REVERT: u 106 LYS cc_start: 0.8645 (tptm) cc_final: 0.8423 (tptm) REVERT: v 204 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8122 (mt-10) REVERT: w 304 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7914 (mm-30) REVERT: w 306 LYS cc_start: 0.8864 (tttt) cc_final: 0.8580 (mttt) REVERT: z 1206 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8456 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7844 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8878 (tttt) cc_final: 0.8292 (tttt) REVERT: F 4 GLU cc_start: 0.7641 (mp0) cc_final: 0.6465 (pm20) REVERT: 1 106 LYS cc_start: 0.8831 (tptm) cc_final: 0.8624 (tptm) REVERT: 3 306 LYS cc_start: 0.8750 (tttt) cc_final: 0.8538 (tttt) REVERT: 5 1106 LYS cc_start: 0.8662 (tptm) cc_final: 0.8164 (tptm) REVERT: 6 1204 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7935 (mt-10) REVERT: 6 1206 LYS cc_start: 0.8841 (ttmm) cc_final: 0.8613 (ttmm) REVERT: 7 1304 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8141 (mm-30) REVERT: 7 1306 LYS cc_start: 0.8993 (tttt) cc_final: 0.8691 (mttt) REVERT: 8 106 LYS cc_start: 0.8725 (tptm) cc_final: 0.8490 (tptm) REVERT: 9 204 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7553 (mt-10) REVERT: CA 1106 LYS cc_start: 0.8638 (tptm) cc_final: 0.8327 (tptm) REVERT: DA 1204 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7576 (mt-10) REVERT: EA 1306 LYS cc_start: 0.8994 (tttt) cc_final: 0.8736 (mttt) REVERT: H 4 GLU cc_start: 0.4369 (pm20) cc_final: 0.3529 (pm20) REVERT: FA 106 LYS cc_start: 0.8732 (tptm) cc_final: 0.8443 (tptm) REVERT: GA 203 PHE cc_start: 0.8822 (m-80) cc_final: 0.8595 (m-80) REVERT: HA 306 LYS cc_start: 0.8929 (tttt) cc_final: 0.8637 (mttt) REVERT: JA 1106 LYS cc_start: 0.8641 (tptm) cc_final: 0.8347 (tptm) REVERT: LA 1306 LYS cc_start: 0.9027 (tttt) cc_final: 0.8736 (mttt) REVERT: MA 106 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8539 (mmmm) REVERT: OA 306 LYS cc_start: 0.8957 (tttt) cc_final: 0.8633 (mttt) REVERT: QA 1106 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8557 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8526 (ttmm) REVERT: SA 1306 LYS cc_start: 0.9079 (tttt) cc_final: 0.8811 (tttt) REVERT: a 2 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8026 (tppt) REVERT: a 3 PHE cc_start: 0.9198 (t80) cc_final: 0.8783 (t80) REVERT: a 7 PHE cc_start: 0.9301 (t80) cc_final: 0.8990 (t80) REVERT: TA 104 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: TA 105 PHE cc_start: 0.9034 (t80) cc_final: 0.8753 (t80) REVERT: UA 202 LYS cc_start: 0.8671 (tttm) cc_final: 0.8265 (mmmm) REVERT: UA 206 LYS cc_start: 0.8718 (tttt) cc_final: 0.8442 (tttm) REVERT: VA 304 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8625 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8181 (ttpt) REVERT: WA 1005 PHE cc_start: 0.8963 (t80) cc_final: 0.8450 (t80) REVERT: XA 1107 PHE cc_start: 0.8854 (t80) cc_final: 0.8453 (t80) REVERT: YA 1202 LYS cc_start: 0.8836 (tttm) cc_final: 0.8425 (tttm) REVERT: YA 1205 PHE cc_start: 0.8568 (t80) cc_final: 0.8174 (t80) REVERT: ZA 1305 PHE cc_start: 0.8625 (t80) cc_final: 0.8303 (t80) REVERT: b 2 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8486 (ttpt) REVERT: b 5 PHE cc_start: 0.9155 (t80) cc_final: 0.8760 (t80) REVERT: b 6 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8454 (ttpt) REVERT: aA 106 LYS cc_start: 0.8557 (tttp) cc_final: 0.8329 (tttp) REVERT: aA 107 PHE cc_start: 0.8830 (t80) cc_final: 0.8586 (t80) REVERT: bA 202 LYS cc_start: 0.8709 (tttm) cc_final: 0.8258 (ttmm) REVERT: cA 304 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8531 (tm-30) REVERT: cA 307 PHE cc_start: 0.8753 (t80) cc_final: 0.8353 (t80) REVERT: fA 1202 LYS cc_start: 0.8657 (tttm) cc_final: 0.8371 (tttm) REVERT: c 2 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8588 (ttpt) REVERT: c 4 GLU cc_start: 0.8042 (tp30) cc_final: 0.7827 (tp30) REVERT: c 5 PHE cc_start: 0.8898 (t80) cc_final: 0.8342 (t80) REVERT: c 7 PHE cc_start: 0.9322 (t80) cc_final: 0.8924 (t80) REVERT: hA 106 LYS cc_start: 0.8705 (tttp) cc_final: 0.8466 (tttp) REVERT: iA 202 LYS cc_start: 0.8912 (tttm) cc_final: 0.8571 (mmmm) REVERT: jA 306 LYS cc_start: 0.8459 (tptp) cc_final: 0.7993 (tptp) REVERT: kA 1005 PHE cc_start: 0.9029 (t80) cc_final: 0.8758 (t80) REVERT: lA 1103 PHE cc_start: 0.8729 (t80) cc_final: 0.8303 (t80) REVERT: mA 1206 LYS cc_start: 0.8476 (tttt) cc_final: 0.8185 (tttm) REVERT: nA 1305 PHE cc_start: 0.8690 (t80) cc_final: 0.8425 (t80) REVERT: d 3 PHE cc_start: 0.9149 (t80) cc_final: 0.8596 (t80) REVERT: d 5 PHE cc_start: 0.8947 (t80) cc_final: 0.8617 (t80) REVERT: d 7 PHE cc_start: 0.9319 (t80) cc_final: 0.8864 (t80) REVERT: oA 107 PHE cc_start: 0.8710 (t80) cc_final: 0.8162 (t80) REVERT: pA 202 LYS cc_start: 0.8637 (tttm) cc_final: 0.8294 (mmmm) REVERT: qA 304 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8571 (tm-30) REVERT: rA 1003 PHE cc_start: 0.9131 (t80) cc_final: 0.8927 (t80) REVERT: rA 1005 PHE cc_start: 0.8917 (t80) cc_final: 0.8611 (t80) REVERT: rA 1006 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8437 (ttpt) REVERT: sA 1103 PHE cc_start: 0.8803 (t80) cc_final: 0.8122 (t80) REVERT: tA 1206 LYS cc_start: 0.8530 (tttt) cc_final: 0.8316 (tttt) REVERT: vA 107 PHE cc_start: 0.8739 (t80) cc_final: 0.8477 (t80) REVERT: wA 202 LYS cc_start: 0.8548 (tttm) cc_final: 0.8282 (mmmm) REVERT: wA 206 LYS cc_start: 0.8455 (tttt) cc_final: 0.8241 (tttt) REVERT: zA 1105 PHE cc_start: 0.8942 (t80) cc_final: 0.8695 (t80) REVERT: 1A 1303 PHE cc_start: 0.8384 (t80) cc_final: 0.7985 (t80) REVERT: f 7 PHE cc_start: 0.9254 (t80) cc_final: 0.9044 (t80) REVERT: 3A 202 LYS cc_start: 0.8770 (tttm) cc_final: 0.8337 (mmmm) REVERT: 4A 305 PHE cc_start: 0.8697 (t80) cc_final: 0.8422 (t80) REVERT: 5A 1003 PHE cc_start: 0.9066 (t80) cc_final: 0.8405 (t80) REVERT: 5A 1005 PHE cc_start: 0.8916 (t80) cc_final: 0.8569 (t80) REVERT: 5A 1007 PHE cc_start: 0.9209 (t80) cc_final: 0.8577 (t80) REVERT: 6A 1103 PHE cc_start: 0.8674 (t80) cc_final: 0.8406 (t80) REVERT: 7A 1205 PHE cc_start: 0.8465 (t80) cc_final: 0.8258 (t80) REVERT: 7A 1206 LYS cc_start: 0.8406 (tttt) cc_final: 0.8191 (tttm) REVERT: g 2 LYS cc_start: 0.8500 (ttpt) cc_final: 0.7927 (tppt) REVERT: 9A 104 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: BB 306 LYS cc_start: 0.8467 (tptp) cc_final: 0.8229 (tptp) REVERT: BB 307 PHE cc_start: 0.8866 (t80) cc_final: 0.8415 (t80) REVERT: CB 1003 PHE cc_start: 0.9009 (t80) cc_final: 0.8289 (t80) REVERT: CB 1005 PHE cc_start: 0.9085 (t80) cc_final: 0.8655 (t80) REVERT: CB 1007 PHE cc_start: 0.9190 (t80) cc_final: 0.8856 (t80) REVERT: DB 1106 LYS cc_start: 0.8464 (tttp) cc_final: 0.8223 (tttp) REVERT: EB 1202 LYS cc_start: 0.8805 (tttm) cc_final: 0.8393 (tttm) REVERT: FB 1303 PHE cc_start: 0.8539 (t80) cc_final: 0.8165 (t80) REVERT: h 3 PHE cc_start: 0.9112 (t80) cc_final: 0.8436 (t80) REVERT: h 5 PHE cc_start: 0.8914 (t80) cc_final: 0.8510 (t80) REVERT: HB 206 LYS cc_start: 0.8882 (tttt) cc_final: 0.8671 (tttt) REVERT: MB 1303 PHE cc_start: 0.8521 (t80) cc_final: 0.8160 (t80) REVERT: i 2 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8228 (ttpt) REVERT: i 6 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8378 (ttpt) REVERT: NB 104 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: NB 107 PHE cc_start: 0.8826 (t80) cc_final: 0.8155 (t80) REVERT: PB 303 PHE cc_start: 0.8007 (t80) cc_final: 0.7723 (t80) REVERT: PB 306 LYS cc_start: 0.8794 (tptp) cc_final: 0.8090 (pptt) REVERT: PB 307 PHE cc_start: 0.8397 (t80) cc_final: 0.7876 (t80) REVERT: QB 1006 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8317 (ttpt) REVERT: SB 1202 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8332 (ttmm) REVERT: SB 1203 PHE cc_start: 0.8773 (t80) cc_final: 0.8515 (t80) REVERT: TB 1305 PHE cc_start: 0.8384 (t80) cc_final: 0.7912 (t80) REVERT: TB 1307 PHE cc_start: 0.8124 (t80) cc_final: 0.7630 (t80) outliers start: 9 outliers final: 3 residues processed: 465 average time/residue: 0.1965 time to fit residues: 113.9975 Evaluate side-chains 460 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 454 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain KA residue 1202 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain NB residue 104 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.076655 restraints weight = 25329.877| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.29 r_work: 0.3008 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.072 12563 Z= 0.715 Angle : 0.945 10.086 16272 Z= 0.436 Chirality : 0.049 0.211 1152 Planarity : 0.004 0.016 2160 Dihedral : 15.391 93.915 1449 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.86 % Allowed : 21.99 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.84 (0.15), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.44 (0.11), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.004 PHEvA 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01591 / 0.72 (12528) covalent geometry : angle 0.94476 / 0.44 (16272) hydrogen bonds : bond 0.04189 / 2.33 ( 278) hydrogen bonds : angle 6.94647 / 3.95 ( 786) Misc. bond : bond 0.00201 / 0.11 ( 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 524 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 482 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8694 (mtmt) REVERT: M 1004 GLU cc_start: 0.7300 (mp0) cc_final: 0.6632 (mp0) REVERT: M 1006 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8437 (mtmt) REVERT: N 1104 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7915 (mm-30) REVERT: N 1106 LYS cc_start: 0.8855 (tptm) cc_final: 0.8251 (tptm) REVERT: O 1206 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8606 (ttmm) REVERT: T 1004 GLU cc_start: 0.7706 (mp0) cc_final: 0.7320 (mp0) REVERT: U 1104 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7768 (mm-30) REVERT: X 102 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8555 (ttpt) REVERT: X 104 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7660 (mm-30) REVERT: j 1004 GLU cc_start: 0.8374 (mp0) cc_final: 0.7272 (mp0) REVERT: j 1006 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8489 (mtmt) REVERT: k 1104 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7779 (mm-30) REVERT: m 1306 LYS cc_start: 0.9075 (tttt) cc_final: 0.8861 (mttt) REVERT: D 6 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8427 (mtmt) REVERT: n 104 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7702 (mm-30) REVERT: r 1104 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7805 (mm-30) REVERT: r 1106 LYS cc_start: 0.8892 (tptm) cc_final: 0.8561 (mptm) REVERT: s 1206 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8710 (ttmm) REVERT: u 106 LYS cc_start: 0.8834 (tptm) cc_final: 0.8471 (tptm) REVERT: w 304 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8383 (mm-30) REVERT: w 306 LYS cc_start: 0.8978 (tttt) cc_final: 0.8716 (mttt) REVERT: x 1004 GLU cc_start: 0.7810 (mp0) cc_final: 0.7573 (mp0) REVERT: y 1106 LYS cc_start: 0.8764 (tptm) cc_final: 0.8457 (tptm) REVERT: z 1206 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8511 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8064 (mm-30) REVERT: 0 1306 LYS cc_start: 0.9138 (tttt) cc_final: 0.8684 (tttt) REVERT: F 4 GLU cc_start: 0.7497 (mp0) cc_final: 0.6441 (pm20) REVERT: 1 106 LYS cc_start: 0.8834 (tptm) cc_final: 0.8433 (tptm) REVERT: 4 1006 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8528 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8815 (tptm) cc_final: 0.8331 (tptm) REVERT: 6 1204 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7598 (mt-10) REVERT: 6 1206 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8730 (ttmm) REVERT: 7 1306 LYS cc_start: 0.9109 (tttt) cc_final: 0.8848 (mttt) REVERT: 8 106 LYS cc_start: 0.8885 (tptm) cc_final: 0.8617 (tptm) REVERT: CA 1106 LYS cc_start: 0.8807 (tptm) cc_final: 0.8406 (tptm) REVERT: EA 1306 LYS cc_start: 0.9117 (tttt) cc_final: 0.8912 (tttt) REVERT: FA 106 LYS cc_start: 0.8854 (tptm) cc_final: 0.8499 (tptm) REVERT: HA 306 LYS cc_start: 0.9075 (tttt) cc_final: 0.8792 (mttt) REVERT: JA 1106 LYS cc_start: 0.8787 (tptm) cc_final: 0.8428 (tptm) REVERT: LA 1304 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7686 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9052 (tttt) cc_final: 0.8785 (mttt) REVERT: MA 106 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8586 (mmmm) REVERT: OA 302 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5167 (tptt) REVERT: QA 1102 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8669 (ttpt) REVERT: QA 1104 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8005 (mm-30) REVERT: RA 1206 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8663 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8154 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9165 (tttt) cc_final: 0.8925 (tttt) REVERT: a 2 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8398 (tppt) REVERT: TA 102 LYS cc_start: 0.9021 (tptm) cc_final: 0.8642 (tptm) REVERT: TA 104 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: TA 105 PHE cc_start: 0.9089 (t80) cc_final: 0.8627 (t80) REVERT: UA 202 LYS cc_start: 0.9024 (tttm) cc_final: 0.8536 (ttmm) REVERT: VA 302 LYS cc_start: 0.8847 (tptp) cc_final: 0.8354 (tptp) REVERT: VA 304 GLU cc_start: 0.9076 (tm-30) cc_final: 0.7907 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8487 (ttpt) REVERT: YA 1202 LYS cc_start: 0.9110 (tttm) cc_final: 0.8691 (tttm) REVERT: ZA 1304 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8225 (tm-30) REVERT: ZA 1305 PHE cc_start: 0.8574 (t80) cc_final: 0.8357 (t80) REVERT: b 2 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8685 (ttpt) REVERT: b 6 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8570 (ttpt) REVERT: aA 102 LYS cc_start: 0.9035 (tptm) cc_final: 0.8725 (tptm) REVERT: aA 104 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8363 (tm-30) REVERT: aA 106 LYS cc_start: 0.8638 (tttp) cc_final: 0.8409 (tttp) REVERT: bA 202 LYS cc_start: 0.8984 (tttm) cc_final: 0.8484 (ttmm) REVERT: bA 204 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7366 (tm-30) REVERT: cA 302 LYS cc_start: 0.8789 (tptp) cc_final: 0.8354 (tptp) REVERT: cA 303 PHE cc_start: 0.8699 (t80) cc_final: 0.8197 (t80) REVERT: cA 304 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8388 (tm-30) REVERT: dA 1005 PHE cc_start: 0.8919 (t80) cc_final: 0.8641 (t80) REVERT: eA 1103 PHE cc_start: 0.8485 (t80) cc_final: 0.8125 (t80) REVERT: eA 1104 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8047 (tm-30) REVERT: c 2 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8842 (ttpt) REVERT: c 4 GLU cc_start: 0.8163 (tp30) cc_final: 0.7899 (tp30) REVERT: c 5 PHE cc_start: 0.8816 (t80) cc_final: 0.8400 (t80) REVERT: iA 202 LYS cc_start: 0.9045 (tttm) cc_final: 0.8642 (ttmm) REVERT: jA 302 LYS cc_start: 0.8604 (tptp) cc_final: 0.8324 (tptp) REVERT: jA 304 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8076 (tm-30) REVERT: jA 306 LYS cc_start: 0.8649 (tptp) cc_final: 0.8346 (tptp) REVERT: jA 307 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8823 (t80) REVERT: kA 1005 PHE cc_start: 0.8966 (t80) cc_final: 0.8674 (t80) REVERT: nA 1302 LYS cc_start: 0.8692 (tptp) cc_final: 0.8329 (tptp) REVERT: nA 1304 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8407 (tm-30) REVERT: nA 1306 LYS cc_start: 0.8567 (tptp) cc_final: 0.8145 (tptp) REVERT: d 2 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8787 (ttpt) REVERT: qA 304 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8605 (tm-30) REVERT: qA 306 LYS cc_start: 0.8529 (tptp) cc_final: 0.8212 (tptp) REVERT: rA 1006 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8488 (ttpt) REVERT: sA 1103 PHE cc_start: 0.8613 (t80) cc_final: 0.8298 (t80) REVERT: tA 1203 PHE cc_start: 0.8929 (t80) cc_final: 0.8706 (t80) REVERT: tA 1204 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7523 (tm-30) REVERT: tA 1206 LYS cc_start: 0.8738 (tttt) cc_final: 0.8518 (tttt) REVERT: uA 1302 LYS cc_start: 0.8848 (tptp) cc_final: 0.8504 (tptp) REVERT: e 2 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8445 (tppt) REVERT: vA 102 LYS cc_start: 0.9037 (tptm) cc_final: 0.8768 (tptm) REVERT: wA 206 LYS cc_start: 0.8624 (tttt) cc_final: 0.8295 (tttt) REVERT: xA 302 LYS cc_start: 0.8678 (tptp) cc_final: 0.8229 (tptp) REVERT: xA 303 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8402 (t80) REVERT: xA 306 LYS cc_start: 0.8490 (tptp) cc_final: 0.8196 (tptp) REVERT: zA 1105 PHE cc_start: 0.8925 (t80) cc_final: 0.8646 (t80) REVERT: 1A 1304 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8128 (tm-30) REVERT: f 2 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8608 (ttpt) REVERT: f 4 GLU cc_start: 0.8350 (tp30) cc_final: 0.8029 (tp30) REVERT: 2A 102 LYS cc_start: 0.8974 (tptm) cc_final: 0.8580 (tptm) REVERT: 3A 202 LYS cc_start: 0.8969 (tttm) cc_final: 0.8464 (ttmm) REVERT: 4A 304 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8984 (tm-30) REVERT: 4A 306 LYS cc_start: 0.8502 (tptp) cc_final: 0.8279 (tptp) REVERT: 4A 307 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8374 (t80) REVERT: 5A 1003 PHE cc_start: 0.9013 (t80) cc_final: 0.8695 (t80) REVERT: 5A 1007 PHE cc_start: 0.9392 (t80) cc_final: 0.8655 (t80) REVERT: g 2 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8420 (tppt) REVERT: g 4 GLU cc_start: 0.8223 (tp30) cc_final: 0.7870 (tp30) REVERT: 9A 102 LYS cc_start: 0.9068 (tptm) cc_final: 0.8741 (tptm) REVERT: 9A 103 PHE cc_start: 0.8807 (t80) cc_final: 0.8396 (t80) REVERT: 9A 104 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: AB 202 LYS cc_start: 0.8977 (tptm) cc_final: 0.8391 (ttmm) REVERT: BB 306 LYS cc_start: 0.8632 (tptp) cc_final: 0.8359 (tptp) REVERT: BB 307 PHE cc_start: 0.9177 (t80) cc_final: 0.8858 (t80) REVERT: CB 1003 PHE cc_start: 0.9029 (t80) cc_final: 0.8695 (t80) REVERT: CB 1004 GLU cc_start: 0.8271 (tp30) cc_final: 0.7803 (tm-30) REVERT: EB 1203 PHE cc_start: 0.8804 (t80) cc_final: 0.8354 (t80) REVERT: FB 1304 GLU cc_start: 0.8996 (tm-30) cc_final: 0.7492 (tm-30) REVERT: FB 1305 PHE cc_start: 0.8543 (t80) cc_final: 0.8292 (t80) REVERT: h 4 GLU cc_start: 0.8050 (tp30) cc_final: 0.7727 (pm20) REVERT: h 5 PHE cc_start: 0.8955 (t80) cc_final: 0.8518 (t80) REVERT: HB 203 PHE cc_start: 0.8800 (t80) cc_final: 0.8453 (t80) REVERT: HB 205 PHE cc_start: 0.8508 (t80) cc_final: 0.8166 (t80) REVERT: HB 206 LYS cc_start: 0.8974 (tttt) cc_final: 0.8660 (tttm) REVERT: IB 302 LYS cc_start: 0.8835 (tptp) cc_final: 0.8514 (tptp) REVERT: IB 303 PHE cc_start: 0.8777 (t80) cc_final: 0.8546 (t80) REVERT: IB 304 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8367 (tm-30) REVERT: JB 1004 GLU cc_start: 0.8048 (tp30) cc_final: 0.7806 (tp30) REVERT: JB 1005 PHE cc_start: 0.8620 (t80) cc_final: 0.8413 (t80) REVERT: KB 1103 PHE cc_start: 0.8761 (t80) cc_final: 0.8083 (t80) REVERT: KB 1105 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8504 (t80) REVERT: MB 1304 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8074 (tm-30) REVERT: i 2 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8627 (ttpt) REVERT: NB 104 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: NB 107 PHE cc_start: 0.9141 (t80) cc_final: 0.8848 (t80) REVERT: OB 202 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8508 (mmmm) REVERT: OB 203 PHE cc_start: 0.8962 (t80) cc_final: 0.8638 (t80) REVERT: PB 302 LYS cc_start: 0.8786 (tptp) cc_final: 0.8532 (tptp) REVERT: PB 306 LYS cc_start: 0.8763 (tptp) cc_final: 0.8520 (tptp) REVERT: PB 307 PHE cc_start: 0.8875 (t80) cc_final: 0.8395 (t80) REVERT: SB 1202 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8522 (ttmm) REVERT: SB 1204 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7191 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8808 (tttt) cc_final: 0.8602 (tmtt) REVERT: TB 1304 GLU cc_start: 0.8676 (tm-30) cc_final: 0.7283 (pm20) REVERT: TB 1305 PHE cc_start: 0.8599 (t80) cc_final: 0.7610 (t80) REVERT: TB 1306 LYS cc_start: 0.8740 (tptp) cc_final: 0.8201 (pptt) REVERT: TB 1307 PHE cc_start: 0.8738 (t80) cc_final: 0.8243 (t80) outliers start: 42 outliers final: 18 residues processed: 483 average time/residue: 0.1952 time to fit residues: 117.4571 Evaluate side-chains 505 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 477 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1006 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain RB residue 1106 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079453 restraints weight = 24054.503| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.25 r_work: 0.3148 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12563 Z= 0.113 Angle : 0.625 9.046 16272 Z= 0.287 Chirality : 0.031 0.093 1152 Planarity : 0.002 0.014 2160 Dihedral : 14.620 83.576 1449 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 28.24 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.35 (0.17), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.13), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.002 PHEnA1303 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (12528) covalent geometry : angle 0.62498 / 0.29 (16272) hydrogen bonds : bond 0.01900 / 1.05 ( 278) hydrogen bonds : angle 6.10950 / 3.48 ( 786) Misc. bond : bond 0.00117 / 0.06 ( 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 460 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 440 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8587 (mtmt) REVERT: J 104 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7850 (mm-30) REVERT: L 302 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8588 (ttpt) REVERT: O 1206 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8574 (ttmm) REVERT: P 1306 LYS cc_start: 0.9018 (tttt) cc_final: 0.8751 (tttt) REVERT: B 4 GLU cc_start: 0.7868 (mp0) cc_final: 0.6839 (mp0) REVERT: T 1004 GLU cc_start: 0.7544 (mp0) cc_final: 0.7245 (mp0) REVERT: X 102 LYS cc_start: 0.8890 (ttpt) cc_final: 0.7756 (ttpt) REVERT: X 104 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7318 (mm-30) REVERT: j 1004 GLU cc_start: 0.8336 (mp0) cc_final: 0.7692 (mp0) REVERT: j 1006 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8416 (mtmt) REVERT: k 1104 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7764 (mm-30) REVERT: l 1202 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8439 (mmmm) REVERT: m 1302 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8711 (ttpt) REVERT: D 4 GLU cc_start: 0.8150 (mp0) cc_final: 0.7862 (mp0) REVERT: r 1104 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7707 (mm-30) REVERT: r 1106 LYS cc_start: 0.8827 (tptm) cc_final: 0.8533 (mptm) REVERT: s 1206 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8637 (ttmm) REVERT: E 4 GLU cc_start: 0.7546 (mp0) cc_final: 0.6813 (mp0) REVERT: u 106 LYS cc_start: 0.8717 (tptm) cc_final: 0.8302 (tptm) REVERT: w 304 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8219 (mm-30) REVERT: x 1006 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8214 (mtmt) REVERT: z 1206 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8520 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8017 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8898 (tttt) cc_final: 0.8289 (tttt) REVERT: F 4 GLU cc_start: 0.7665 (mp0) cc_final: 0.6501 (pm20) REVERT: 1 103 PHE cc_start: 0.9036 (m-80) cc_final: 0.8791 (m-80) REVERT: 4 1006 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8365 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8729 (tptm) cc_final: 0.8258 (tptm) REVERT: 6 1206 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8682 (ttmm) REVERT: 7 1306 LYS cc_start: 0.9031 (tttt) cc_final: 0.8742 (mttt) REVERT: G 6 LYS cc_start: 0.8864 (mtmt) cc_final: 0.7974 (mtmt) REVERT: 8 106 LYS cc_start: 0.8845 (tptm) cc_final: 0.8540 (tptm) REVERT: 9 204 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7829 (mt-10) REVERT: CA 1106 LYS cc_start: 0.8803 (tptm) cc_final: 0.8158 (tptm) REVERT: EA 1306 LYS cc_start: 0.9016 (tttt) cc_final: 0.8756 (tttt) REVERT: FA 106 LYS cc_start: 0.8736 (tptm) cc_final: 0.8359 (tptm) REVERT: HA 306 LYS cc_start: 0.8974 (tttt) cc_final: 0.8686 (mttt) REVERT: JA 1106 LYS cc_start: 0.8696 (tptm) cc_final: 0.8339 (tptm) REVERT: KA 1202 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8578 (pptt) REVERT: LA 1306 LYS cc_start: 0.9019 (tttt) cc_final: 0.8760 (mttt) REVERT: OA 302 LYS cc_start: 0.7068 (tptt) cc_final: 0.6768 (tppt) REVERT: OA 304 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8069 (mm-30) REVERT: PA 1006 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8547 (ttmt) REVERT: QA 1102 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8316 (ttpt) REVERT: QA 1104 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7893 (mm-30) REVERT: QA 1106 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8187 (mmmm) REVERT: RA 1204 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8071 (mt-10) REVERT: RA 1206 LYS cc_start: 0.8845 (ttmm) cc_final: 0.8499 (ttmm) REVERT: SA 1302 LYS cc_start: 0.6372 (tptt) cc_final: 0.5726 (tppt) REVERT: SA 1306 LYS cc_start: 0.9055 (tttt) cc_final: 0.8758 (tttt) REVERT: a 2 LYS cc_start: 0.8574 (ttpt) cc_final: 0.7959 (tppt) REVERT: TA 104 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: TA 105 PHE cc_start: 0.9090 (t80) cc_final: 0.8548 (t80) REVERT: TA 106 LYS cc_start: 0.8808 (tmtp) cc_final: 0.8560 (tmtp) REVERT: UA 202 LYS cc_start: 0.8775 (tttm) cc_final: 0.8302 (ttmm) REVERT: UA 206 LYS cc_start: 0.8794 (tttt) cc_final: 0.8553 (tttm) REVERT: VA 307 PHE cc_start: 0.8570 (t80) cc_final: 0.8300 (t80) REVERT: WA 1003 PHE cc_start: 0.9006 (t80) cc_final: 0.8649 (t80) REVERT: YA 1202 LYS cc_start: 0.8859 (tttm) cc_final: 0.8464 (tttm) REVERT: ZA 1305 PHE cc_start: 0.8489 (t80) cc_final: 0.8126 (t80) REVERT: b 2 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8235 (ttpt) REVERT: b 6 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8340 (ttpt) REVERT: aA 102 LYS cc_start: 0.8807 (tptm) cc_final: 0.8455 (tptm) REVERT: bA 202 LYS cc_start: 0.8675 (tttm) cc_final: 0.8067 (ttmm) REVERT: cA 304 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8322 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9121 (t80) cc_final: 0.8872 (t80) REVERT: c 2 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8261 (tppt) REVERT: c 4 GLU cc_start: 0.8171 (tp30) cc_final: 0.7877 (tp30) REVERT: c 5 PHE cc_start: 0.8792 (t80) cc_final: 0.8107 (t80) REVERT: c 6 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8416 (ttpt) REVERT: iA 202 LYS cc_start: 0.8940 (tttm) cc_final: 0.8635 (mtpp) REVERT: kA 1002 LYS cc_start: 0.8490 (ttpt) cc_final: 0.7991 (tppt) REVERT: kA 1005 PHE cc_start: 0.8959 (t80) cc_final: 0.8528 (t80) REVERT: d 2 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8517 (ttpt) REVERT: pA 202 LYS cc_start: 0.8667 (tttm) cc_final: 0.8334 (ttmm) REVERT: qA 304 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8620 (tm-30) REVERT: rA 1002 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8053 (tppt) REVERT: rA 1006 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8403 (ttpt) REVERT: sA 1103 PHE cc_start: 0.8501 (t80) cc_final: 0.8081 (t80) REVERT: tA 1203 PHE cc_start: 0.8889 (t80) cc_final: 0.8675 (t80) REVERT: uA 1303 PHE cc_start: 0.8446 (t80) cc_final: 0.8119 (t80) REVERT: xA 302 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7972 (tptp) REVERT: f 2 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8052 (tppt) REVERT: 3A 202 LYS cc_start: 0.8817 (tttm) cc_final: 0.8423 (ttmm) REVERT: 4A 302 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8108 (tptp) REVERT: 5A 1002 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8114 (ttpt) REVERT: 5A 1003 PHE cc_start: 0.8951 (t80) cc_final: 0.8607 (t80) REVERT: 5A 1007 PHE cc_start: 0.9216 (t80) cc_final: 0.8672 (t80) REVERT: 7A 1205 PHE cc_start: 0.8661 (t80) cc_final: 0.8387 (t80) REVERT: 7A 1206 LYS cc_start: 0.8504 (tttt) cc_final: 0.8088 (tttm) REVERT: 8A 1303 PHE cc_start: 0.8805 (t80) cc_final: 0.8535 (t80) REVERT: g 4 GLU cc_start: 0.8035 (tp30) cc_final: 0.7559 (tp30) REVERT: 9A 102 LYS cc_start: 0.8618 (tptm) cc_final: 0.8124 (tptm) REVERT: 9A 104 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: AB 202 LYS cc_start: 0.8729 (tptm) cc_final: 0.8145 (ttmm) REVERT: BB 306 LYS cc_start: 0.8648 (tptp) cc_final: 0.8389 (tptp) REVERT: BB 307 PHE cc_start: 0.9075 (t80) cc_final: 0.8810 (t80) REVERT: CB 1003 PHE cc_start: 0.8961 (t80) cc_final: 0.8562 (t80) REVERT: CB 1004 GLU cc_start: 0.8121 (tp30) cc_final: 0.7867 (tp30) REVERT: DB 1106 LYS cc_start: 0.8539 (tttp) cc_final: 0.8295 (tttp) REVERT: EB 1203 PHE cc_start: 0.8824 (t80) cc_final: 0.8393 (t80) REVERT: FB 1305 PHE cc_start: 0.8327 (t80) cc_final: 0.8023 (t80) REVERT: h 5 PHE cc_start: 0.8930 (t80) cc_final: 0.8658 (t80) REVERT: HB 203 PHE cc_start: 0.8759 (t80) cc_final: 0.8212 (t80) REVERT: HB 205 PHE cc_start: 0.8437 (t80) cc_final: 0.8178 (t80) REVERT: HB 206 LYS cc_start: 0.8755 (tttt) cc_final: 0.8501 (tttm) REVERT: JB 1005 PHE cc_start: 0.8630 (t80) cc_final: 0.8005 (t80) REVERT: MB 1304 GLU cc_start: 0.8871 (tm-30) cc_final: 0.7405 (tm-30) REVERT: i 2 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8408 (ttpt) REVERT: NB 104 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7984 (pm20) REVERT: NB 107 PHE cc_start: 0.8989 (t80) cc_final: 0.8745 (t80) REVERT: OB 202 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8337 (mmmm) REVERT: OB 203 PHE cc_start: 0.8852 (t80) cc_final: 0.8591 (t80) REVERT: PB 302 LYS cc_start: 0.8683 (tptp) cc_final: 0.8201 (tptp) REVERT: PB 304 GLU cc_start: 0.8828 (tm-30) cc_final: 0.6699 (pm20) REVERT: PB 305 PHE cc_start: 0.8245 (t80) cc_final: 0.7282 (t80) REVERT: PB 306 LYS cc_start: 0.8733 (tptp) cc_final: 0.8381 (tptp) REVERT: PB 307 PHE cc_start: 0.8672 (t80) cc_final: 0.8250 (t80) REVERT: SB 1202 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8413 (ttmm) REVERT: SB 1203 PHE cc_start: 0.8774 (t80) cc_final: 0.8316 (t80) REVERT: TB 1305 PHE cc_start: 0.8403 (t80) cc_final: 0.8156 (t80) REVERT: TB 1306 LYS cc_start: 0.8648 (tptp) cc_final: 0.7941 (pptt) REVERT: TB 1307 PHE cc_start: 0.8421 (t80) cc_final: 0.7854 (t80) outliers start: 20 outliers final: 3 residues processed: 445 average time/residue: 0.2053 time to fit residues: 113.5427 Evaluate side-chains 438 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 429 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KA residue 1202 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 9A residue 104 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.077455 restraints weight = 25311.003| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.22 r_work: 0.3029 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.070 12563 Z= 0.710 Angle : 0.920 9.394 16272 Z= 0.425 Chirality : 0.048 0.150 1152 Planarity : 0.004 0.018 2160 Dihedral : 14.899 90.274 1446 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.32 % Allowed : 27.55 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.62 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.12), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.004 PHEnA1303 Details of bonding type rmsd/Z covalent geometry : bond 0.01583 / 0.71 (12528) covalent geometry : angle 0.91992 / 0.42 (16272) hydrogen bonds : bond 0.03893 / 2.17 ( 278) hydrogen bonds : angle 6.61639 / 3.77 ( 786) Misc. bond : bond 0.00190 / 0.11 ( 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 524 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 478 time to evaluate : 0.354 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: J 106 LYS cc_start: 0.9029 (tptm) cc_final: 0.8577 (tptm) REVERT: L 302 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8491 (ttpt) REVERT: L 304 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8171 (mm-30) REVERT: N 1104 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8010 (mm-30) REVERT: N 1106 LYS cc_start: 0.8890 (tptm) cc_final: 0.8308 (tptm) REVERT: B 4 GLU cc_start: 0.7849 (mp0) cc_final: 0.5945 (mp0) REVERT: U 1104 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7658 (mm-30) REVERT: X 104 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7882 (mm-30) REVERT: Y 204 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8332 (mm-30) REVERT: Y 206 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8596 (ttmm) REVERT: j 1004 GLU cc_start: 0.8403 (mp0) cc_final: 0.7548 (mp0) REVERT: k 1104 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7883 (mm-30) REVERT: m 1306 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8663 (mttt) REVERT: D 4 GLU cc_start: 0.8003 (mp0) cc_final: 0.7702 (mp0) REVERT: n 104 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7463 (mm-30) REVERT: n 106 LYS cc_start: 0.8848 (tptm) cc_final: 0.8332 (tptm) REVERT: p 306 LYS cc_start: 0.8911 (tttt) cc_final: 0.8697 (tttt) REVERT: q 1004 GLU cc_start: 0.8524 (mp0) cc_final: 0.8131 (mp0) REVERT: r 1104 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7924 (mm-30) REVERT: s 1202 LYS cc_start: 0.9298 (ttpt) cc_final: 0.8938 (ttpt) REVERT: s 1206 LYS cc_start: 0.9005 (ttmm) cc_final: 0.8727 (ttmm) REVERT: E 4 GLU cc_start: 0.7706 (mp0) cc_final: 0.6793 (mp0) REVERT: E 6 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8514 (mtmt) REVERT: u 106 LYS cc_start: 0.8757 (tptm) cc_final: 0.8416 (tptm) REVERT: w 304 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8339 (mm-30) REVERT: y 1106 LYS cc_start: 0.8695 (tptm) cc_final: 0.8410 (tptm) REVERT: z 1206 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8562 (ttmm) REVERT: 0 1302 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8957 (mtpt) REVERT: 0 1304 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7991 (mm-30) REVERT: 0 1306 LYS cc_start: 0.9107 (tttt) cc_final: 0.8820 (tttt) REVERT: F 4 GLU cc_start: 0.7608 (mp0) cc_final: 0.6585 (pm20) REVERT: 1 106 LYS cc_start: 0.8811 (tptm) cc_final: 0.8413 (tptm) REVERT: 4 1006 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8608 (ttmt) REVERT: 5 1102 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8433 (ttpt) REVERT: 5 1106 LYS cc_start: 0.8789 (tptm) cc_final: 0.8321 (tptm) REVERT: 6 1206 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8699 (ttmm) REVERT: 7 1306 LYS cc_start: 0.9117 (tttt) cc_final: 0.8821 (mttt) REVERT: G 4 GLU cc_start: 0.7811 (mp0) cc_final: 0.6750 (mp0) REVERT: 8 106 LYS cc_start: 0.8973 (tptm) cc_final: 0.8611 (tptm) REVERT: 9 204 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8012 (mt-10) REVERT: CA 1104 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7858 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8796 (tptm) cc_final: 0.8170 (tptm) REVERT: EA 1306 LYS cc_start: 0.9119 (tttt) cc_final: 0.8900 (tttt) REVERT: FA 106 LYS cc_start: 0.8764 (tptm) cc_final: 0.8376 (tptm) REVERT: HA 306 LYS cc_start: 0.9048 (tttt) cc_final: 0.8768 (mttt) REVERT: JA 1106 LYS cc_start: 0.8825 (tptm) cc_final: 0.8404 (tptm) REVERT: LA 1304 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8063 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9040 (tttt) cc_final: 0.8793 (mttt) REVERT: I 6 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8417 (mtmt) REVERT: MA 106 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8576 (mmmm) REVERT: OA 302 LYS cc_start: 0.6293 (tptt) cc_final: 0.5837 (tptt) REVERT: OA 304 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8070 (mm-30) REVERT: OA 306 LYS cc_start: 0.9107 (mttt) cc_final: 0.8818 (mttt) REVERT: PA 1006 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8616 (ttmt) REVERT: QA 1102 LYS cc_start: 0.9213 (ttpt) cc_final: 0.8618 (ttpt) REVERT: QA 1104 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8064 (mm-30) REVERT: QA 1106 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8246 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8658 (ttmm) REVERT: SA 1302 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.4007 (tptt) REVERT: SA 1304 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8077 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9125 (tttt) cc_final: 0.8866 (tttt) REVERT: a 2 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8378 (tppt) REVERT: TA 102 LYS cc_start: 0.9040 (tptm) cc_final: 0.8607 (tptm) REVERT: TA 104 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: TA 106 LYS cc_start: 0.8906 (tmtp) cc_final: 0.8650 (tmtp) REVERT: UA 202 LYS cc_start: 0.8986 (tttm) cc_final: 0.8470 (ttmm) REVERT: VA 302 LYS cc_start: 0.8834 (tptp) cc_final: 0.8391 (tptp) REVERT: VA 307 PHE cc_start: 0.8959 (t80) cc_final: 0.8723 (t80) REVERT: YA 1202 LYS cc_start: 0.9088 (tttm) cc_final: 0.8787 (tttm) REVERT: ZA 1305 PHE cc_start: 0.8634 (t80) cc_final: 0.8430 (t80) REVERT: b 2 LYS cc_start: 0.9016 (ttpt) cc_final: 0.8682 (ttpt) REVERT: b 6 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8458 (ttpt) REVERT: aA 102 LYS cc_start: 0.9050 (tptm) cc_final: 0.8733 (tptm) REVERT: bA 202 LYS cc_start: 0.8976 (tttm) cc_final: 0.8341 (ttmm) REVERT: cA 302 LYS cc_start: 0.8762 (tptp) cc_final: 0.8416 (tptp) REVERT: cA 303 PHE cc_start: 0.8767 (t80) cc_final: 0.8512 (t80) REVERT: cA 304 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8256 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8720 (t80) REVERT: c 2 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8531 (tppt) REVERT: c 3 PHE cc_start: 0.9138 (t80) cc_final: 0.8698 (t80) REVERT: c 4 GLU cc_start: 0.8177 (tp30) cc_final: 0.7834 (tm-30) REVERT: c 5 PHE cc_start: 0.8799 (t80) cc_final: 0.8357 (t80) REVERT: c 6 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8694 (ttpt) REVERT: iA 202 LYS cc_start: 0.9092 (tttm) cc_final: 0.8577 (ttmm) REVERT: jA 304 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8296 (tm-30) REVERT: kA 1005 PHE cc_start: 0.8953 (t80) cc_final: 0.8627 (t80) REVERT: lA 1103 PHE cc_start: 0.8819 (t80) cc_final: 0.8300 (t80) REVERT: nA 1302 LYS cc_start: 0.8723 (tptp) cc_final: 0.8340 (tptp) REVERT: nA 1304 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8383 (tm-30) REVERT: nA 1306 LYS cc_start: 0.8583 (tptp) cc_final: 0.8201 (tptp) REVERT: d 2 LYS cc_start: 0.9041 (ttpt) cc_final: 0.8806 (ttpt) REVERT: d 4 GLU cc_start: 0.8015 (tp30) cc_final: 0.7751 (tp30) REVERT: oA 102 LYS cc_start: 0.8778 (tptm) cc_final: 0.8352 (tptm) REVERT: oA 104 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8091 (tm-30) REVERT: pA 202 LYS cc_start: 0.8888 (tttm) cc_final: 0.8436 (mtpp) REVERT: qA 304 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8034 (tm-30) REVERT: qA 306 LYS cc_start: 0.8606 (tptp) cc_final: 0.8239 (tptp) REVERT: rA 1006 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8440 (ttpt) REVERT: sA 1103 PHE cc_start: 0.8536 (t80) cc_final: 0.8246 (t80) REVERT: tA 1204 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7221 (tm-30) REVERT: tA 1206 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8345 (tptt) REVERT: uA 1302 LYS cc_start: 0.8806 (tptp) cc_final: 0.8496 (tptp) REVERT: e 2 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8377 (tppt) REVERT: vA 102 LYS cc_start: 0.9019 (tptm) cc_final: 0.8738 (tptm) REVERT: wA 206 LYS cc_start: 0.8642 (tttt) cc_final: 0.8402 (tptt) REVERT: xA 302 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8312 (tptp) REVERT: xA 303 PHE cc_start: 0.8774 (t80) cc_final: 0.8449 (t80) REVERT: xA 306 LYS cc_start: 0.8521 (tptp) cc_final: 0.8180 (tptp) REVERT: 1A 1302 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8290 (tptp) REVERT: f 2 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8589 (ttpt) REVERT: 2A 102 LYS cc_start: 0.8895 (tptm) cc_final: 0.8519 (tptm) REVERT: 3A 202 LYS cc_start: 0.8915 (tttm) cc_final: 0.8467 (mmmm) REVERT: 4A 302 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8383 (tptp) REVERT: 4A 304 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8648 (tm-30) REVERT: 4A 306 LYS cc_start: 0.8595 (tptp) cc_final: 0.8316 (tptp) REVERT: 4A 307 PHE cc_start: 0.8930 (t80) cc_final: 0.8512 (t80) REVERT: 5A 1003 PHE cc_start: 0.9004 (t80) cc_final: 0.8636 (t80) REVERT: 7A 1205 PHE cc_start: 0.8972 (t80) cc_final: 0.8218 (t80) REVERT: 7A 1206 LYS cc_start: 0.8618 (tttt) cc_final: 0.8347 (tttm) REVERT: 8A 1302 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8217 (tptp) REVERT: 8A 1304 GLU cc_start: 0.8898 (tm-30) cc_final: 0.7418 (tm-30) REVERT: g 2 LYS cc_start: 0.9081 (ttpt) cc_final: 0.8462 (tppt) REVERT: g 4 GLU cc_start: 0.8207 (tp30) cc_final: 0.7789 (tp30) REVERT: 9A 102 LYS cc_start: 0.8975 (tptm) cc_final: 0.8686 (tptm) REVERT: 9A 103 PHE cc_start: 0.8610 (t80) cc_final: 0.8211 (t80) REVERT: 9A 104 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: AB 202 LYS cc_start: 0.9041 (tptm) cc_final: 0.8393 (ttmm) REVERT: BB 306 LYS cc_start: 0.8709 (tptp) cc_final: 0.8462 (tptp) REVERT: CB 1003 PHE cc_start: 0.9066 (t80) cc_final: 0.8828 (t80) REVERT: EB 1203 PHE cc_start: 0.8838 (t80) cc_final: 0.8325 (t80) REVERT: h 5 PHE cc_start: 0.9026 (t80) cc_final: 0.8760 (t80) REVERT: HB 202 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8760 (ttmm) REVERT: HB 203 PHE cc_start: 0.8820 (t80) cc_final: 0.8488 (t80) REVERT: IB 302 LYS cc_start: 0.8757 (tptp) cc_final: 0.8424 (tptp) REVERT: IB 303 PHE cc_start: 0.8801 (t80) cc_final: 0.8499 (t80) REVERT: IB 304 GLU cc_start: 0.9033 (tm-30) cc_final: 0.7973 (tm-30) REVERT: KB 1104 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7778 (tm-30) REVERT: KB 1105 PHE cc_start: 0.8945 (t80) cc_final: 0.8284 (t80) REVERT: MB 1304 GLU cc_start: 0.9071 (tm-30) cc_final: 0.7727 (tm-30) REVERT: i 2 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8659 (ttpt) REVERT: i 4 GLU cc_start: 0.8195 (tp30) cc_final: 0.7888 (tm-30) REVERT: NB 104 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8095 (pm20) REVERT: OB 202 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8488 (mmmm) REVERT: OB 203 PHE cc_start: 0.8984 (t80) cc_final: 0.8784 (t80) REVERT: PB 304 GLU cc_start: 0.8966 (tm-30) cc_final: 0.7026 (pm20) REVERT: PB 306 LYS cc_start: 0.8734 (tptp) cc_final: 0.8476 (tptp) REVERT: PB 307 PHE cc_start: 0.8957 (t80) cc_final: 0.8537 (t80) REVERT: SB 1203 PHE cc_start: 0.8692 (t80) cc_final: 0.8284 (t80) REVERT: SB 1206 LYS cc_start: 0.8794 (tmtt) cc_final: 0.8500 (tmtt) REVERT: TB 1302 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8567 (tptp) REVERT: TB 1305 PHE cc_start: 0.8727 (t80) cc_final: 0.8208 (t80) REVERT: TB 1306 LYS cc_start: 0.8742 (tptp) cc_final: 0.8533 (tptp) REVERT: TB 1307 PHE cc_start: 0.8833 (t80) cc_final: 0.8518 (t80) outliers start: 46 outliers final: 24 residues processed: 482 average time/residue: 0.2033 time to fit residues: 120.9011 Evaluate side-chains 514 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 477 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 206 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 202 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain RB residue 1106 LYS Chi-restraints excluded: chain TB residue 1302 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.096852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.083142 restraints weight = 23700.814| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.22 r_work: 0.3167 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12563 Z= 0.114 Angle : 0.641 9.496 16272 Z= 0.299 Chirality : 0.031 0.105 1152 Planarity : 0.002 0.015 2160 Dihedral : 14.306 84.338 1446 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.01 % Allowed : 30.09 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.13 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.13), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHE2A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (12528) covalent geometry : angle 0.64084 / 0.30 (16272) hydrogen bonds : bond 0.01912 / 1.05 ( 278) hydrogen bonds : angle 5.87915 / 3.34 ( 786) Misc. bond : bond 0.00143 / 0.07 ( 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 463 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 437 time to evaluate : 0.284 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: J 104 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7872 (mm-30) REVERT: J 106 LYS cc_start: 0.8891 (tptm) cc_final: 0.8352 (tptm) REVERT: L 302 LYS cc_start: 0.8661 (ttpt) cc_final: 0.8349 (ttpt) REVERT: N 1104 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7866 (mm-30) REVERT: B 4 GLU cc_start: 0.7806 (mp0) cc_final: 0.6067 (mp0) REVERT: T 1004 GLU cc_start: 0.7293 (mp0) cc_final: 0.6892 (mp0) REVERT: T 1006 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8344 (mtmt) REVERT: C 6 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8443 (mtmt) REVERT: X 102 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8405 (ttpt) REVERT: Y 206 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8443 (ttmm) REVERT: Z 304 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8045 (mm-30) REVERT: j 1004 GLU cc_start: 0.8446 (mp0) cc_final: 0.7435 (mp0) REVERT: j 1006 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8529 (mtmt) REVERT: k 1104 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7683 (mm-30) REVERT: l 1202 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8551 (mmmm) REVERT: m 1306 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8496 (mttt) REVERT: n 104 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7318 (mm-30) REVERT: q 1005 PHE cc_start: 0.9065 (m-80) cc_final: 0.8846 (m-80) REVERT: r 1102 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7509 (ttpt) REVERT: r 1104 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7546 (mm-30) REVERT: s 1202 LYS cc_start: 0.9262 (ttpt) cc_final: 0.8948 (ttpt) REVERT: s 1206 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8642 (ttmm) REVERT: t 1302 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8869 (tttt) REVERT: E 4 GLU cc_start: 0.7601 (mp0) cc_final: 0.7342 (mp0) REVERT: E 6 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8408 (mtmt) REVERT: u 106 LYS cc_start: 0.8720 (tptm) cc_final: 0.8318 (tptm) REVERT: w 304 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8199 (mm-30) REVERT: z 1206 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8478 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7953 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8903 (tttt) cc_final: 0.8437 (tttt) REVERT: 1 103 PHE cc_start: 0.9061 (m-80) cc_final: 0.8786 (m-80) REVERT: 1 106 LYS cc_start: 0.8769 (tptm) cc_final: 0.8404 (tptm) REVERT: 4 1006 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8500 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8698 (tptm) cc_final: 0.8186 (tptm) REVERT: 5 1107 PHE cc_start: 0.8696 (m-80) cc_final: 0.8392 (m-10) REVERT: 6 1206 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8692 (ttmm) REVERT: 7 1306 LYS cc_start: 0.9056 (tttt) cc_final: 0.8748 (mttt) REVERT: G 4 GLU cc_start: 0.7509 (mp0) cc_final: 0.6511 (mp0) REVERT: G 5 PHE cc_start: 0.8886 (m-80) cc_final: 0.8662 (m-80) REVERT: 8 106 LYS cc_start: 0.8897 (tptm) cc_final: 0.8561 (tptm) REVERT: 9 204 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7825 (mt-10) REVERT: CA 1106 LYS cc_start: 0.8822 (tptm) cc_final: 0.8182 (tptm) REVERT: FA 106 LYS cc_start: 0.8682 (tptm) cc_final: 0.8314 (tptm) REVERT: HA 306 LYS cc_start: 0.8978 (tttt) cc_final: 0.8692 (mttt) REVERT: JA 1106 LYS cc_start: 0.8709 (tptm) cc_final: 0.8307 (tptm) REVERT: KA 1202 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8683 (pptt) REVERT: LA 1306 LYS cc_start: 0.8993 (tttt) cc_final: 0.8736 (mttt) REVERT: I 4 GLU cc_start: 0.7785 (mp0) cc_final: 0.7463 (mp0) REVERT: I 6 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8412 (mtmt) REVERT: MA 106 LYS cc_start: 0.8668 (mmmm) cc_final: 0.8371 (mmmm) REVERT: OA 302 LYS cc_start: 0.6807 (tptt) cc_final: 0.6564 (tppt) REVERT: OA 304 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7894 (mm-30) REVERT: OA 306 LYS cc_start: 0.9002 (mttt) cc_final: 0.8718 (mttt) REVERT: PA 1006 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8591 (ttmt) REVERT: QA 1104 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7980 (mm-30) REVERT: QA 1106 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8237 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8466 (ttmm) REVERT: SA 1302 LYS cc_start: 0.6618 (tptt) cc_final: 0.5982 (tppt) REVERT: SA 1306 LYS cc_start: 0.9059 (tttt) cc_final: 0.8785 (tttt) REVERT: a 2 LYS cc_start: 0.8587 (ttpt) cc_final: 0.7916 (tppt) REVERT: TA 104 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: TA 105 PHE cc_start: 0.9051 (t80) cc_final: 0.8732 (t80) REVERT: TA 106 LYS cc_start: 0.8781 (tmtp) cc_final: 0.8531 (tmtp) REVERT: UA 202 LYS cc_start: 0.8825 (tttm) cc_final: 0.8385 (ttmm) REVERT: VA 302 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8118 (tptp) REVERT: YA 1202 LYS cc_start: 0.8900 (tttm) cc_final: 0.8592 (tttm) REVERT: aA 102 LYS cc_start: 0.8833 (tptm) cc_final: 0.8441 (tptm) REVERT: bA 202 LYS cc_start: 0.8792 (tttm) cc_final: 0.8356 (ttmm) REVERT: cA 304 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8659 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9094 (t80) cc_final: 0.8570 (t80) REVERT: gA 1302 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8201 (tptp) REVERT: c 2 LYS cc_start: 0.8817 (ttpt) cc_final: 0.8223 (tppt) REVERT: c 4 GLU cc_start: 0.8146 (tp30) cc_final: 0.7824 (tp30) REVERT: c 5 PHE cc_start: 0.8730 (t80) cc_final: 0.8065 (t80) REVERT: c 6 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8326 (ttpt) REVERT: hA 107 PHE cc_start: 0.9082 (t80) cc_final: 0.8751 (t80) REVERT: iA 202 LYS cc_start: 0.8897 (tttm) cc_final: 0.8613 (mmmm) REVERT: jA 302 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8012 (tptp) REVERT: kA 1002 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8085 (tppt) REVERT: kA 1005 PHE cc_start: 0.8936 (t80) cc_final: 0.8498 (t80) REVERT: lA 1103 PHE cc_start: 0.8474 (t80) cc_final: 0.8169 (t80) REVERT: mA 1206 LYS cc_start: 0.8354 (tttt) cc_final: 0.8132 (tptt) REVERT: nA 1302 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8007 (tptp) REVERT: d 2 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8528 (ttpt) REVERT: oA 107 PHE cc_start: 0.9068 (t80) cc_final: 0.8741 (t80) REVERT: pA 202 LYS cc_start: 0.8700 (tttm) cc_final: 0.8324 (mmmm) REVERT: qA 302 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7922 (tptp) REVERT: qA 304 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8584 (tm-30) REVERT: qA 306 LYS cc_start: 0.8570 (tptp) cc_final: 0.8173 (tptp) REVERT: tA 1206 LYS cc_start: 0.8610 (tttt) cc_final: 0.8377 (tptt) REVERT: vA 102 LYS cc_start: 0.8835 (tptm) cc_final: 0.8453 (tptm) REVERT: xA 302 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8067 (tptp) REVERT: xA 303 PHE cc_start: 0.8602 (t80) cc_final: 0.8333 (t80) REVERT: 1A 1302 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8051 (tptp) REVERT: f 2 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7976 (tppt) REVERT: 3A 202 LYS cc_start: 0.8866 (tttm) cc_final: 0.8315 (ttmm) REVERT: 4A 302 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8237 (tptp) REVERT: 4A 304 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8288 (tm-30) REVERT: 4A 306 LYS cc_start: 0.8572 (tptp) cc_final: 0.8283 (tptp) REVERT: 5A 1002 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8243 (ttpt) REVERT: 5A 1007 PHE cc_start: 0.9257 (t80) cc_final: 0.8713 (t80) REVERT: 7A 1205 PHE cc_start: 0.8911 (t80) cc_final: 0.8221 (t80) REVERT: 7A 1206 LYS cc_start: 0.8492 (tttt) cc_final: 0.8278 (tttm) REVERT: 8A 1302 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8088 (tptp) REVERT: 8A 1303 PHE cc_start: 0.8763 (t80) cc_final: 0.8203 (t80) REVERT: g 4 GLU cc_start: 0.8081 (tp30) cc_final: 0.7590 (tp30) REVERT: 9A 102 LYS cc_start: 0.8604 (tptm) cc_final: 0.8101 (tptm) REVERT: AB 202 LYS cc_start: 0.8764 (tptm) cc_final: 0.8181 (ttmm) REVERT: AB 205 PHE cc_start: 0.8676 (t80) cc_final: 0.8346 (t80) REVERT: BB 302 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7680 (tptp) REVERT: BB 306 LYS cc_start: 0.8659 (tptp) cc_final: 0.8423 (tptp) REVERT: CB 1003 PHE cc_start: 0.8981 (t80) cc_final: 0.8647 (t80) REVERT: EB 1203 PHE cc_start: 0.8897 (t80) cc_final: 0.8419 (t80) REVERT: FB 1304 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8272 (tm-30) REVERT: h 4 GLU cc_start: 0.8127 (tp30) cc_final: 0.7905 (pm20) REVERT: h 5 PHE cc_start: 0.8965 (t80) cc_final: 0.8519 (t80) REVERT: HB 203 PHE cc_start: 0.8817 (t80) cc_final: 0.8232 (t80) REVERT: HB 205 PHE cc_start: 0.8505 (t80) cc_final: 0.8159 (t80) REVERT: JB 1005 PHE cc_start: 0.8635 (t80) cc_final: 0.8356 (t80) REVERT: KB 1105 PHE cc_start: 0.9005 (t80) cc_final: 0.8360 (t80) REVERT: MB 1304 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8697 (tm-30) REVERT: i 2 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8538 (tppt) REVERT: i 4 GLU cc_start: 0.8191 (tp30) cc_final: 0.7791 (tp30) REVERT: NB 104 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7895 (pm20) REVERT: NB 105 PHE cc_start: 0.8396 (t80) cc_final: 0.7930 (t80) REVERT: NB 107 PHE cc_start: 0.9191 (t80) cc_final: 0.8890 (t80) REVERT: OB 202 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8330 (mmmm) REVERT: OB 203 PHE cc_start: 0.8956 (t80) cc_final: 0.8719 (t80) REVERT: PB 304 GLU cc_start: 0.8787 (tm-30) cc_final: 0.6927 (pm20) REVERT: PB 305 PHE cc_start: 0.8240 (t80) cc_final: 0.7263 (t80) REVERT: PB 306 LYS cc_start: 0.8735 (tptp) cc_final: 0.8452 (tptp) REVERT: PB 307 PHE cc_start: 0.8808 (t80) cc_final: 0.8426 (t80) REVERT: SB 1202 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8336 (ttmm) REVERT: SB 1203 PHE cc_start: 0.8828 (t80) cc_final: 0.8391 (t80) REVERT: SB 1206 LYS cc_start: 0.8514 (tmtt) cc_final: 0.8130 (tmtt) REVERT: TB 1302 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8219 (tptp) REVERT: TB 1305 PHE cc_start: 0.8590 (t80) cc_final: 0.8046 (t80) outliers start: 26 outliers final: 5 residues processed: 449 average time/residue: 0.2002 time to fit residues: 111.0596 Evaluate side-chains 449 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 431 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain qA residue 302 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain TB residue 1302 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.090670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077897 restraints weight = 25219.337| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.21 r_work: 0.3041 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.060 12563 Z= 0.712 Angle : 0.922 9.990 16272 Z= 0.427 Chirality : 0.048 0.142 1152 Planarity : 0.004 0.015 2160 Dihedral : 14.338 87.730 1443 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.79 % Allowed : 28.01 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.47 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.12), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.004 PHE4A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.01586 / 0.71 (12528) covalent geometry : angle 0.92206 / 0.43 (16272) hydrogen bonds : bond 0.03845 / 2.12 ( 278) hydrogen bonds : angle 6.51618 / 3.72 ( 786) Misc. bond : bond 0.00195 / 0.11 ( 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 526 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 476 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.9046 (m-80) cc_final: 0.8532 (m-80) REVERT: J 106 LYS cc_start: 0.9044 (tptm) cc_final: 0.8610 (tptm) REVERT: L 302 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8565 (ttpt) REVERT: M 1004 GLU cc_start: 0.6947 (mp0) cc_final: 0.6258 (mp0) REVERT: N 1104 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7979 (mm-30) REVERT: N 1106 LYS cc_start: 0.8922 (tptm) cc_final: 0.8332 (tptm) REVERT: B 4 GLU cc_start: 0.7926 (mp0) cc_final: 0.6064 (mp0) REVERT: Q 106 LYS cc_start: 0.8721 (tptm) cc_final: 0.8295 (tptm) REVERT: T 1004 GLU cc_start: 0.7571 (mp0) cc_final: 0.7303 (mp0) REVERT: T 1006 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8456 (mtmt) REVERT: U 1104 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7741 (mm-30) REVERT: X 104 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7536 (mm-30) REVERT: Y 204 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8279 (mm-30) REVERT: Y 206 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8611 (ttmm) REVERT: Z 304 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8159 (mm-30) REVERT: j 1004 GLU cc_start: 0.8426 (mp0) cc_final: 0.7541 (mp0) REVERT: k 1104 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7775 (mm-30) REVERT: l 1202 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8362 (ttmm) REVERT: m 1306 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8652 (mttt) REVERT: n 104 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7438 (mm-30) REVERT: n 106 LYS cc_start: 0.8817 (tptm) cc_final: 0.8310 (tptm) REVERT: r 1102 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7912 (ttpt) REVERT: r 1104 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7706 (mm-30) REVERT: s 1202 LYS cc_start: 0.9258 (ttpt) cc_final: 0.8945 (ttpt) REVERT: t 1304 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7913 (mm-30) REVERT: E 4 GLU cc_start: 0.7719 (mp0) cc_final: 0.6847 (mp0) REVERT: E 6 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8471 (mtmt) REVERT: u 106 LYS cc_start: 0.8756 (tptm) cc_final: 0.8400 (tptm) REVERT: w 304 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8334 (mm-30) REVERT: z 1206 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8546 (ttmm) REVERT: 0 1306 LYS cc_start: 0.9127 (tttt) cc_final: 0.8880 (tttt) REVERT: F 4 GLU cc_start: 0.7999 (mp0) cc_final: 0.6933 (mp0) REVERT: 4 1006 LYS cc_start: 0.8869 (mtmt) cc_final: 0.8442 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8780 (tptm) cc_final: 0.8245 (tptm) REVERT: 5 1107 PHE cc_start: 0.8826 (m-80) cc_final: 0.8486 (m-10) REVERT: 6 1206 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8696 (ttmm) REVERT: 7 1306 LYS cc_start: 0.9112 (tttt) cc_final: 0.8762 (mttt) REVERT: G 4 GLU cc_start: 0.7807 (mp0) cc_final: 0.6824 (mp0) REVERT: 8 106 LYS cc_start: 0.8974 (tptm) cc_final: 0.8590 (tptm) REVERT: 9 204 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8015 (mt-10) REVERT: CA 1106 LYS cc_start: 0.8800 (tptm) cc_final: 0.8202 (tptm) REVERT: FA 106 LYS cc_start: 0.8782 (tptm) cc_final: 0.8446 (tptm) REVERT: HA 306 LYS cc_start: 0.8993 (tttt) cc_final: 0.8697 (mttt) REVERT: JA 1106 LYS cc_start: 0.8799 (tptm) cc_final: 0.8413 (tptm) REVERT: LA 1304 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8145 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9056 (tttt) cc_final: 0.8806 (mttt) REVERT: I 4 GLU cc_start: 0.7868 (mp0) cc_final: 0.7561 (mp0) REVERT: I 6 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8443 (mtmt) REVERT: MA 106 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8458 (mmmm) REVERT: OA 304 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7990 (mm-30) REVERT: OA 306 LYS cc_start: 0.9060 (mttt) cc_final: 0.8769 (mttt) REVERT: PA 1006 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8596 (ttmt) REVERT: QA 1104 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8092 (mm-30) REVERT: QA 1106 LYS cc_start: 0.8506 (mmmm) cc_final: 0.8208 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8971 (ttmm) cc_final: 0.8656 (ttmm) REVERT: SA 1302 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.3914 (tptt) REVERT: SA 1304 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8065 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9073 (tttt) cc_final: 0.8823 (tttt) REVERT: a 2 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8385 (tppt) REVERT: TA 102 LYS cc_start: 0.9023 (tptm) cc_final: 0.8576 (tptm) REVERT: TA 103 PHE cc_start: 0.8514 (t80) cc_final: 0.8277 (t80) REVERT: TA 106 LYS cc_start: 0.8887 (tmtp) cc_final: 0.8640 (tmtp) REVERT: UA 202 LYS cc_start: 0.9007 (tttm) cc_final: 0.8503 (ttmm) REVERT: VA 302 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8324 (tptp) REVERT: YA 1202 LYS cc_start: 0.9102 (tttm) cc_final: 0.8823 (tttm) REVERT: b 2 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8637 (ttpt) REVERT: b 6 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8575 (tppt) REVERT: aA 102 LYS cc_start: 0.9058 (tptm) cc_final: 0.8723 (tptm) REVERT: bA 202 LYS cc_start: 0.8978 (tttm) cc_final: 0.8334 (ttmm) REVERT: cA 302 LYS cc_start: 0.8737 (tptp) cc_final: 0.8397 (tptp) REVERT: cA 304 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8516 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9088 (t80) cc_final: 0.8666 (t80) REVERT: gA 1302 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8332 (tptp) REVERT: c 2 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8519 (tppt) REVERT: c 3 PHE cc_start: 0.9157 (t80) cc_final: 0.8761 (t80) REVERT: c 5 PHE cc_start: 0.8782 (t80) cc_final: 0.8445 (t80) REVERT: iA 202 LYS cc_start: 0.9092 (tttm) cc_final: 0.8700 (ttmm) REVERT: kA 1005 PHE cc_start: 0.8935 (t80) cc_final: 0.8627 (t80) REVERT: lA 1103 PHE cc_start: 0.8735 (t80) cc_final: 0.8200 (t80) REVERT: mA 1206 LYS cc_start: 0.8593 (tttt) cc_final: 0.8334 (tptt) REVERT: nA 1302 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8257 (tptp) REVERT: nA 1306 LYS cc_start: 0.8564 (tptp) cc_final: 0.8206 (tptp) REVERT: d 2 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8803 (ttpt) REVERT: d 4 GLU cc_start: 0.7998 (tp30) cc_final: 0.7757 (tp30) REVERT: oA 102 LYS cc_start: 0.8790 (tptm) cc_final: 0.8311 (tptm) REVERT: pA 202 LYS cc_start: 0.8882 (tttm) cc_final: 0.8268 (mtpp) REVERT: pA 203 PHE cc_start: 0.9064 (t80) cc_final: 0.8812 (t80) REVERT: qA 304 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8060 (tm-30) REVERT: qA 306 LYS cc_start: 0.8605 (tptp) cc_final: 0.8288 (tptp) REVERT: sA 1103 PHE cc_start: 0.8423 (t80) cc_final: 0.8165 (t80) REVERT: tA 1202 LYS cc_start: 0.8866 (tttm) cc_final: 0.8609 (tttm) REVERT: tA 1204 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7069 (tm-30) REVERT: uA 1302 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8398 (tptp) REVERT: uA 1303 PHE cc_start: 0.8297 (t80) cc_final: 0.8026 (t80) REVERT: e 2 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8297 (tppt) REVERT: vA 102 LYS cc_start: 0.9025 (tptm) cc_final: 0.8728 (tptm) REVERT: xA 302 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8367 (tptp) REVERT: xA 303 PHE cc_start: 0.8812 (t80) cc_final: 0.8552 (t80) REVERT: xA 306 LYS cc_start: 0.8510 (tptp) cc_final: 0.8207 (tptp) REVERT: yA 1002 LYS cc_start: 0.8864 (ttpt) cc_final: 0.8557 (ttpt) REVERT: 1A 1302 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8326 (tptp) REVERT: f 2 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8538 (ttpt) REVERT: 2A 102 LYS cc_start: 0.8868 (tptm) cc_final: 0.8513 (tptm) REVERT: 2A 106 LYS cc_start: 0.8859 (tmtp) cc_final: 0.8595 (tmtp) REVERT: 3A 202 LYS cc_start: 0.8945 (tttm) cc_final: 0.8493 (mmmm) REVERT: 4A 302 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8391 (tptp) REVERT: 4A 304 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8473 (tm-30) REVERT: 4A 306 LYS cc_start: 0.8540 (tptp) cc_final: 0.8233 (tptp) REVERT: 4A 307 PHE cc_start: 0.8964 (t80) cc_final: 0.8620 (t80) REVERT: 5A 1002 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8701 (ttpt) REVERT: 8A 1302 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8239 (tptp) REVERT: 8A 1303 PHE cc_start: 0.8971 (t80) cc_final: 0.8302 (t80) REVERT: 8A 1304 GLU cc_start: 0.8957 (tm-30) cc_final: 0.7485 (tm-30) REVERT: g 2 LYS cc_start: 0.9085 (ttpt) cc_final: 0.8438 (tppt) REVERT: g 4 GLU cc_start: 0.8170 (tp30) cc_final: 0.7762 (tp30) REVERT: 9A 102 LYS cc_start: 0.8950 (tptm) cc_final: 0.8680 (tptm) REVERT: 9A 103 PHE cc_start: 0.8524 (t80) cc_final: 0.8127 (t80) REVERT: AB 202 LYS cc_start: 0.9024 (tptm) cc_final: 0.8406 (ttmm) REVERT: BB 302 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8026 (tptp) REVERT: BB 306 LYS cc_start: 0.8722 (tptp) cc_final: 0.8432 (tptp) REVERT: CB 1002 LYS cc_start: 0.8965 (ttpt) cc_final: 0.8643 (ttpt) REVERT: DB 1102 LYS cc_start: 0.8782 (tptm) cc_final: 0.8361 (tptm) REVERT: EB 1203 PHE cc_start: 0.8868 (t80) cc_final: 0.8270 (t80) REVERT: FB 1305 PHE cc_start: 0.8334 (t80) cc_final: 0.8110 (t80) REVERT: HB 202 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8758 (ttmm) REVERT: HB 203 PHE cc_start: 0.8817 (t80) cc_final: 0.8388 (t80) REVERT: IB 302 LYS cc_start: 0.8686 (tptp) cc_final: 0.8334 (tptp) REVERT: IB 304 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8299 (tm-30) REVERT: KB 1105 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8382 (t80) REVERT: MB 1304 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8748 (tm-30) REVERT: i 2 LYS cc_start: 0.9069 (ttpt) cc_final: 0.8713 (ttpt) REVERT: i 4 GLU cc_start: 0.8206 (tp30) cc_final: 0.7973 (tm-30) REVERT: NB 104 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8096 (pm20) REVERT: NB 105 PHE cc_start: 0.8720 (t80) cc_final: 0.8364 (t80) REVERT: NB 107 PHE cc_start: 0.9269 (t80) cc_final: 0.9023 (t80) REVERT: PB 304 GLU cc_start: 0.8924 (tm-30) cc_final: 0.6975 (pm20) REVERT: PB 305 PHE cc_start: 0.8372 (t80) cc_final: 0.7759 (t80) REVERT: PB 306 LYS cc_start: 0.8812 (tptp) cc_final: 0.8547 (tptp) REVERT: PB 307 PHE cc_start: 0.9066 (t80) cc_final: 0.8766 (t80) REVERT: SB 1202 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8479 (ttmm) REVERT: SB 1203 PHE cc_start: 0.8685 (t80) cc_final: 0.8289 (t80) REVERT: TB 1302 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8468 (tptp) REVERT: TB 1303 PHE cc_start: 0.8247 (t80) cc_final: 0.7920 (t80) REVERT: TB 1305 PHE cc_start: 0.8701 (t80) cc_final: 0.8279 (t80) REVERT: TB 1306 LYS cc_start: 0.8715 (tptp) cc_final: 0.8361 (tptp) outliers start: 50 outliers final: 28 residues processed: 482 average time/residue: 0.2008 time to fit residues: 119.2902 Evaluate side-chains 517 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 474 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain uA residue 1302 LYS Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 206 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 202 LYS Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain RB residue 1106 LYS Chi-restraints excluded: chain TB residue 1302 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.095936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.082553 restraints weight = 23760.616| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.22 r_work: 0.3167 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12563 Z= 0.123 Angle : 0.656 9.977 16272 Z= 0.310 Chirality : 0.031 0.114 1152 Planarity : 0.002 0.015 2160 Dihedral : 13.364 88.717 1440 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.24 % Allowed : 31.48 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.04 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHEKB1103 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (12528) covalent geometry : angle 0.65614 / 0.31 (16272) hydrogen bonds : bond 0.02008 / 1.11 ( 278) hydrogen bonds : angle 5.81046 / 3.30 ( 786) Misc. bond : bond 0.00080 / 0.05 ( 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 454 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 426 time to evaluate : 0.467 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: J 106 LYS cc_start: 0.8937 (tptm) cc_final: 0.8474 (tptm) REVERT: L 302 LYS cc_start: 0.8722 (ttpt) cc_final: 0.8347 (ttpt) REVERT: N 1104 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7880 (mm-30) REVERT: N 1106 LYS cc_start: 0.8824 (tptm) cc_final: 0.8203 (tptm) REVERT: B 4 GLU cc_start: 0.7787 (mp0) cc_final: 0.6879 (mp0) REVERT: Q 106 LYS cc_start: 0.8705 (tptm) cc_final: 0.8253 (tptm) REVERT: T 1006 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8353 (mtmt) REVERT: C 6 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8462 (mtmt) REVERT: X 103 PHE cc_start: 0.8997 (m-80) cc_final: 0.8708 (m-80) REVERT: X 104 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7529 (mm-30) REVERT: Y 204 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8136 (mm-30) REVERT: Z 304 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8058 (mm-30) REVERT: j 1004 GLU cc_start: 0.8444 (mp0) cc_final: 0.7459 (mp0) REVERT: j 1006 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8471 (mtmt) REVERT: k 1104 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7625 (mm-30) REVERT: l 1206 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8719 (ttmm) REVERT: m 1306 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8496 (mttt) REVERT: D 4 GLU cc_start: 0.7959 (mp0) cc_final: 0.7741 (mp0) REVERT: n 104 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7728 (mm-30) REVERT: q 1004 GLU cc_start: 0.8359 (mp0) cc_final: 0.7783 (mp0) REVERT: r 1102 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7807 (ttpt) REVERT: r 1103 PHE cc_start: 0.8688 (m-80) cc_final: 0.8151 (m-80) REVERT: r 1104 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7781 (mm-30) REVERT: s 1202 LYS cc_start: 0.9274 (ttpt) cc_final: 0.8974 (ttpt) REVERT: E 4 GLU cc_start: 0.7560 (mp0) cc_final: 0.6879 (mp0) REVERT: E 6 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8371 (mtmt) REVERT: u 106 LYS cc_start: 0.8744 (tptm) cc_final: 0.8320 (tptm) REVERT: w 304 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8168 (mm-30) REVERT: z 1206 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8475 (ttmm) REVERT: 0 1306 LYS cc_start: 0.8943 (tttt) cc_final: 0.8503 (tttt) REVERT: 1 103 PHE cc_start: 0.9013 (m-80) cc_final: 0.8795 (m-10) REVERT: 4 1006 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8550 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8774 (tptm) cc_final: 0.8299 (tptm) REVERT: 5 1107 PHE cc_start: 0.8674 (m-80) cc_final: 0.8423 (m-10) REVERT: 6 1206 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8727 (ttmm) REVERT: 7 1306 LYS cc_start: 0.9095 (tttt) cc_final: 0.8736 (mttt) REVERT: G 5 PHE cc_start: 0.8899 (m-80) cc_final: 0.8669 (m-80) REVERT: 8 106 LYS cc_start: 0.8977 (tptm) cc_final: 0.8596 (tptm) REVERT: 9 204 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7799 (mt-10) REVERT: CA 1106 LYS cc_start: 0.8838 (tptm) cc_final: 0.8189 (tptm) REVERT: FA 106 LYS cc_start: 0.8730 (tptm) cc_final: 0.8303 (tptm) REVERT: GA 206 LYS cc_start: 0.4863 (OUTLIER) cc_final: 0.3839 (pptt) REVERT: HA 306 LYS cc_start: 0.8958 (tttt) cc_final: 0.8689 (mttt) REVERT: JA 1106 LYS cc_start: 0.8688 (tptm) cc_final: 0.8298 (tptm) REVERT: KA 1202 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8668 (pptt) REVERT: LA 1304 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8036 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9027 (tttt) cc_final: 0.8769 (mttt) REVERT: I 4 GLU cc_start: 0.7761 (mp0) cc_final: 0.7422 (mp0) REVERT: I 6 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8342 (mtmt) REVERT: MA 106 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8312 (mmmm) REVERT: OA 304 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7793 (mm-30) REVERT: OA 306 LYS cc_start: 0.8980 (mttt) cc_final: 0.8649 (mttt) REVERT: PA 1006 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8580 (ttmt) REVERT: QA 1102 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8295 (ttpt) REVERT: QA 1104 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8003 (mm-30) REVERT: QA 1106 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8241 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8590 (ttmm) REVERT: SA 1302 LYS cc_start: 0.6444 (tptt) cc_final: 0.5813 (tppt) REVERT: SA 1306 LYS cc_start: 0.9065 (tttt) cc_final: 0.8838 (tttt) REVERT: TA 105 PHE cc_start: 0.9101 (t80) cc_final: 0.8757 (t80) REVERT: TA 106 LYS cc_start: 0.8778 (tmtp) cc_final: 0.8532 (tmtp) REVERT: UA 202 LYS cc_start: 0.8751 (tttm) cc_final: 0.8320 (ttmm) REVERT: VA 302 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8029 (tptp) REVERT: YA 1202 LYS cc_start: 0.8912 (tttm) cc_final: 0.8656 (tttm) REVERT: b 6 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8505 (tppt) REVERT: aA 102 LYS cc_start: 0.8791 (tptm) cc_final: 0.8407 (tptm) REVERT: bA 202 LYS cc_start: 0.8701 (tttm) cc_final: 0.8111 (ttmm) REVERT: cA 302 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8166 (tptp) REVERT: cA 304 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8583 (tm-30) REVERT: cA 305 PHE cc_start: 0.8707 (t80) cc_final: 0.8491 (t80) REVERT: eA 1105 PHE cc_start: 0.9053 (t80) cc_final: 0.8550 (t80) REVERT: gA 1302 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8206 (tptp) REVERT: c 2 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8195 (tppt) REVERT: c 5 PHE cc_start: 0.8716 (t80) cc_final: 0.8433 (t80) REVERT: iA 202 LYS cc_start: 0.8936 (tttm) cc_final: 0.8662 (mmmm) REVERT: kA 1002 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8100 (tppt) REVERT: kA 1005 PHE cc_start: 0.8947 (t80) cc_final: 0.8570 (t80) REVERT: lA 1103 PHE cc_start: 0.8460 (t80) cc_final: 0.8152 (t80) REVERT: mA 1206 LYS cc_start: 0.8370 (tttt) cc_final: 0.8161 (tptt) REVERT: nA 1302 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8057 (tptp) REVERT: pA 202 LYS cc_start: 0.8759 (tttm) cc_final: 0.8367 (mtpp) REVERT: qA 304 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8612 (tm-30) REVERT: qA 306 LYS cc_start: 0.8588 (tptp) cc_final: 0.8256 (tptp) REVERT: tA 1202 LYS cc_start: 0.8772 (tttm) cc_final: 0.8495 (tttm) REVERT: tA 1206 LYS cc_start: 0.8643 (tttt) cc_final: 0.8371 (tptt) REVERT: uA 1302 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7889 (tptp) REVERT: vA 102 LYS cc_start: 0.8835 (tptm) cc_final: 0.8473 (tptm) REVERT: xA 302 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8104 (tptp) REVERT: xA 303 PHE cc_start: 0.8604 (t80) cc_final: 0.8211 (t80) REVERT: xA 306 LYS cc_start: 0.8403 (tptp) cc_final: 0.8034 (tptp) REVERT: f 2 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8066 (tppt) REVERT: 3A 202 LYS cc_start: 0.8796 (tttm) cc_final: 0.8289 (ttmm) REVERT: 4A 302 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8205 (tptp) REVERT: 4A 306 LYS cc_start: 0.8556 (tptp) cc_final: 0.8228 (tptp) REVERT: 5A 1003 PHE cc_start: 0.8928 (t80) cc_final: 0.8506 (t80) REVERT: 5A 1007 PHE cc_start: 0.9261 (t80) cc_final: 0.8712 (t80) REVERT: 7A 1205 PHE cc_start: 0.8932 (t80) cc_final: 0.8180 (t80) REVERT: 8A 1302 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8085 (tptp) REVERT: 8A 1303 PHE cc_start: 0.8706 (t80) cc_final: 0.8263 (t80) REVERT: g 4 GLU cc_start: 0.8048 (tp30) cc_final: 0.7555 (tp30) REVERT: 9A 102 LYS cc_start: 0.8590 (tptm) cc_final: 0.8110 (tptm) REVERT: 9A 103 PHE cc_start: 0.8464 (t80) cc_final: 0.7956 (t80) REVERT: AB 202 LYS cc_start: 0.8799 (tptm) cc_final: 0.8119 (ttmm) REVERT: AB 205 PHE cc_start: 0.8703 (t80) cc_final: 0.8377 (t80) REVERT: BB 302 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7674 (tptp) REVERT: BB 306 LYS cc_start: 0.8654 (tptp) cc_final: 0.8405 (tptp) REVERT: EB 1202 LYS cc_start: 0.8786 (tttm) cc_final: 0.8483 (tttm) REVERT: EB 1203 PHE cc_start: 0.8927 (t80) cc_final: 0.8408 (t80) REVERT: HB 203 PHE cc_start: 0.8843 (t80) cc_final: 0.8189 (t80) REVERT: HB 205 PHE cc_start: 0.8528 (t80) cc_final: 0.8158 (t80) REVERT: IB 304 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8150 (tm-30) REVERT: JB 1005 PHE cc_start: 0.8626 (t80) cc_final: 0.8341 (t80) REVERT: KB 1105 PHE cc_start: 0.8998 (t80) cc_final: 0.8433 (t80) REVERT: MB 1304 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8678 (tm-30) REVERT: i 2 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8377 (tppt) REVERT: i 4 GLU cc_start: 0.8172 (tp30) cc_final: 0.7810 (tp30) REVERT: NB 104 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7963 (pm20) REVERT: NB 105 PHE cc_start: 0.8357 (t80) cc_final: 0.7901 (t80) REVERT: PB 304 GLU cc_start: 0.8782 (tm-30) cc_final: 0.7087 (pm20) REVERT: PB 305 PHE cc_start: 0.8314 (t80) cc_final: 0.7391 (t80) REVERT: PB 306 LYS cc_start: 0.8764 (tptp) cc_final: 0.8495 (tptp) REVERT: PB 307 PHE cc_start: 0.8874 (t80) cc_final: 0.8583 (t80) REVERT: SB 1202 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8331 (ttmm) REVERT: SB 1203 PHE cc_start: 0.8811 (t80) cc_final: 0.8452 (t80) REVERT: SB 1206 LYS cc_start: 0.8566 (tmtt) cc_final: 0.8262 (tmtt) REVERT: TB 1302 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8206 (tptp) REVERT: TB 1305 PHE cc_start: 0.8592 (t80) cc_final: 0.8027 (t80) outliers start: 28 outliers final: 11 residues processed: 438 average time/residue: 0.2027 time to fit residues: 109.9707 Evaluate side-chains 445 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 422 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain uA residue 1302 LYS Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain TB residue 1302 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078338 restraints weight = 24895.719| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.18 r_work: 0.3048 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.062 12563 Z= 0.714 Angle : 0.965 10.058 16272 Z= 0.447 Chirality : 0.049 0.153 1152 Planarity : 0.004 0.021 2160 Dihedral : 13.865 87.693 1440 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.75 % Allowed : 31.48 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.33 (0.17), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.13), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.040 0.004 PHEGB 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01594 / 0.72 (12528) covalent geometry : angle 0.96480 / 0.45 (16272) hydrogen bonds : bond 0.03873 / 2.14 ( 278) hydrogen bonds : angle 6.53798 / 3.72 ( 786) Misc. bond : bond 0.00263 / 0.14 ( 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 512 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 471 time to evaluate : 0.450 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 5 PHE cc_start: 0.9060 (m-80) cc_final: 0.8653 (m-80) REVERT: J 104 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8127 (mm-30) REVERT: J 106 LYS cc_start: 0.9053 (tptm) cc_final: 0.8532 (tptm) REVERT: L 302 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8518 (ttpt) REVERT: N 1104 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7991 (mm-30) REVERT: N 1106 LYS cc_start: 0.8918 (tptm) cc_final: 0.8349 (tptm) REVERT: B 4 GLU cc_start: 0.7842 (mp0) cc_final: 0.6232 (mp0) REVERT: Q 106 LYS cc_start: 0.8720 (tptm) cc_final: 0.8329 (tptm) REVERT: T 1006 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8506 (mtmt) REVERT: U 1104 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7396 (mm-30) REVERT: C 2 LYS cc_start: 0.8111 (tttm) cc_final: 0.7870 (tttm) REVERT: X 104 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7563 (mm-30) REVERT: Y 204 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8330 (mm-30) REVERT: Y 206 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8634 (ttmm) REVERT: Z 304 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8088 (mm-30) REVERT: j 1004 GLU cc_start: 0.8431 (mp0) cc_final: 0.7555 (mp0) REVERT: k 1104 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7835 (mm-30) REVERT: k 1106 LYS cc_start: 0.8730 (mptm) cc_final: 0.8458 (tptm) REVERT: l 1202 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8263 (tppp) REVERT: m 1306 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8655 (mttt) REVERT: n 104 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7723 (mm-30) REVERT: n 106 LYS cc_start: 0.8834 (tptm) cc_final: 0.8329 (tptm) REVERT: q 1004 GLU cc_start: 0.8469 (mp0) cc_final: 0.7899 (mp0) REVERT: r 1102 LYS cc_start: 0.8403 (ttpt) cc_final: 0.7701 (ttpt) REVERT: r 1104 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7676 (mm-30) REVERT: r 1106 LYS cc_start: 0.8856 (mptm) cc_final: 0.8540 (mptm) REVERT: s 1202 LYS cc_start: 0.9259 (ttpt) cc_final: 0.8951 (ttpt) REVERT: t 1304 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7936 (mm-30) REVERT: E 4 GLU cc_start: 0.7756 (mp0) cc_final: 0.6888 (mp0) REVERT: E 6 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8498 (mtmt) REVERT: u 102 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8742 (ttpt) REVERT: u 106 LYS cc_start: 0.8778 (tptm) cc_final: 0.8375 (tptm) REVERT: w 304 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8350 (mm-30) REVERT: z 1206 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8520 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8177 (mm-30) REVERT: 0 1306 LYS cc_start: 0.9125 (tttt) cc_final: 0.8758 (tttt) REVERT: F 4 GLU cc_start: 0.7891 (mp0) cc_final: 0.6906 (mp0) REVERT: 4 1006 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8412 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8797 (tptm) cc_final: 0.8290 (tptm) REVERT: 5 1107 PHE cc_start: 0.8840 (m-80) cc_final: 0.8490 (m-10) REVERT: 6 1206 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8722 (ttmm) REVERT: 7 1306 LYS cc_start: 0.9118 (tttt) cc_final: 0.8762 (mttt) REVERT: G 4 GLU cc_start: 0.7765 (mp0) cc_final: 0.6811 (mp0) REVERT: 8 106 LYS cc_start: 0.8978 (tptm) cc_final: 0.8567 (tptm) REVERT: CA 1106 LYS cc_start: 0.8801 (tptm) cc_final: 0.8188 (tptm) REVERT: FA 106 LYS cc_start: 0.8723 (tptm) cc_final: 0.8378 (tptm) REVERT: GA 206 LYS cc_start: 0.4695 (OUTLIER) cc_final: 0.2660 (pptt) REVERT: HA 306 LYS cc_start: 0.8989 (tttt) cc_final: 0.8697 (mttt) REVERT: JA 1104 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7762 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8795 (tptm) cc_final: 0.8405 (tptm) REVERT: LA 1304 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8156 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9070 (tttt) cc_final: 0.8831 (mttt) REVERT: I 4 GLU cc_start: 0.7899 (mp0) cc_final: 0.7619 (mp0) REVERT: I 6 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8389 (mtmt) REVERT: MA 106 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8398 (mmmm) REVERT: OA 304 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7885 (mm-30) REVERT: OA 306 LYS cc_start: 0.9030 (mttt) cc_final: 0.8684 (mttt) REVERT: PA 1006 LYS cc_start: 0.8896 (ttmt) cc_final: 0.8565 (ttmt) REVERT: QA 1106 LYS cc_start: 0.8484 (mmmm) cc_final: 0.8174 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8967 (ttmm) cc_final: 0.8703 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8089 (mm-30) REVERT: a 2 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8368 (tppt) REVERT: TA 102 LYS cc_start: 0.9039 (tptm) cc_final: 0.8596 (tptm) REVERT: TA 106 LYS cc_start: 0.8851 (tmtp) cc_final: 0.8608 (tmtp) REVERT: UA 202 LYS cc_start: 0.9005 (tttm) cc_final: 0.8497 (ttmm) REVERT: VA 302 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8320 (tptp) REVERT: YA 1202 LYS cc_start: 0.9118 (tttm) cc_final: 0.8865 (tttm) REVERT: b 2 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8610 (ttpt) REVERT: b 6 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8582 (tppt) REVERT: aA 102 LYS cc_start: 0.9052 (tptm) cc_final: 0.8703 (tptm) REVERT: bA 202 LYS cc_start: 0.8967 (tttm) cc_final: 0.8426 (ttmm) REVERT: cA 302 LYS cc_start: 0.8715 (tptp) cc_final: 0.8381 (tptp) REVERT: cA 304 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8283 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9066 (t80) cc_final: 0.8654 (t80) REVERT: gA 1302 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8349 (tptp) REVERT: c 2 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8472 (tppt) REVERT: c 3 PHE cc_start: 0.9158 (t80) cc_final: 0.8737 (t80) REVERT: c 5 PHE cc_start: 0.8814 (t80) cc_final: 0.8542 (t80) REVERT: iA 202 LYS cc_start: 0.9104 (tttm) cc_final: 0.8722 (ttmm) REVERT: kA 1005 PHE cc_start: 0.8954 (t80) cc_final: 0.8651 (t80) REVERT: lA 1103 PHE cc_start: 0.8658 (t80) cc_final: 0.8176 (t80) REVERT: mA 1206 LYS cc_start: 0.8626 (tttt) cc_final: 0.8380 (tptt) REVERT: nA 1302 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8216 (tptp) REVERT: nA 1306 LYS cc_start: 0.8609 (tptp) cc_final: 0.8232 (tptp) REVERT: d 2 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8807 (ttpt) REVERT: pA 202 LYS cc_start: 0.8904 (tttm) cc_final: 0.8288 (mtpp) REVERT: pA 203 PHE cc_start: 0.9048 (t80) cc_final: 0.8700 (t80) REVERT: qA 304 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8098 (tm-30) REVERT: qA 306 LYS cc_start: 0.8614 (tptp) cc_final: 0.8257 (tptp) REVERT: sA 1103 PHE cc_start: 0.8424 (t80) cc_final: 0.8150 (t80) REVERT: tA 1202 LYS cc_start: 0.8858 (tttm) cc_final: 0.8608 (tttm) REVERT: tA 1204 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7053 (tm-30) REVERT: uA 1302 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8352 (tptp) REVERT: uA 1303 PHE cc_start: 0.8305 (t80) cc_final: 0.8053 (t80) REVERT: e 2 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8309 (tppt) REVERT: vA 102 LYS cc_start: 0.9033 (tptm) cc_final: 0.8736 (tptm) REVERT: xA 302 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8348 (tptp) REVERT: xA 303 PHE cc_start: 0.8841 (t80) cc_final: 0.8602 (t80) REVERT: xA 306 LYS cc_start: 0.8492 (tptp) cc_final: 0.8147 (tptp) REVERT: yA 1002 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8563 (ttpt) REVERT: 1A 1302 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8309 (tptp) REVERT: f 2 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8525 (ttpt) REVERT: 2A 102 LYS cc_start: 0.8891 (tptm) cc_final: 0.8523 (tptm) REVERT: 3A 202 LYS cc_start: 0.8912 (tttm) cc_final: 0.8478 (mmmm) REVERT: 4A 302 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8443 (tptp) REVERT: 4A 304 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8455 (tm-30) REVERT: 4A 306 LYS cc_start: 0.8561 (tptp) cc_final: 0.8283 (tptp) REVERT: 4A 307 PHE cc_start: 0.8962 (t80) cc_final: 0.8607 (t80) REVERT: 5A 1002 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8691 (ttpt) REVERT: 8A 1302 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8209 (tptp) REVERT: 8A 1303 PHE cc_start: 0.8949 (t80) cc_final: 0.8389 (t80) REVERT: 8A 1304 GLU cc_start: 0.8977 (tm-30) cc_final: 0.7594 (tm-30) REVERT: g 2 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8464 (tppt) REVERT: g 4 GLU cc_start: 0.8141 (tp30) cc_final: 0.7742 (tp30) REVERT: 9A 102 LYS cc_start: 0.8934 (tptm) cc_final: 0.8656 (tptm) REVERT: 9A 103 PHE cc_start: 0.8497 (t80) cc_final: 0.8095 (t80) REVERT: AB 202 LYS cc_start: 0.9024 (tptm) cc_final: 0.8388 (ttmm) REVERT: BB 302 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8119 (tptp) REVERT: BB 306 LYS cc_start: 0.8733 (tptp) cc_final: 0.8441 (tptp) REVERT: CB 1002 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8681 (ttpt) REVERT: CB 1004 GLU cc_start: 0.8134 (tp30) cc_final: 0.7835 (tp30) REVERT: DB 1102 LYS cc_start: 0.8793 (tptm) cc_final: 0.8399 (tptm) REVERT: EB 1203 PHE cc_start: 0.8892 (t80) cc_final: 0.8283 (t80) REVERT: HB 203 PHE cc_start: 0.8824 (t80) cc_final: 0.8398 (t80) REVERT: IB 302 LYS cc_start: 0.8648 (tptp) cc_final: 0.8309 (tptp) REVERT: IB 304 GLU cc_start: 0.8878 (tm-30) cc_final: 0.7787 (tm-30) REVERT: KB 1105 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8421 (t80) REVERT: MB 1304 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8100 (tm-30) REVERT: i 2 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8773 (tppt) REVERT: i 4 GLU cc_start: 0.8190 (tp30) cc_final: 0.7981 (tm-30) REVERT: NB 104 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8118 (pm20) REVERT: NB 105 PHE cc_start: 0.8682 (t80) cc_final: 0.8326 (t80) REVERT: NB 107 PHE cc_start: 0.9272 (t80) cc_final: 0.8905 (t80) REVERT: PB 304 GLU cc_start: 0.8919 (tm-30) cc_final: 0.7014 (pm20) REVERT: PB 305 PHE cc_start: 0.8501 (t80) cc_final: 0.7849 (t80) REVERT: PB 306 LYS cc_start: 0.8754 (tptp) cc_final: 0.8498 (tptp) REVERT: PB 307 PHE cc_start: 0.9110 (t80) cc_final: 0.8800 (t80) REVERT: SB 1202 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8448 (ttmm) REVERT: SB 1203 PHE cc_start: 0.8704 (t80) cc_final: 0.8349 (t80) REVERT: SB 1206 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8487 (tmtt) REVERT: TB 1302 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8451 (tptp) REVERT: TB 1305 PHE cc_start: 0.8707 (t80) cc_final: 0.8276 (t80) outliers start: 41 outliers final: 21 residues processed: 476 average time/residue: 0.2005 time to fit residues: 117.8695 Evaluate side-chains 505 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 469 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain l residue 1202 LYS Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 7 residue 1302 LYS Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain uA residue 1302 LYS Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1302 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.094678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.081729 restraints weight = 23819.834| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.16 r_work: 0.3194 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12563 Z= 0.132 Angle : 0.718 9.976 16272 Z= 0.342 Chirality : 0.032 0.124 1152 Planarity : 0.002 0.018 2160 Dihedral : 13.257 85.141 1440 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.55 % Allowed : 34.03 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.93 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.002 PHEKB1103 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (12528) covalent geometry : angle 0.71790 / 0.34 (16272) hydrogen bonds : bond 0.02117 / 1.17 ( 278) hydrogen bonds : angle 5.87866 / 3.32 ( 786) Misc. bond : bond 0.00161 / 0.08 ( 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 440 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 418 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8029 (mm-30) REVERT: J 106 LYS cc_start: 0.8978 (tptm) cc_final: 0.8533 (tptm) REVERT: L 302 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8345 (ttpt) REVERT: N 1104 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7933 (mm-30) REVERT: N 1106 LYS cc_start: 0.8859 (tptm) cc_final: 0.8279 (tptm) REVERT: B 4 GLU cc_start: 0.7845 (mp0) cc_final: 0.6943 (mp0) REVERT: Q 106 LYS cc_start: 0.8704 (tptm) cc_final: 0.8266 (tptm) REVERT: T 1006 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8425 (mtmt) REVERT: C 6 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8499 (mtmt) REVERT: X 104 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7544 (mm-30) REVERT: Y 204 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8179 (mm-30) REVERT: Y 206 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8426 (ttmm) REVERT: Z 304 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8001 (mm-30) REVERT: j 1004 GLU cc_start: 0.8420 (mp0) cc_final: 0.7353 (mp0) REVERT: k 1104 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7609 (mm-30) REVERT: l 1202 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8029 (tppp) REVERT: l 1206 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8715 (ttmm) REVERT: m 1306 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8390 (mttt) REVERT: q 1004 GLU cc_start: 0.8266 (mp0) cc_final: 0.7761 (mp0) REVERT: q 1005 PHE cc_start: 0.9054 (m-80) cc_final: 0.8602 (m-80) REVERT: r 1102 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7754 (ttpt) REVERT: r 1103 PHE cc_start: 0.8612 (m-80) cc_final: 0.8065 (m-80) REVERT: r 1104 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7602 (mm-30) REVERT: s 1202 LYS cc_start: 0.9270 (ttpt) cc_final: 0.8948 (ttpt) REVERT: E 4 GLU cc_start: 0.7554 (mp0) cc_final: 0.6914 (mp0) REVERT: E 6 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8422 (mtmt) REVERT: u 106 LYS cc_start: 0.8735 (tptm) cc_final: 0.8311 (tptm) REVERT: w 304 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8169 (mm-30) REVERT: x 1004 GLU cc_start: 0.7778 (mp0) cc_final: 0.7176 (mp0) REVERT: z 1202 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8456 (ttpt) REVERT: z 1206 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8445 (ttmm) REVERT: 0 1306 LYS cc_start: 0.8871 (tttt) cc_final: 0.8430 (tttt) REVERT: F 6 LYS cc_start: 0.8844 (mtmt) cc_final: 0.7895 (mtmt) REVERT: 1 103 PHE cc_start: 0.8897 (m-80) cc_final: 0.8679 (m-10) REVERT: 4 1006 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8535 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8760 (tptm) cc_final: 0.8277 (tptm) REVERT: 5 1107 PHE cc_start: 0.8646 (m-80) cc_final: 0.8416 (m-10) REVERT: 6 1206 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8662 (ttmm) REVERT: 7 1306 LYS cc_start: 0.9092 (tttt) cc_final: 0.8704 (mttt) REVERT: G 5 PHE cc_start: 0.8832 (m-80) cc_final: 0.8618 (m-80) REVERT: 8 106 LYS cc_start: 0.8944 (tptm) cc_final: 0.8598 (tptm) REVERT: CA 1106 LYS cc_start: 0.8797 (tptm) cc_final: 0.8169 (tptm) REVERT: FA 106 LYS cc_start: 0.8629 (tptm) cc_final: 0.8158 (tptm) REVERT: HA 306 LYS cc_start: 0.8914 (tttt) cc_final: 0.8607 (mttt) REVERT: JA 1106 LYS cc_start: 0.8742 (tptm) cc_final: 0.8340 (tptm) REVERT: KA 1202 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8688 (pptt) REVERT: LA 1304 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8091 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9008 (tttt) cc_final: 0.8757 (mttt) REVERT: I 4 GLU cc_start: 0.7786 (mp0) cc_final: 0.7496 (mp0) REVERT: I 6 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8345 (mtmt) REVERT: MA 106 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8284 (mmmm) REVERT: OA 304 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7661 (mm-30) REVERT: OA 306 LYS cc_start: 0.8958 (mttt) cc_final: 0.8563 (mttt) REVERT: PA 1006 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8599 (ttmt) REVERT: QA 1102 LYS cc_start: 0.9123 (ttpt) cc_final: 0.8902 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8211 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8571 (ttmm) REVERT: SA 1302 LYS cc_start: 0.6535 (tptt) cc_final: 0.5942 (tppt) REVERT: TA 105 PHE cc_start: 0.9092 (t80) cc_final: 0.8670 (t80) REVERT: TA 106 LYS cc_start: 0.8775 (tmtp) cc_final: 0.8542 (tmtp) REVERT: VA 302 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8043 (tptp) REVERT: WA 1003 PHE cc_start: 0.9002 (t80) cc_final: 0.8609 (t80) REVERT: YA 1202 LYS cc_start: 0.8899 (tttm) cc_final: 0.8609 (tttm) REVERT: b 6 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8468 (tppt) REVERT: aA 102 LYS cc_start: 0.8833 (tptm) cc_final: 0.8395 (tptm) REVERT: bA 202 LYS cc_start: 0.8766 (tttm) cc_final: 0.8157 (ttmm) REVERT: cA 304 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8228 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9073 (t80) cc_final: 0.8635 (t80) REVERT: c 2 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8194 (tppt) REVERT: c 5 PHE cc_start: 0.8696 (t80) cc_final: 0.8325 (t80) REVERT: iA 202 LYS cc_start: 0.8980 (tttm) cc_final: 0.8607 (ttmm) REVERT: kA 1002 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8050 (tppt) REVERT: kA 1005 PHE cc_start: 0.8954 (t80) cc_final: 0.8586 (t80) REVERT: lA 1103 PHE cc_start: 0.8435 (t80) cc_final: 0.8118 (t80) REVERT: mA 1206 LYS cc_start: 0.8360 (tttt) cc_final: 0.8121 (tptt) REVERT: nA 1302 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8040 (tptp) REVERT: pA 202 LYS cc_start: 0.8803 (tttm) cc_final: 0.8269 (mtpp) REVERT: qA 306 LYS cc_start: 0.8613 (tptp) cc_final: 0.8303 (tptp) REVERT: tA 1202 LYS cc_start: 0.8752 (tttm) cc_final: 0.8478 (tttm) REVERT: tA 1206 LYS cc_start: 0.8642 (tttt) cc_final: 0.8372 (tptt) REVERT: uA 1302 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7838 (tptp) REVERT: xA 306 LYS cc_start: 0.8385 (tptp) cc_final: 0.7976 (tptp) REVERT: f 2 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8063 (ttpt) REVERT: 3A 202 LYS cc_start: 0.8764 (tttm) cc_final: 0.8277 (ttmm) REVERT: 4A 306 LYS cc_start: 0.8582 (tptp) cc_final: 0.8275 (tptp) REVERT: 5A 1003 PHE cc_start: 0.8915 (t80) cc_final: 0.8519 (t80) REVERT: 5A 1007 PHE cc_start: 0.9256 (t80) cc_final: 0.8641 (t80) REVERT: 7A 1205 PHE cc_start: 0.8955 (t80) cc_final: 0.8147 (t80) REVERT: 8A 1302 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8050 (tptp) REVERT: 8A 1303 PHE cc_start: 0.8700 (t80) cc_final: 0.8334 (t80) REVERT: g 4 GLU cc_start: 0.8057 (tp30) cc_final: 0.7550 (tp30) REVERT: 9A 102 LYS cc_start: 0.8603 (tptm) cc_final: 0.8094 (tptm) REVERT: 9A 103 PHE cc_start: 0.8399 (t80) cc_final: 0.7911 (t80) REVERT: AB 202 LYS cc_start: 0.8794 (tptm) cc_final: 0.8074 (ttmm) REVERT: AB 205 PHE cc_start: 0.8693 (t80) cc_final: 0.8374 (t80) REVERT: BB 302 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7645 (tptp) REVERT: BB 306 LYS cc_start: 0.8673 (tptp) cc_final: 0.8388 (tptp) REVERT: EB 1203 PHE cc_start: 0.8920 (t80) cc_final: 0.8407 (t80) REVERT: FB 1304 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8254 (tm-30) REVERT: HB 203 PHE cc_start: 0.8795 (t80) cc_final: 0.8226 (t80) REVERT: HB 205 PHE cc_start: 0.8534 (t80) cc_final: 0.8297 (t80) REVERT: JB 1005 PHE cc_start: 0.8589 (t80) cc_final: 0.8342 (t80) REVERT: KB 1105 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8484 (t80) REVERT: MB 1304 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8671 (tm-30) REVERT: i 2 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8330 (tppt) REVERT: i 4 GLU cc_start: 0.8153 (tp30) cc_final: 0.7755 (tp30) REVERT: NB 102 LYS cc_start: 0.8452 (tptm) cc_final: 0.8093 (tptm) REVERT: NB 104 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7984 (pm20) REVERT: NB 105 PHE cc_start: 0.8274 (t80) cc_final: 0.7855 (t80) REVERT: NB 107 PHE cc_start: 0.9119 (t80) cc_final: 0.8731 (t80) REVERT: PB 304 GLU cc_start: 0.8821 (tm-30) cc_final: 0.7133 (pm20) REVERT: PB 305 PHE cc_start: 0.8305 (t80) cc_final: 0.7749 (t80) REVERT: PB 306 LYS cc_start: 0.8786 (tptp) cc_final: 0.8502 (tptp) REVERT: PB 307 PHE cc_start: 0.8920 (t80) cc_final: 0.8642 (t80) REVERT: SB 1202 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8311 (ttmm) REVERT: SB 1203 PHE cc_start: 0.8785 (t80) cc_final: 0.8488 (t80) REVERT: SB 1206 LYS cc_start: 0.8603 (tmtt) cc_final: 0.8254 (tmtt) REVERT: TB 1302 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8236 (tptp) REVERT: TB 1305 PHE cc_start: 0.8578 (t80) cc_final: 0.7970 (t80) outliers start: 22 outliers final: 9 residues processed: 425 average time/residue: 0.2021 time to fit residues: 106.0701 Evaluate side-chains 433 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 414 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain T residue 1006 LYS Chi-restraints excluded: chain l residue 1202 LYS Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 7 residue 1302 LYS Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain uA residue 1302 LYS Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain TB residue 1302 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.078245 restraints weight = 24991.331| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.22 r_work: 0.3052 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.064 12563 Z= 0.715 Angle : 0.979 10.458 16272 Z= 0.457 Chirality : 0.050 0.151 1152 Planarity : 0.004 0.025 2160 Dihedral : 13.672 85.327 1440 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.36 % Allowed : 33.56 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.30 (0.17), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.13), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.043 0.004 PHE j1005 Details of bonding type rmsd/Z covalent geometry : bond 0.01596 / 0.72 (12528) covalent geometry : angle 0.97908 / 0.46 (16272) hydrogen bonds : bond 0.03859 / 2.12 ( 278) hydrogen bonds : angle 6.58149 / 3.74 ( 786) Misc. bond : bond 0.00231 / 0.13 ( 35) =============================================================================== Job complete usr+sys time: 2778.62 seconds wall clock time: 48 minutes 29.13 seconds (2909.13 seconds total)