Starting phenix.real_space_refine on Sat Oct 24 02:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lqg_23485/10_2026/7lqg_23485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqg_23485/10_2026/7lqg_23485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqg_23485/10_2026/7lqg_23485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqg_23485/10_2026/7lqg_23485.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lqg_23485/10_2026/7lqg_23485.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lqg_23485/10_2026/7lqg_23485.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lqg_23485/10_2026/7lqg_23485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqg_23485/10_2026/7lqg_23485.cif" } 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= 0.030 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): 0.01s 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: 2.85, per 1000 atoms: 0.24 Number of scatterers: 12096 At special positions: 0 Unit cell: (89.64, 89.64, 108, 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=36, symmetry=0 Number of additional bonds: simple=36, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 133.4 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: 0.30 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: 3.536A pdb=" N PHEGB 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE h 5 " --> pdb=" O PHEGB 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE2A 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.536A 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: 3.536A 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: 3.624A 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: 3.676A 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: 1.85 Time building geometry restraints manager: 1.11 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: 1530 1.26 - 1.33: 1350 1.33 - 1.41: 3600 1.41 - 1.48: 1300 1.48 - 1.56: 4748 Bond restraints: 12528 Sorted by residual: 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 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 3.48e+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 3.46e+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 5CRQB1001 " pdb=" CAL 5CRQB1001 " 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: 14236 1.98 - 3.95: 1586 3.95 - 5.93: 324 5.93 - 7.91: 108 7.91 - 9.88: 18 Bond angle restraints: 16272 Sorted by residual: 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 f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 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 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 1.08e+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 angle pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " pdb=" CAA 5CR i 1 " 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: 4840 15.26 - 30.52: 794 30.52 - 45.78: 342 45.78 - 61.04: 198 61.04 - 76.30: 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 1.29 58.71 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 8 106 " pdb=" CB LYS 8 106 " pdb=" CG LYS 8 106 " pdb=" CD LYS 8 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.30 58.70 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: 404 0.018 - 0.036: 326 0.036 - 0.054: 308 0.054 - 0.072: 88 0.072 - 0.090: 26 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 2.02e-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 l1202 " pdb=" N LYS l1202 " pdb=" C LYS l1202 " pdb=" CB LYS l1202 " 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 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 PHEUA 205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-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 PHESB1205 " -0.008 2.00e-02 2.50e+03 6.92e-03 8.39e-01 pdb=" CG PHESB1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHESB1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHESB1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHESB1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHESB1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHESB1205 " -0.002 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 48 2.45 - 3.07: 6870 3.07 - 3.68: 18066 3.68 - 4.29: 29438 4.29 - 4.90: 49356 Nonbonded interactions: 103778 Sorted by model distance: nonbonded pdb=" CD LYS A 2 " pdb=" OE2 GMADA1208 " model vdw 1.842 2.752 nonbonded pdb=" CD LYS M1002 " pdb=" OE2 GMA 9 208 " model vdw 1.842 2.752 nonbonded pdb=" OE2 GMA V1208 " pdb=" CD LYS H 2 " model vdw 1.868 2.752 nonbonded pdb=" OE2 GMA R 208 " pdb=" CD LYSIA1002 " model vdw 1.868 2.752 nonbonded pdb=" OE2 GMA l1208 " pdb=" NZ LYS D 2 " model vdw 1.870 2.496 ... (remaining 103773 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.720 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.026 0.570 12564 Z= 2.184 Angle : 1.417 9.883 16272 Z= 0.592 Chirality : 0.035 0.090 1152 Planarity : 0.002 0.009 2160 Dihedral : 20.718 76.303 3888 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 31.55 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 1.41747 / 0.59 (16272) hydrogen bonds : bond 0.31156 / 16.93 ( 278) hydrogen bonds : angle 15.44566 / 8.75 ( 786) Misc. bond : bond 0.38093 / 21.06 ( 36) *********************** 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 628 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 502 time to evaluate : 0.441 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: 0.7489 (mp0) cc_final: 0.6989 (pm20) REVERT: A 6 LYS cc_start: 0.8409 (mtmt) cc_final: 0.7960 (mtmt) REVERT: M 1004 GLU cc_start: 0.7511 (mp0) cc_final: 0.7009 (pm20) REVERT: M 1006 LYS cc_start: 0.8412 (mtmt) cc_final: 0.7962 (mtmt) REVERT: P 1302 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8557 (ttmm) REVERT: B 4 GLU cc_start: 0.7388 (mp0) cc_final: 0.6353 (pm20) REVERT: T 1004 GLU cc_start: 0.7416 (mp0) cc_final: 0.6369 (pm20) REVERT: W 1302 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8394 (ttmm) REVERT: C 6 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8165 (mtmt) REVERT: Z 306 LYS cc_start: 0.8670 (tttt) cc_final: 0.8388 (tttt) REVERT: j 1006 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8135 (mtmt) REVERT: m 1306 LYS cc_start: 0.8682 (tttt) cc_final: 0.8399 (tttt) REVERT: n 104 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6299 (mm-30) REVERT: p 306 LYS cc_start: 0.8718 (tttt) cc_final: 0.8460 (tttt) REVERT: r 1104 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6342 (mm-30) REVERT: t 1306 LYS cc_start: 0.8723 (tttt) cc_final: 0.8465 (tttt) REVERT: E 4 GLU cc_start: 0.7450 (mp0) cc_final: 0.7098 (mp0) REVERT: E 6 LYS cc_start: 0.8375 (mtmt) cc_final: 0.8101 (mtmt) REVERT: u 102 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8441 (mtpp) REVERT: u 104 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7138 (mm-30) REVERT: w 304 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7102 (mm-30) REVERT: w 306 LYS cc_start: 0.8688 (tttt) cc_final: 0.8360 (tttt) REVERT: x 1004 GLU cc_start: 0.7478 (mp0) cc_final: 0.7137 (mp0) REVERT: x 1006 LYS cc_start: 0.8388 (mtmt) cc_final: 0.8119 (mtmt) REVERT: y 1102 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8446 (mtpp) REVERT: y 1104 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7164 (mm-30) REVERT: z 1202 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8300 (mtpt) REVERT: 0 1302 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8519 (ttmm) REVERT: 0 1304 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7083 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8695 (tttt) cc_final: 0.8386 (tttt) REVERT: F 4 GLU cc_start: 0.7395 (mp0) cc_final: 0.6854 (pm20) REVERT: 2 206 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8189 (ttmm) REVERT: 3 306 LYS cc_start: 0.8751 (tttt) cc_final: 0.8442 (tttt) REVERT: 4 1004 GLU cc_start: 0.7422 (mp0) cc_final: 0.6862 (pm20) REVERT: 6 1206 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8193 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8759 (tttt) cc_final: 0.8423 (tttt) REVERT: G 4 GLU cc_start: 0.7499 (mp0) cc_final: 0.6447 (mp0) REVERT: 9 202 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8270 (mtpt) REVERT: 9 204 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6821 (mt-10) REVERT: AA 306 LYS cc_start: 0.8758 (tttt) cc_final: 0.8472 (tttt) REVERT: BA 1004 GLU cc_start: 0.7517 (mp0) cc_final: 0.6466 (mp0) REVERT: DA 1202 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8302 (mtpt) REVERT: DA 1204 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6824 (mt-10) REVERT: EA 1302 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8628 (ttmm) REVERT: EA 1304 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6981 (mm-30) REVERT: EA 1306 LYS cc_start: 0.8759 (tttt) cc_final: 0.8463 (tttt) REVERT: I 4 GLU cc_start: 0.7640 (mp0) cc_final: 0.7419 (mp0) REVERT: OA 306 LYS cc_start: 0.8620 (tttt) cc_final: 0.8201 (tttt) REVERT: RA 1204 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7135 (mt-10) REVERT: SA 1306 LYS cc_start: 0.8631 (tttt) cc_final: 0.8226 (tttt) REVERT: a 3 PHE cc_start: 0.9236 (t80) cc_final: 0.9008 (t80) REVERT: a 5 PHE cc_start: 0.9036 (t80) cc_final: 0.8632 (t80) REVERT: a 7 PHE cc_start: 0.9251 (t80) cc_final: 0.8950 (t80) REVERT: TA 103 PHE cc_start: 0.9011 (t80) cc_final: 0.8762 (t80) REVERT: TA 107 PHE cc_start: 0.8855 (t80) cc_final: 0.8646 (t80) REVERT: UA 202 LYS cc_start: 0.8743 (tttm) cc_final: 0.8497 (mmmm) REVERT: UA 206 LYS cc_start: 0.8907 (tttt) cc_final: 0.8690 (tttt) REVERT: VA 304 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8172 (tm-30) REVERT: WA 1003 PHE cc_start: 0.9236 (t80) cc_final: 0.9018 (t80) REVERT: WA 1005 PHE cc_start: 0.9054 (t80) cc_final: 0.8646 (t80) REVERT: WA 1007 PHE cc_start: 0.9255 (t80) cc_final: 0.8979 (t80) REVERT: XA 1103 PHE cc_start: 0.8981 (t80) cc_final: 0.8746 (t80) REVERT: XA 1107 PHE cc_start: 0.8879 (t80) cc_final: 0.8668 (t80) REVERT: YA 1202 LYS cc_start: 0.8721 (tttm) cc_final: 0.8422 (tttm) REVERT: YA 1206 LYS cc_start: 0.8892 (tttt) cc_final: 0.8671 (tttt) REVERT: ZA 1304 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8173 (tm-30) REVERT: bA 202 LYS cc_start: 0.8657 (tttm) cc_final: 0.8266 (mmmm) REVERT: fA 1202 LYS cc_start: 0.8629 (tttm) cc_final: 0.8365 (tttm) REVERT: hA 103 PHE cc_start: 0.8994 (t80) cc_final: 0.8568 (t80) REVERT: hA 107 PHE cc_start: 0.8728 (t80) cc_final: 0.8372 (t80) REVERT: iA 202 LYS cc_start: 0.8724 (tttm) cc_final: 0.8387 (ttmm) REVERT: iA 204 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6966 (tm-30) REVERT: iA 206 LYS cc_start: 0.8950 (tttt) cc_final: 0.8476 (tttm) REVERT: jA 305 PHE cc_start: 0.8812 (t80) cc_final: 0.8586 (t80) REVERT: lA 1103 PHE cc_start: 0.8962 (t80) cc_final: 0.8549 (t80) REVERT: lA 1107 PHE cc_start: 0.8750 (t80) cc_final: 0.8441 (t80) REVERT: mA 1204 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6926 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8933 (tttt) cc_final: 0.8409 (tttt) REVERT: nA 1305 PHE cc_start: 0.8820 (t80) cc_final: 0.8601 (t80) REVERT: d 5 PHE cc_start: 0.9042 (t80) cc_final: 0.8631 (t80) REVERT: oA 103 PHE cc_start: 0.9060 (t80) cc_final: 0.8390 (t80) REVERT: pA 202 LYS cc_start: 0.8764 (tttm) cc_final: 0.8397 (mmmm) REVERT: pA 206 LYS cc_start: 0.8962 (tttt) cc_final: 0.8485 (tttt) REVERT: rA 1005 PHE cc_start: 0.9060 (t80) cc_final: 0.8811 (t80) REVERT: sA 1103 PHE cc_start: 0.9029 (t80) cc_final: 0.8379 (t80) REVERT: tA 1202 LYS cc_start: 0.8745 (tttm) cc_final: 0.8479 (tttm) REVERT: tA 1206 LYS cc_start: 0.8945 (tttt) cc_final: 0.8470 (tttt) REVERT: e 5 PHE cc_start: 0.9202 (t80) cc_final: 0.8927 (t80) REVERT: wA 202 LYS cc_start: 0.8607 (tttm) cc_final: 0.8261 (tppp) REVERT: wA 206 LYS cc_start: 0.8849 (tttt) cc_final: 0.8513 (tttm) REVERT: xA 303 PHE cc_start: 0.8785 (t80) cc_final: 0.8524 (t80) REVERT: xA 305 PHE cc_start: 0.8647 (t80) cc_final: 0.8384 (t80) REVERT: yA 1005 PHE cc_start: 0.9221 (t80) cc_final: 0.8952 (t80) REVERT: 1A 1303 PHE cc_start: 0.8787 (t80) cc_final: 0.8526 (t80) REVERT: 1A 1305 PHE cc_start: 0.8655 (t80) cc_final: 0.8381 (t80) REVERT: f 3 PHE cc_start: 0.9281 (t80) cc_final: 0.9054 (t80) REVERT: f 7 PHE cc_start: 0.9110 (t80) cc_final: 0.8576 (t80) REVERT: 2A 102 LYS cc_start: 0.8748 (tptm) cc_final: 0.8306 (tptm) REVERT: 2A 106 LYS cc_start: 0.8921 (tttp) cc_final: 0.8703 (tttp) REVERT: 2A 107 PHE cc_start: 0.8737 (t80) cc_final: 0.8279 (t80) REVERT: 3A 202 LYS cc_start: 0.8895 (tttm) cc_final: 0.8665 (tttm) REVERT: 3A 206 LYS cc_start: 0.8907 (tttt) cc_final: 0.8676 (tttm) REVERT: 4A 304 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8244 (tm-30) REVERT: 5A 1003 PHE cc_start: 0.9280 (t80) cc_final: 0.9058 (t80) REVERT: 5A 1007 PHE cc_start: 0.9116 (t80) cc_final: 0.8614 (t80) REVERT: 6A 1102 LYS cc_start: 0.8733 (tptm) cc_final: 0.8313 (tptm) REVERT: 6A 1106 LYS cc_start: 0.8924 (tttp) cc_final: 0.8702 (tttp) REVERT: 6A 1107 PHE cc_start: 0.8759 (t80) cc_final: 0.8326 (t80) REVERT: 7A 1202 LYS cc_start: 0.8870 (tttm) cc_final: 0.8637 (tttm) REVERT: 8A 1304 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8243 (tm-30) REVERT: g 7 PHE cc_start: 0.9090 (t80) cc_final: 0.8841 (t80) REVERT: 9A 102 LYS cc_start: 0.8869 (tptm) cc_final: 0.8366 (tptm) REVERT: 9A 106 LYS cc_start: 0.8870 (tttp) cc_final: 0.8562 (tttm) REVERT: 9A 107 PHE cc_start: 0.8870 (t80) cc_final: 0.8327 (t80) REVERT: AB 202 LYS cc_start: 0.8868 (tttm) cc_final: 0.8520 (mtpp) REVERT: AB 206 LYS cc_start: 0.8933 (tttt) cc_final: 0.8727 (tttm) REVERT: BB 304 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8195 (tm-30) REVERT: BB 306 LYS cc_start: 0.8697 (tptp) cc_final: 0.8278 (tptp) REVERT: CB 1003 PHE cc_start: 0.9292 (t80) cc_final: 0.9085 (t80) REVERT: CB 1005 PHE cc_start: 0.9156 (t80) cc_final: 0.8840 (t80) REVERT: CB 1007 PHE cc_start: 0.9095 (t80) cc_final: 0.8864 (t80) REVERT: DB 1106 LYS cc_start: 0.8873 (tttp) cc_final: 0.8661 (tttp) REVERT: DB 1107 PHE cc_start: 0.8888 (t80) cc_final: 0.8277 (t80) REVERT: FB 1304 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8168 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8682 (tptp) cc_final: 0.8281 (tptp) REVERT: GB 102 LYS cc_start: 0.8922 (tptm) cc_final: 0.8611 (tptm) REVERT: GB 106 LYS cc_start: 0.8740 (tttp) cc_final: 0.8378 (tttm) REVERT: HB 202 LYS cc_start: 0.8580 (tttm) cc_final: 0.8273 (mmmm) REVERT: IB 303 PHE cc_start: 0.8740 (t80) cc_final: 0.8458 (t80) REVERT: IB 304 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8502 (tm-30) REVERT: IB 306 LYS cc_start: 0.8769 (tptp) cc_final: 0.8562 (tptp) REVERT: KB 1102 LYS cc_start: 0.8919 (tptm) cc_final: 0.8619 (tptm) REVERT: MB 1303 PHE cc_start: 0.8741 (t80) cc_final: 0.8454 (t80) REVERT: MB 1306 LYS cc_start: 0.8749 (tptp) cc_final: 0.8547 (tptp) REVERT: OB 204 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7338 (tm-30) REVERT: OB 206 LYS cc_start: 0.8959 (tttt) cc_final: 0.8503 (tttt) REVERT: PB 305 PHE cc_start: 0.8500 (t80) cc_final: 0.8208 (t80) REVERT: PB 307 PHE cc_start: 0.8156 (t80) cc_final: 0.7803 (t80) REVERT: SB 1204 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7295 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8938 (tttt) cc_final: 0.8488 (tttt) REVERT: TB 1305 PHE cc_start: 0.8511 (t80) cc_final: 0.8219 (t80) REVERT: TB 1307 PHE cc_start: 0.8172 (t80) cc_final: 0.7811 (t80) outliers start: 126 outliers final: 85 residues processed: 528 average time/residue: 0.1958 time to fit residues: 128.4164 Evaluate side-chains 583 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 492 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain P residue 1302 LYS Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain S residue 302 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 0 residue 1302 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 106 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 EA residue 1302 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 102 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain QA residue 1102 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 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 dA residue 1006 LYS 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 e residue 6 LYS 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 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 4 GLU Chi-restraints excluded: chain h residue 6 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 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: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.088073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.076450 restraints weight = 25295.086| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.23 r_work: 0.3022 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.057 12564 Z= 0.605 Angle : 0.903 8.835 16272 Z= 0.417 Chirality : 0.045 0.141 1152 Planarity : 0.004 0.015 2160 Dihedral : 17.758 86.845 1786 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.44 % Allowed : 19.21 % Favored : 75.35 % 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: -6.08 (0.14), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.11), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.004 PHE8A1305 Details of bonding type rmsd/Z covalent geometry : bond 0.01343 / 0.61 (12528) covalent geometry : angle 0.90331 / 0.42 (16272) hydrogen bonds : bond 0.04598 / 2.51 ( 278) hydrogen bonds : angle 7.38976 / 4.16 ( 786) Misc. bond : bond 0.00207 / 0.11 ( 36) *********************** 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 565 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 518 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8498 (mtmt) REVERT: J 106 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8534 (mmmm) REVERT: M 1006 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8512 (mtmt) REVERT: P 1302 LYS cc_start: 0.9306 (ttpt) cc_final: 0.8788 (ttmm) REVERT: S 302 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8675 (ttmm) REVERT: W 1302 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8652 (ttmm) REVERT: C 6 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8283 (mtmt) REVERT: X 102 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8132 (ttmm) REVERT: X 104 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7384 (mm-30) REVERT: X 106 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8502 (mmmt) REVERT: Z 302 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8599 (ttmm) REVERT: Z 306 LYS cc_start: 0.9119 (tttt) cc_final: 0.8813 (mttt) REVERT: j 1006 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8775 (mtmt) REVERT: k 1102 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8087 (ttpp) REVERT: k 1104 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7323 (mm-30) REVERT: k 1106 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8487 (mmmt) REVERT: m 1302 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8444 (ttmm) REVERT: m 1306 LYS cc_start: 0.9127 (tttt) cc_final: 0.8844 (mttt) REVERT: D 6 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8592 (mtmt) REVERT: n 104 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7454 (mm-30) REVERT: o 206 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8668 (ttmm) REVERT: p 306 LYS cc_start: 0.8987 (tttt) cc_final: 0.8729 (tttt) REVERT: q 1006 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8607 (mtmt) REVERT: r 1104 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7428 (mm-30) REVERT: s 1204 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7991 (mt-10) REVERT: s 1206 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8668 (ttmm) REVERT: t 1306 LYS cc_start: 0.9002 (tttt) cc_final: 0.8744 (tttt) REVERT: E 4 GLU cc_start: 0.7629 (mp0) cc_final: 0.7096 (mp0) REVERT: E 6 LYS cc_start: 0.8830 (mtmt) cc_final: 0.7890 (mtmt) REVERT: u 102 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8096 (ttmm) REVERT: u 104 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7118 (mm-30) REVERT: v 206 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8517 (ttmm) REVERT: w 304 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8104 (mm-30) REVERT: w 306 LYS cc_start: 0.9095 (tttt) cc_final: 0.8835 (tttt) REVERT: x 1006 LYS cc_start: 0.8813 (mtmt) cc_final: 0.7898 (mtmt) REVERT: y 1102 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8467 (ttmm) REVERT: y 1104 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7143 (mm-30) REVERT: 0 1302 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8615 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8209 (mm-30) REVERT: 0 1306 LYS cc_start: 0.9103 (tttt) cc_final: 0.8873 (tttt) REVERT: F 4 GLU cc_start: 0.7574 (mp0) cc_final: 0.6684 (mp0) REVERT: 3 304 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8093 (mm-30) REVERT: 4 1004 GLU cc_start: 0.7555 (mp0) cc_final: 0.6642 (mp0) REVERT: 6 1206 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8698 (ttmm) REVERT: 7 1304 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7989 (mm-30) REVERT: G 4 GLU cc_start: 0.7442 (mp0) cc_final: 0.6161 (mp0) REVERT: 8 102 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8795 (mtpt) REVERT: AA 306 LYS cc_start: 0.9110 (tttt) cc_final: 0.8894 (tttt) REVERT: BA 1004 GLU cc_start: 0.7359 (mp0) cc_final: 0.6085 (mp0) REVERT: CA 1102 LYS cc_start: 0.9037 (ttpt) cc_final: 0.8776 (mtpt) REVERT: DA 1202 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8756 (mtpt) REVERT: EA 1304 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7911 (mm-30) REVERT: FA 102 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8055 (ttmm) REVERT: FA 104 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7643 (mm-30) REVERT: HA 304 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8048 (mm-30) REVERT: JA 1102 LYS cc_start: 0.8452 (ttpt) cc_final: 0.7955 (ttmm) REVERT: JA 1104 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7587 (mm-30) REVERT: LA 1304 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8062 (mm-30) REVERT: I 2 LYS cc_start: 0.8987 (tttt) cc_final: 0.8644 (tttt) REVERT: MA 102 LYS cc_start: 0.9273 (ttpt) cc_final: 0.9047 (ttpt) REVERT: MA 106 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8475 (mmmm) REVERT: NA 206 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8709 (ttmm) REVERT: OA 302 LYS cc_start: 0.9187 (ttpt) cc_final: 0.8585 (ttmm) REVERT: OA 304 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8244 (mm-30) REVERT: OA 306 LYS cc_start: 0.9073 (tttt) cc_final: 0.8813 (tppt) REVERT: QA 1102 LYS cc_start: 0.9281 (ttpt) cc_final: 0.9021 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8477 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8702 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9218 (ttpt) cc_final: 0.8585 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8203 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9093 (tttt) cc_final: 0.8841 (mmmt) REVERT: a 2 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8533 (ttpt) REVERT: a 4 GLU cc_start: 0.8400 (tp30) cc_final: 0.8199 (tp30) REVERT: UA 202 LYS cc_start: 0.9085 (tttm) cc_final: 0.8773 (mmmm) REVERT: UA 204 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7111 (tm-30) REVERT: VA 304 GLU cc_start: 0.8936 (tm-30) cc_final: 0.7919 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8500 (ttpt) REVERT: WA 1004 GLU cc_start: 0.8345 (tp30) cc_final: 0.7961 (tp30) REVERT: WA 1006 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8564 (ttpt) REVERT: YA 1202 LYS cc_start: 0.9060 (tttm) cc_final: 0.8717 (tttm) REVERT: YA 1204 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7188 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.8914 (tm-30) cc_final: 0.7888 (tm-30) REVERT: b 4 GLU cc_start: 0.8224 (tp30) cc_final: 0.7853 (tp30) REVERT: b 5 PHE cc_start: 0.9074 (t80) cc_final: 0.8704 (t80) REVERT: aA 102 LYS cc_start: 0.8983 (tptm) cc_final: 0.8349 (tptm) REVERT: aA 103 PHE cc_start: 0.8736 (t80) cc_final: 0.8087 (t80) REVERT: bA 203 PHE cc_start: 0.9104 (t80) cc_final: 0.8887 (t80) REVERT: dA 1002 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8521 (tppt) REVERT: dA 1005 PHE cc_start: 0.9091 (t80) cc_final: 0.8818 (t80) REVERT: eA 1104 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7947 (tm-30) REVERT: eA 1107 PHE cc_start: 0.9138 (t80) cc_final: 0.8859 (t80) REVERT: fA 1203 PHE cc_start: 0.9123 (t80) cc_final: 0.8917 (t80) REVERT: c 2 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8738 (ttpt) REVERT: hA 102 LYS cc_start: 0.8864 (tptm) cc_final: 0.8592 (tptm) REVERT: iA 202 LYS cc_start: 0.8940 (tttm) cc_final: 0.8501 (mtpp) REVERT: iA 204 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7267 (tm-30) REVERT: iA 206 LYS cc_start: 0.8854 (tttt) cc_final: 0.8195 (tttm) REVERT: jA 306 LYS cc_start: 0.8751 (tptp) cc_final: 0.8272 (tptp) REVERT: kA 1002 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8474 (ttpt) REVERT: lA 1102 LYS cc_start: 0.8867 (tptm) cc_final: 0.8592 (tptm) REVERT: mA 1204 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7205 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8862 (tttt) cc_final: 0.8468 (tttt) REVERT: nA 1306 LYS cc_start: 0.8749 (tptp) cc_final: 0.8317 (tptp) REVERT: d 2 LYS cc_start: 0.9176 (ttpt) cc_final: 0.8717 (tppt) REVERT: d 4 GLU cc_start: 0.8188 (tp30) cc_final: 0.7901 (tp30) REVERT: d 5 PHE cc_start: 0.8883 (t80) cc_final: 0.8371 (t80) REVERT: oA 102 LYS cc_start: 0.8931 (tptm) cc_final: 0.8602 (tptm) REVERT: oA 103 PHE cc_start: 0.8728 (t80) cc_final: 0.7676 (t80) REVERT: pA 202 LYS cc_start: 0.8824 (tttm) cc_final: 0.8367 (mtpp) REVERT: pA 204 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7521 (tm-30) REVERT: pA 206 LYS cc_start: 0.8901 (tttt) cc_final: 0.8675 (tttt) REVERT: qA 306 LYS cc_start: 0.8754 (tptp) cc_final: 0.8464 (tptp) REVERT: rA 1005 PHE cc_start: 0.8924 (t80) cc_final: 0.8570 (t80) REVERT: sA 1102 LYS cc_start: 0.8933 (tptm) cc_final: 0.8640 (tptm) REVERT: sA 1103 PHE cc_start: 0.8778 (t80) cc_final: 0.8152 (t80) REVERT: tA 1204 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7508 (tm-30) REVERT: tA 1206 LYS cc_start: 0.8887 (tttt) cc_final: 0.8678 (tttt) REVERT: uA 1306 LYS cc_start: 0.8720 (tptp) cc_final: 0.8449 (tptp) REVERT: e 2 LYS cc_start: 0.8990 (ttpt) cc_final: 0.8718 (ttpt) REVERT: e 5 PHE cc_start: 0.8979 (t80) cc_final: 0.8765 (t80) REVERT: wA 202 LYS cc_start: 0.8844 (tttm) cc_final: 0.8382 (ttmm) REVERT: wA 204 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7644 (tm-30) REVERT: wA 206 LYS cc_start: 0.8790 (tttt) cc_final: 0.8399 (tttm) REVERT: xA 304 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8168 (tm-30) REVERT: yA 1002 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8608 (ttpt) REVERT: yA 1005 PHE cc_start: 0.8991 (t80) cc_final: 0.8772 (t80) REVERT: 0A 1204 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7634 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.8807 (tm-30) cc_final: 0.7558 (tm-30) REVERT: 1A 1307 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8918 (t80) REVERT: f 2 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8755 (ttpt) REVERT: f 4 GLU cc_start: 0.8369 (tp30) cc_final: 0.7481 (tp30) REVERT: f 7 PHE cc_start: 0.9325 (t80) cc_final: 0.8616 (t80) REVERT: 2A 102 LYS cc_start: 0.8829 (tptm) cc_final: 0.8166 (tptm) REVERT: 3A 205 PHE cc_start: 0.8870 (t80) cc_final: 0.8541 (t80) REVERT: 3A 206 LYS cc_start: 0.8980 (tttt) cc_final: 0.8758 (tttm) REVERT: 5A 1004 GLU cc_start: 0.8377 (tp30) cc_final: 0.7404 (tp30) REVERT: 5A 1007 PHE cc_start: 0.9330 (t80) cc_final: 0.8667 (t80) REVERT: 6A 1102 LYS cc_start: 0.8803 (tptm) cc_final: 0.8061 (tptm) REVERT: 6A 1103 PHE cc_start: 0.8631 (t80) cc_final: 0.7521 (t80) REVERT: 7A 1205 PHE cc_start: 0.8840 (t80) cc_final: 0.8500 (t80) REVERT: 7A 1206 LYS cc_start: 0.8970 (tttm) cc_final: 0.8752 (tttm) REVERT: g 2 LYS cc_start: 0.8935 (ttpt) cc_final: 0.8698 (ttpt) REVERT: g 4 GLU cc_start: 0.8379 (tp30) cc_final: 0.7919 (tp30) REVERT: 9A 102 LYS cc_start: 0.9070 (tptm) cc_final: 0.8677 (tptm) REVERT: 9A 106 LYS cc_start: 0.8741 (tttp) cc_final: 0.8506 (tttp) REVERT: AB 202 LYS cc_start: 0.8843 (tttm) cc_final: 0.8442 (mtpp) REVERT: AB 203 PHE cc_start: 0.8843 (t80) cc_final: 0.8567 (t80) REVERT: BB 304 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8324 (tm-30) REVERT: BB 305 PHE cc_start: 0.8862 (t80) cc_final: 0.8655 (t80) REVERT: BB 306 LYS cc_start: 0.8689 (tptp) cc_final: 0.8196 (tptp) REVERT: CB 1003 PHE cc_start: 0.9179 (t80) cc_final: 0.8887 (t80) REVERT: CB 1004 GLU cc_start: 0.8329 (tp30) cc_final: 0.7693 (tp30) REVERT: DB 1102 LYS cc_start: 0.9040 (tptm) cc_final: 0.8489 (tptm) REVERT: DB 1106 LYS cc_start: 0.8705 (tttp) cc_final: 0.8454 (tttp) REVERT: DB 1107 PHE cc_start: 0.9060 (t80) cc_final: 0.7877 (t80) REVERT: EB 1202 LYS cc_start: 0.8848 (tttm) cc_final: 0.8503 (tttm) REVERT: EB 1203 PHE cc_start: 0.8837 (t80) cc_final: 0.8591 (t80) REVERT: EB 1204 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7018 (tm-30) REVERT: EB 1206 LYS cc_start: 0.8796 (tttm) cc_final: 0.8564 (tttm) REVERT: FB 1304 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8227 (tm-30) REVERT: FB 1305 PHE cc_start: 0.8866 (t80) cc_final: 0.8658 (t80) REVERT: h 4 GLU cc_start: 0.8122 (tp30) cc_final: 0.7581 (tp30) REVERT: GB 102 LYS cc_start: 0.8901 (tptm) cc_final: 0.8501 (tptm) REVERT: GB 103 PHE cc_start: 0.8772 (t80) cc_final: 0.7877 (t80) REVERT: HB 202 LYS cc_start: 0.8826 (tttm) cc_final: 0.8488 (mmmm) REVERT: IB 304 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8379 (tm-30) REVERT: IB 306 LYS cc_start: 0.8693 (tptp) cc_final: 0.8398 (tptp) REVERT: JB 1004 GLU cc_start: 0.8098 (tp30) cc_final: 0.7520 (tp30) REVERT: KB 1102 LYS cc_start: 0.8901 (tptm) cc_final: 0.8460 (tptm) REVERT: KB 1103 PHE cc_start: 0.8760 (t80) cc_final: 0.7770 (t80) REVERT: MB 1304 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8389 (tm-30) REVERT: MB 1306 LYS cc_start: 0.8702 (tptp) cc_final: 0.8405 (tptp) REVERT: i 6 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8598 (ttpt) REVERT: OB 204 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7711 (tm-30) REVERT: OB 206 LYS cc_start: 0.8877 (tttt) cc_final: 0.8387 (tttt) REVERT: PB 304 GLU cc_start: 0.8644 (tm-30) cc_final: 0.7459 (pm20) REVERT: PB 305 PHE cc_start: 0.8717 (t80) cc_final: 0.7727 (t80) REVERT: PB 306 LYS cc_start: 0.8868 (tptp) cc_final: 0.8151 (pptt) REVERT: PB 307 PHE cc_start: 0.8795 (t80) cc_final: 0.8135 (t80) REVERT: RB 1102 LYS cc_start: 0.8906 (tptm) cc_final: 0.8473 (tptm) REVERT: SB 1204 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7638 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8858 (tttt) cc_final: 0.8493 (tttt) REVERT: TB 1304 GLU cc_start: 0.8623 (tm-30) cc_final: 0.7478 (pm20) REVERT: TB 1305 PHE cc_start: 0.8702 (t80) cc_final: 0.7713 (t80) REVERT: TB 1306 LYS cc_start: 0.8872 (tptp) cc_final: 0.8164 (pptt) REVERT: TB 1307 PHE cc_start: 0.8785 (t80) cc_final: 0.8136 (t80) outliers start: 47 outliers final: 19 residues processed: 520 average time/residue: 0.1918 time to fit residues: 124.0742 Evaluate side-chains 537 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 512 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain Q residue 102 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain k residue 1106 LYS Chi-restraints excluded: chain m residue 1302 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain r residue 1106 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.093171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081394 restraints weight = 24758.050| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.13 r_work: 0.3145 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12564 Z= 0.108 Angle : 0.642 8.995 16272 Z= 0.291 Chirality : 0.031 0.101 1152 Planarity : 0.002 0.013 2160 Dihedral : 16.113 89.871 1472 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.43 % Allowed : 26.39 % Favored : 71.18 % 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: -5.40 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.12), 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 0.00250 / 0.11 (12528) covalent geometry : angle 0.64208 / 0.29 (16272) hydrogen bonds : bond 0.01787 / 0.99 ( 278) hydrogen bonds : angle 6.26814 / 3.55 ( 786) Misc. bond : bond 0.00106 / 0.05 ( 36) *********************** 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 505 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 484 time to evaluate : 0.648 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: A 6 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8293 (mtmt) REVERT: M 1006 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8294 (mtmt) REVERT: P 1302 LYS cc_start: 0.9140 (ttpt) cc_final: 0.8615 (ttmm) REVERT: B 6 LYS cc_start: 0.8828 (mtmt) cc_final: 0.7881 (mtmt) REVERT: Q 106 LYS cc_start: 0.8816 (tptm) cc_final: 0.8477 (tptm) REVERT: T 1006 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8520 (mtmt) REVERT: U 1106 LYS cc_start: 0.8808 (tptm) cc_final: 0.8472 (tptm) REVERT: W 1302 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8506 (ttmm) REVERT: C 2 LYS cc_start: 0.7495 (tttt) cc_final: 0.6758 (tttt) REVERT: C 4 GLU cc_start: 0.7643 (mp0) cc_final: 0.7308 (mp0) REVERT: X 102 LYS cc_start: 0.8509 (ttpt) cc_final: 0.7431 (ttpp) REVERT: X 104 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7180 (mm-30) REVERT: X 106 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8434 (mmmt) REVERT: Z 306 LYS cc_start: 0.8980 (tttt) cc_final: 0.8691 (mttt) REVERT: j 1002 LYS cc_start: 0.7486 (tttt) cc_final: 0.6684 (tttt) REVERT: j 1004 GLU cc_start: 0.7720 (mp0) cc_final: 0.7081 (mp0) REVERT: j 1006 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8706 (mtmt) REVERT: k 1102 LYS cc_start: 0.8514 (ttpt) cc_final: 0.7371 (ttpp) REVERT: k 1104 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7249 (mm-30) REVERT: k 1106 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8417 (mmmt) REVERT: m 1302 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8238 (ttmm) REVERT: m 1306 LYS cc_start: 0.8989 (tttt) cc_final: 0.8709 (mttt) REVERT: D 4 GLU cc_start: 0.8250 (mp0) cc_final: 0.7987 (mp0) REVERT: n 102 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7790 (ttpt) REVERT: n 104 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7678 (mm-30) REVERT: n 106 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8410 (mmmt) REVERT: p 306 LYS cc_start: 0.8905 (tttt) cc_final: 0.8663 (tttt) REVERT: q 1004 GLU cc_start: 0.8195 (mp0) cc_final: 0.7940 (mp0) REVERT: q 1006 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8595 (mtmt) REVERT: r 1102 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7842 (ttpt) REVERT: r 1104 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7674 (mm-30) REVERT: r 1106 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8537 (mmmm) REVERT: t 1306 LYS cc_start: 0.8918 (tttt) cc_final: 0.8656 (tttt) REVERT: E 6 LYS cc_start: 0.8662 (mtmt) cc_final: 0.7762 (mtmt) REVERT: u 102 LYS cc_start: 0.8879 (ttpt) cc_final: 0.7951 (ttmm) REVERT: u 104 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7831 (mm-30) REVERT: v 206 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8454 (ttmm) REVERT: w 304 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8014 (mm-30) REVERT: w 306 LYS cc_start: 0.8801 (tttt) cc_final: 0.8526 (tttt) REVERT: x 1006 LYS cc_start: 0.8675 (mtmt) cc_final: 0.7764 (mtmt) REVERT: y 1102 LYS cc_start: 0.8877 (ttpt) cc_final: 0.8340 (ttmm) REVERT: y 1104 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7864 (mm-30) REVERT: z 1206 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8297 (ttmm) REVERT: 0 1302 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8467 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7930 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8828 (tttt) cc_final: 0.8397 (tttt) REVERT: F 4 GLU cc_start: 0.7637 (mp0) cc_final: 0.7132 (mp0) REVERT: 2 206 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8556 (ttmm) REVERT: 3 306 LYS cc_start: 0.8947 (tttt) cc_final: 0.8647 (tttt) REVERT: 4 1004 GLU cc_start: 0.7572 (mp0) cc_final: 0.6998 (mp0) REVERT: 6 1206 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8593 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8944 (tttt) cc_final: 0.8638 (tttt) REVERT: G 4 GLU cc_start: 0.7491 (mp0) cc_final: 0.6623 (mp0) REVERT: BA 1004 GLU cc_start: 0.7437 (mp0) cc_final: 0.6654 (mp0) REVERT: CA 1102 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8852 (mtpt) REVERT: EA 1306 LYS cc_start: 0.8949 (tttt) cc_final: 0.8628 (tttt) REVERT: FA 106 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8749 (mmmt) REVERT: JA 1104 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7860 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8752 (mmmt) REVERT: I 6 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8746 (mtmt) REVERT: MA 102 LYS cc_start: 0.9248 (ttpt) cc_final: 0.8915 (ttpt) REVERT: MA 106 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8327 (mmmm) REVERT: OA 302 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8796 (ttpt) REVERT: QA 1102 LYS cc_start: 0.9259 (ttpt) cc_final: 0.8951 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8382 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8594 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8468 (ttpt) REVERT: SA 1304 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8090 (mm-30) REVERT: a 3 PHE cc_start: 0.9147 (t80) cc_final: 0.8905 (t80) REVERT: a 7 PHE cc_start: 0.9204 (t80) cc_final: 0.8998 (t80) REVERT: UA 202 LYS cc_start: 0.8870 (tttm) cc_final: 0.8458 (mmmm) REVERT: UA 204 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7262 (tm-30) REVERT: VA 304 GLU cc_start: 0.8728 (tm-30) cc_final: 0.7533 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8251 (ttpt) REVERT: WA 1003 PHE cc_start: 0.9158 (t80) cc_final: 0.8837 (t80) REVERT: YA 1202 LYS cc_start: 0.8854 (tttm) cc_final: 0.8462 (tttm) REVERT: YA 1204 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7207 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.8729 (tm-30) cc_final: 0.7651 (tm-30) REVERT: b 4 GLU cc_start: 0.8087 (tp30) cc_final: 0.7805 (tp30) REVERT: b 5 PHE cc_start: 0.9057 (t80) cc_final: 0.8849 (t80) REVERT: aA 103 PHE cc_start: 0.8504 (t80) cc_final: 0.7953 (t80) REVERT: aA 105 PHE cc_start: 0.9265 (t80) cc_final: 0.8964 (t80) REVERT: bA 202 LYS cc_start: 0.8811 (tttm) cc_final: 0.8431 (mtpp) REVERT: bA 206 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8215 (tttm) REVERT: dA 1003 PHE cc_start: 0.9250 (t80) cc_final: 0.9010 (t80) REVERT: eA 1107 PHE cc_start: 0.9051 (t80) cc_final: 0.8760 (t80) REVERT: gA 1307 PHE cc_start: 0.8931 (t80) cc_final: 0.8709 (t80) REVERT: c 2 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8353 (tppt) REVERT: hA 103 PHE cc_start: 0.8652 (t80) cc_final: 0.8301 (t80) REVERT: iA 202 LYS cc_start: 0.8737 (tttm) cc_final: 0.8291 (mtpp) REVERT: iA 204 GLU cc_start: 0.7708 (tm-30) cc_final: 0.6863 (tm-30) REVERT: iA 206 LYS cc_start: 0.8583 (tttt) cc_final: 0.8252 (tttt) REVERT: jA 306 LYS cc_start: 0.8683 (tptp) cc_final: 0.8178 (tptp) REVERT: kA 1002 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8093 (tppt) REVERT: mA 1204 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6888 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8578 (tttt) cc_final: 0.8259 (tttt) REVERT: nA 1306 LYS cc_start: 0.8708 (tptp) cc_final: 0.8227 (tptp) REVERT: d 2 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8398 (tppt) REVERT: d 4 GLU cc_start: 0.8099 (tp30) cc_final: 0.7770 (tp30) REVERT: d 5 PHE cc_start: 0.8842 (t80) cc_final: 0.8240 (t80) REVERT: oA 102 LYS cc_start: 0.8669 (tptm) cc_final: 0.8332 (tptm) REVERT: oA 103 PHE cc_start: 0.8523 (t80) cc_final: 0.7533 (t80) REVERT: pA 202 LYS cc_start: 0.8590 (tttm) cc_final: 0.8191 (mtpp) REVERT: pA 204 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7041 (tm-30) REVERT: qA 306 LYS cc_start: 0.8646 (tptp) cc_final: 0.8348 (tptp) REVERT: rA 1002 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8371 (tppt) REVERT: rA 1005 PHE cc_start: 0.8871 (t80) cc_final: 0.8554 (t80) REVERT: sA 1102 LYS cc_start: 0.8689 (tptm) cc_final: 0.8381 (tptm) REVERT: sA 1103 PHE cc_start: 0.8544 (t80) cc_final: 0.8071 (t80) REVERT: tA 1202 LYS cc_start: 0.8592 (tttm) cc_final: 0.8239 (ttmm) REVERT: tA 1204 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7015 (tm-30) REVERT: uA 1306 LYS cc_start: 0.8625 (tptp) cc_final: 0.8337 (tptp) REVERT: e 2 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8414 (tppt) REVERT: wA 202 LYS cc_start: 0.8698 (tttm) cc_final: 0.8386 (mtpp) REVERT: wA 204 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7384 (tm-30) REVERT: wA 206 LYS cc_start: 0.8620 (tttt) cc_final: 0.8308 (tttm) REVERT: xA 304 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8090 (tm-30) REVERT: xA 307 PHE cc_start: 0.8859 (t80) cc_final: 0.8499 (t80) REVERT: yA 1002 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8440 (ttpt) REVERT: 0A 1204 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7429 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.8724 (tm-30) cc_final: 0.7974 (tm-30) REVERT: 1A 1307 PHE cc_start: 0.8949 (t80) cc_final: 0.8648 (t80) REVERT: f 2 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8388 (ttpt) REVERT: f 3 PHE cc_start: 0.9039 (t80) cc_final: 0.8708 (t80) REVERT: f 7 PHE cc_start: 0.9209 (t80) cc_final: 0.8611 (t80) REVERT: 4A 303 PHE cc_start: 0.8351 (t80) cc_final: 0.7965 (t80) REVERT: 5A 1002 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8181 (ttpt) REVERT: 5A 1003 PHE cc_start: 0.9047 (t80) cc_final: 0.8598 (t80) REVERT: 5A 1007 PHE cc_start: 0.9228 (t80) cc_final: 0.8638 (t80) REVERT: g 2 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8451 (ttpt) REVERT: g 4 GLU cc_start: 0.8202 (tp30) cc_final: 0.7996 (tp30) REVERT: g 7 PHE cc_start: 0.9223 (t80) cc_final: 0.8810 (t80) REVERT: 9A 102 LYS cc_start: 0.8887 (tptm) cc_final: 0.8435 (tptm) REVERT: 9A 106 LYS cc_start: 0.8631 (tttp) cc_final: 0.8268 (tttm) REVERT: AB 202 LYS cc_start: 0.8679 (tttm) cc_final: 0.8289 (mtpp) REVERT: AB 203 PHE cc_start: 0.8815 (t80) cc_final: 0.8479 (t80) REVERT: AB 204 GLU cc_start: 0.7868 (tm-30) cc_final: 0.6864 (tm-30) REVERT: CB 1003 PHE cc_start: 0.9167 (t80) cc_final: 0.8889 (t80) REVERT: CB 1007 PHE cc_start: 0.9216 (t80) cc_final: 0.8828 (t80) REVERT: DB 1102 LYS cc_start: 0.8859 (tptm) cc_final: 0.8412 (tptm) REVERT: EB 1202 LYS cc_start: 0.8714 (tttm) cc_final: 0.8349 (tttm) REVERT: EB 1203 PHE cc_start: 0.8833 (t80) cc_final: 0.8548 (t80) REVERT: EB 1204 GLU cc_start: 0.7832 (tm-30) cc_final: 0.6817 (tm-30) REVERT: FB 1304 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8317 (tm-30) REVERT: h 4 GLU cc_start: 0.7946 (tp30) cc_final: 0.7722 (tp30) REVERT: HB 202 LYS cc_start: 0.8745 (tttm) cc_final: 0.8440 (mmmm) REVERT: IB 304 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8395 (tm-30) REVERT: IB 307 PHE cc_start: 0.8889 (t80) cc_final: 0.8419 (t80) REVERT: JB 1004 GLU cc_start: 0.7982 (tp30) cc_final: 0.7743 (tp30) REVERT: MB 1304 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8418 (tm-30) REVERT: MB 1307 PHE cc_start: 0.8853 (t80) cc_final: 0.8409 (t80) REVERT: i 6 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8483 (ttpt) REVERT: OB 203 PHE cc_start: 0.8825 (t80) cc_final: 0.8545 (t80) REVERT: OB 204 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7575 (tm-30) REVERT: PB 304 GLU cc_start: 0.8642 (tm-30) cc_final: 0.7463 (pm20) REVERT: PB 305 PHE cc_start: 0.8488 (t80) cc_final: 0.7558 (t80) REVERT: PB 306 LYS cc_start: 0.8778 (tptp) cc_final: 0.7970 (pptt) REVERT: PB 307 PHE cc_start: 0.8530 (t80) cc_final: 0.7822 (t80) REVERT: QB 1002 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8210 (tppt) REVERT: RB 1102 LYS cc_start: 0.8743 (tptm) cc_final: 0.8339 (tptm) REVERT: SB 1203 PHE cc_start: 0.8822 (t80) cc_final: 0.8529 (t80) REVERT: SB 1204 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7347 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8701 (tttt) cc_final: 0.8490 (tttt) REVERT: TB 1304 GLU cc_start: 0.8582 (tm-30) cc_final: 0.7457 (pm20) REVERT: TB 1305 PHE cc_start: 0.8461 (t80) cc_final: 0.7510 (t80) REVERT: TB 1306 LYS cc_start: 0.8791 (tptp) cc_final: 0.7982 (pptt) REVERT: TB 1307 PHE cc_start: 0.8526 (t80) cc_final: 0.7838 (t80) outliers start: 21 outliers final: 10 residues processed: 485 average time/residue: 0.1971 time to fit residues: 118.9454 Evaluate side-chains 486 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 473 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain Q residue 102 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain r residue 1106 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain bA residue 206 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain QB residue 1006 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.093894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082144 restraints weight = 24489.171| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.09 r_work: 0.3169 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12564 Z= 0.112 Angle : 0.617 9.054 16272 Z= 0.280 Chirality : 0.030 0.092 1152 Planarity : 0.002 0.012 2160 Dihedral : 15.387 88.574 1464 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 26.97 % Favored : 70.72 % 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: -5.12 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.12), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHEFB1303 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (12528) covalent geometry : angle 0.61696 / 0.28 (16272) hydrogen bonds : bond 0.01555 / 0.87 ( 278) hydrogen bonds : angle 5.67462 / 3.22 ( 786) Misc. bond : bond 0.00103 / 0.05 ( 36) *********************** 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 501 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 481 time to evaluate : 0.355 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: J 106 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8225 (mmmm) REVERT: L 304 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8052 (mm-30) REVERT: N 1105 PHE cc_start: 0.8872 (m-80) cc_final: 0.8636 (m-10) REVERT: P 1302 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8587 (ttmm) REVERT: B 4 GLU cc_start: 0.7616 (mp0) cc_final: 0.7169 (mp0) REVERT: Q 106 LYS cc_start: 0.8806 (tptm) cc_final: 0.8508 (tptm) REVERT: S 302 LYS cc_start: 0.9128 (mtpt) cc_final: 0.8592 (ttmm) REVERT: T 1004 GLU cc_start: 0.7602 (mp0) cc_final: 0.7279 (mp0) REVERT: U 1106 LYS cc_start: 0.8817 (tptm) cc_final: 0.8521 (tptm) REVERT: W 1302 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8537 (ttmm) REVERT: C 6 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8081 (mtmt) REVERT: X 102 LYS cc_start: 0.8452 (ttpt) cc_final: 0.7483 (ttpp) REVERT: X 104 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7417 (mm-30) REVERT: X 106 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8449 (mmmt) REVERT: Z 304 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7999 (mm-30) REVERT: Z 306 LYS cc_start: 0.8904 (tttt) cc_final: 0.8607 (mttt) REVERT: j 1002 LYS cc_start: 0.7501 (tttt) cc_final: 0.6815 (tttt) REVERT: j 1004 GLU cc_start: 0.7974 (mp0) cc_final: 0.7714 (mp0) REVERT: j 1006 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8620 (mtmt) REVERT: k 1102 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7390 (ttpp) REVERT: k 1104 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7144 (mm-30) REVERT: k 1106 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8379 (mmmt) REVERT: l 1203 PHE cc_start: 0.8803 (m-80) cc_final: 0.8498 (m-80) REVERT: m 1302 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8309 (ttmm) REVERT: m 1306 LYS cc_start: 0.8920 (tttt) cc_final: 0.8645 (mttt) REVERT: D 2 LYS cc_start: 0.7485 (tttt) cc_final: 0.6694 (tttt) REVERT: n 102 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7623 (ttpt) REVERT: n 104 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7471 (mm-30) REVERT: q 1006 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8542 (mtmt) REVERT: r 1102 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7643 (ttpt) REVERT: r 1104 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7452 (mm-30) REVERT: r 1106 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8288 (mmmm) REVERT: s 1202 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8661 (mtpt) REVERT: s 1204 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7900 (mt-10) REVERT: t 1306 LYS cc_start: 0.8926 (tttt) cc_final: 0.8628 (tttt) REVERT: E 6 LYS cc_start: 0.8654 (mtmt) cc_final: 0.7899 (mtmt) REVERT: v 204 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6837 (tm-30) REVERT: v 206 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8509 (ttmm) REVERT: w 304 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7726 (mm-30) REVERT: w 306 LYS cc_start: 0.8782 (tttt) cc_final: 0.8432 (tttt) REVERT: x 1006 LYS cc_start: 0.8696 (mtmt) cc_final: 0.7834 (mtmt) REVERT: y 1102 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8501 (ttmm) REVERT: z 1206 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8383 (ttmm) REVERT: 0 1302 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8336 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7814 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8785 (tttt) cc_final: 0.8330 (tttt) REVERT: 2 206 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8608 (ttmm) REVERT: 3 304 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7914 (mm-30) REVERT: 3 306 LYS cc_start: 0.8914 (tttt) cc_final: 0.8680 (tttt) REVERT: 4 1004 GLU cc_start: 0.7609 (mp0) cc_final: 0.7251 (mp0) REVERT: 6 1206 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8618 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8903 (tttt) cc_final: 0.8679 (tttt) REVERT: G 4 GLU cc_start: 0.7495 (mp0) cc_final: 0.7147 (mp0) REVERT: 8 104 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8121 (mm-30) REVERT: 9 204 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7662 (mt-10) REVERT: AA 306 LYS cc_start: 0.8871 (tttt) cc_final: 0.8634 (tttt) REVERT: BA 1004 GLU cc_start: 0.7455 (mp0) cc_final: 0.7206 (mp0) REVERT: CA 1102 LYS cc_start: 0.9145 (ttpt) cc_final: 0.8682 (mtpt) REVERT: DA 1204 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7655 (mt-10) REVERT: EA 1306 LYS cc_start: 0.8928 (tttt) cc_final: 0.8607 (tttt) REVERT: GA 206 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8759 (pptt) REVERT: KA 1206 LYS cc_start: 0.8961 (ttmm) cc_final: 0.8728 (pptt) REVERT: MA 102 LYS cc_start: 0.9203 (ttpt) cc_final: 0.8872 (ttpt) REVERT: MA 106 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8332 (mmmm) REVERT: NA 206 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8627 (ttmm) REVERT: OA 302 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8420 (ttmm) REVERT: OA 304 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7761 (mm-30) REVERT: PA 1004 GLU cc_start: 0.8430 (mp0) cc_final: 0.7952 (mp0) REVERT: QA 1102 LYS cc_start: 0.9210 (ttpt) cc_final: 0.8914 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8367 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8564 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8375 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8073 (mm-30) REVERT: a 3 PHE cc_start: 0.9148 (t80) cc_final: 0.8772 (t80) REVERT: a 7 PHE cc_start: 0.9185 (t80) cc_final: 0.8588 (t80) REVERT: UA 202 LYS cc_start: 0.8764 (tttm) cc_final: 0.8412 (mmmm) REVERT: UA 204 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7118 (tm-30) REVERT: VA 303 PHE cc_start: 0.8376 (t80) cc_final: 0.7976 (t80) REVERT: VA 304 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8266 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8212 (ttpt) REVERT: WA 1003 PHE cc_start: 0.9126 (t80) cc_final: 0.8746 (t80) REVERT: WA 1005 PHE cc_start: 0.8785 (t80) cc_final: 0.8575 (t80) REVERT: WA 1007 PHE cc_start: 0.9255 (t80) cc_final: 0.8715 (t80) REVERT: YA 1202 LYS cc_start: 0.8774 (tttm) cc_final: 0.8436 (tttm) REVERT: YA 1204 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7032 (tm-30) REVERT: b 2 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8341 (tppt) REVERT: b 5 PHE cc_start: 0.9021 (t80) cc_final: 0.8736 (t80) REVERT: aA 105 PHE cc_start: 0.9232 (t80) cc_final: 0.8926 (t80) REVERT: aA 107 PHE cc_start: 0.9016 (t80) cc_final: 0.8762 (t80) REVERT: cA 307 PHE cc_start: 0.8774 (t80) cc_final: 0.8458 (t80) REVERT: dA 1003 PHE cc_start: 0.9172 (t80) cc_final: 0.8947 (t80) REVERT: eA 1103 PHE cc_start: 0.8180 (t80) cc_final: 0.7954 (t80) REVERT: eA 1107 PHE cc_start: 0.9002 (t80) cc_final: 0.8779 (t80) REVERT: gA 1307 PHE cc_start: 0.8985 (t80) cc_final: 0.8753 (t80) REVERT: c 2 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8216 (tppt) REVERT: hA 102 LYS cc_start: 0.8586 (tptm) cc_final: 0.7922 (tptm) REVERT: hA 103 PHE cc_start: 0.8660 (t80) cc_final: 0.8420 (t80) REVERT: iA 202 LYS cc_start: 0.8706 (tttm) cc_final: 0.8274 (mtpp) REVERT: iA 204 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7175 (tm-30) REVERT: iA 206 LYS cc_start: 0.8593 (tttt) cc_final: 0.8388 (tttt) REVERT: jA 306 LYS cc_start: 0.8662 (tptp) cc_final: 0.8154 (tptp) REVERT: kA 1002 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8004 (tppt) REVERT: lA 1102 LYS cc_start: 0.8581 (tptm) cc_final: 0.8102 (tptm) REVERT: lA 1103 PHE cc_start: 0.8593 (t80) cc_final: 0.8035 (t80) REVERT: mA 1204 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7119 (tm-30) REVERT: nA 1306 LYS cc_start: 0.8669 (tptp) cc_final: 0.8108 (tptp) REVERT: d 2 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8390 (tppt) REVERT: oA 102 LYS cc_start: 0.8624 (tptm) cc_final: 0.8262 (tptm) REVERT: oA 103 PHE cc_start: 0.8500 (t80) cc_final: 0.7983 (t80) REVERT: pA 202 LYS cc_start: 0.8592 (tttm) cc_final: 0.8209 (mtpp) REVERT: pA 204 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7469 (tp30) REVERT: pA 206 LYS cc_start: 0.8727 (tttt) cc_final: 0.8445 (tptt) REVERT: qA 303 PHE cc_start: 0.8153 (t80) cc_final: 0.7468 (t80) REVERT: qA 306 LYS cc_start: 0.8672 (tptp) cc_final: 0.8348 (tptp) REVERT: rA 1002 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8223 (tppt) REVERT: rA 1005 PHE cc_start: 0.8788 (t80) cc_final: 0.8466 (t80) REVERT: sA 1102 LYS cc_start: 0.8662 (tptm) cc_final: 0.8355 (tptm) REVERT: sA 1103 PHE cc_start: 0.8459 (t80) cc_final: 0.7962 (t80) REVERT: tA 1202 LYS cc_start: 0.8584 (tttm) cc_final: 0.8240 (ttmm) REVERT: tA 1204 GLU cc_start: 0.7701 (tm-30) cc_final: 0.6971 (tm-30) REVERT: tA 1206 LYS cc_start: 0.8723 (tttt) cc_final: 0.8415 (tptt) REVERT: uA 1306 LYS cc_start: 0.8651 (tptp) cc_final: 0.8336 (tptp) REVERT: e 2 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8394 (tppt) REVERT: wA 202 LYS cc_start: 0.8713 (tttm) cc_final: 0.8398 (mtpp) REVERT: wA 204 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7398 (tm-30) REVERT: wA 206 LYS cc_start: 0.8571 (tttt) cc_final: 0.8273 (tttm) REVERT: xA 307 PHE cc_start: 0.8948 (t80) cc_final: 0.8564 (t80) REVERT: yA 1002 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8289 (tppt) REVERT: yA 1005 PHE cc_start: 0.8872 (t80) cc_final: 0.8464 (t80) REVERT: 1A 1307 PHE cc_start: 0.8983 (t80) cc_final: 0.8733 (t80) REVERT: f 2 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8368 (ttpt) REVERT: f 7 PHE cc_start: 0.9163 (t80) cc_final: 0.8572 (t80) REVERT: 4A 303 PHE cc_start: 0.8334 (t80) cc_final: 0.8133 (t80) REVERT: 5A 1002 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8154 (ttpt) REVERT: 5A 1003 PHE cc_start: 0.9045 (t80) cc_final: 0.8816 (t80) REVERT: 5A 1007 PHE cc_start: 0.9166 (t80) cc_final: 0.8671 (t80) REVERT: 6A 1102 LYS cc_start: 0.8520 (tptm) cc_final: 0.8036 (tptm) REVERT: g 2 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8293 (ttpt) REVERT: g 7 PHE cc_start: 0.9225 (t80) cc_final: 0.8820 (t80) REVERT: 9A 102 LYS cc_start: 0.8702 (tptm) cc_final: 0.8200 (tptm) REVERT: AB 202 LYS cc_start: 0.8670 (tttm) cc_final: 0.8303 (mtpp) REVERT: AB 203 PHE cc_start: 0.8888 (t80) cc_final: 0.8536 (t80) REVERT: AB 204 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7207 (tm-30) REVERT: CB 1003 PHE cc_start: 0.9174 (t80) cc_final: 0.8857 (t80) REVERT: CB 1007 PHE cc_start: 0.9228 (t80) cc_final: 0.8867 (t80) REVERT: DB 1102 LYS cc_start: 0.8717 (tptm) cc_final: 0.8232 (tptm) REVERT: EB 1202 LYS cc_start: 0.8679 (tttm) cc_final: 0.8349 (tttm) REVERT: EB 1203 PHE cc_start: 0.8870 (t80) cc_final: 0.8548 (t80) REVERT: EB 1204 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7149 (tm-30) REVERT: FB 1304 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8077 (tm-30) REVERT: h 3 PHE cc_start: 0.9146 (t80) cc_final: 0.8803 (t80) REVERT: HB 202 LYS cc_start: 0.8719 (tttm) cc_final: 0.8379 (mmmm) REVERT: IB 307 PHE cc_start: 0.8942 (t80) cc_final: 0.8508 (t80) REVERT: JB 1003 PHE cc_start: 0.9132 (t80) cc_final: 0.8767 (t80) REVERT: JB 1004 GLU cc_start: 0.7923 (tp30) cc_final: 0.7704 (tp30) REVERT: MB 1307 PHE cc_start: 0.8913 (t80) cc_final: 0.8465 (t80) REVERT: i 6 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8432 (ttpt) REVERT: OB 204 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7466 (tm-30) REVERT: PB 302 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8153 (tptp) REVERT: PB 303 PHE cc_start: 0.7877 (t80) cc_final: 0.7472 (t80) REVERT: PB 304 GLU cc_start: 0.8673 (tm-30) cc_final: 0.7439 (pm20) REVERT: PB 305 PHE cc_start: 0.8503 (t80) cc_final: 0.7540 (t80) REVERT: PB 306 LYS cc_start: 0.8833 (tptp) cc_final: 0.8064 (pptt) REVERT: PB 307 PHE cc_start: 0.8530 (t80) cc_final: 0.7892 (t80) REVERT: QB 1002 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8111 (tppt) REVERT: RB 1102 LYS cc_start: 0.8683 (tptm) cc_final: 0.8272 (tptm) REVERT: SB 1203 PHE cc_start: 0.8718 (t80) cc_final: 0.8514 (t80) REVERT: SB 1204 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7313 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8698 (tttt) cc_final: 0.8458 (tttt) REVERT: TB 1304 GLU cc_start: 0.8629 (tm-30) cc_final: 0.7422 (pm20) REVERT: TB 1305 PHE cc_start: 0.8494 (t80) cc_final: 0.7566 (t80) REVERT: TB 1306 LYS cc_start: 0.8814 (tptp) cc_final: 0.8057 (pptt) REVERT: TB 1307 PHE cc_start: 0.8520 (t80) cc_final: 0.7900 (t80) outliers start: 20 outliers final: 11 residues processed: 482 average time/residue: 0.1971 time to fit residues: 118.2262 Evaluate side-chains 481 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 467 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain Q residue 102 LYS Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain V residue 1202 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain PB residue 302 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.093031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.081205 restraints weight = 24337.891| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.13 r_work: 0.3189 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12564 Z= 0.119 Angle : 0.612 8.986 16272 Z= 0.280 Chirality : 0.029 0.090 1152 Planarity : 0.002 0.014 2160 Dihedral : 14.786 88.872 1456 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.43 % Allowed : 28.36 % Favored : 69.21 % 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: -5.01 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.12), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.002 PHEjA 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (12528) covalent geometry : angle 0.61236 / 0.28 (16272) hydrogen bonds : bond 0.01630 / 0.91 ( 278) hydrogen bonds : angle 5.37529 / 3.04 ( 786) Misc. bond : bond 0.00103 / 0.05 ( 36) *********************** 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 493 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 472 time to evaluate : 0.435 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: J 106 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8472 (tmmm) REVERT: L 304 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7985 (mm-30) REVERT: N 1105 PHE cc_start: 0.8813 (m-80) cc_final: 0.8553 (m-10) REVERT: N 1106 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8381 (tmtm) REVERT: P 1302 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8785 (ttpt) REVERT: B 4 GLU cc_start: 0.7667 (mp0) cc_final: 0.7466 (mp0) REVERT: Q 106 LYS cc_start: 0.8752 (tptm) cc_final: 0.8452 (tptm) REVERT: S 302 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8587 (ttmm) REVERT: T 1004 GLU cc_start: 0.7581 (mp0) cc_final: 0.7304 (mp0) REVERT: T 1006 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8263 (mtmt) REVERT: U 1106 LYS cc_start: 0.8832 (tptm) cc_final: 0.8545 (tptm) REVERT: W 1302 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8470 (ttmm) REVERT: C 2 LYS cc_start: 0.7471 (tttt) cc_final: 0.6720 (tttt) REVERT: X 102 LYS cc_start: 0.8510 (ttpt) cc_final: 0.7544 (ttpp) REVERT: X 104 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7321 (mm-30) REVERT: X 106 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8447 (mmmt) REVERT: Z 304 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7869 (mm-30) REVERT: Z 306 LYS cc_start: 0.8864 (tttt) cc_final: 0.8571 (mttt) REVERT: j 1002 LYS cc_start: 0.7480 (tttt) cc_final: 0.6697 (tttt) REVERT: j 1006 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8601 (mtmt) REVERT: k 1102 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7355 (ttpp) REVERT: k 1104 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7196 (mm-30) REVERT: k 1106 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8404 (mmmt) REVERT: m 1302 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8224 (ttmm) REVERT: m 1306 LYS cc_start: 0.8883 (tttt) cc_final: 0.8647 (mttt) REVERT: n 104 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7721 (mm-30) REVERT: n 106 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8443 (mmmt) REVERT: o 202 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8332 (mtpt) REVERT: q 1006 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8601 (mtmt) REVERT: r 1102 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7747 (ttpt) REVERT: r 1104 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7547 (mm-30) REVERT: r 1106 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8246 (mmmm) REVERT: s 1202 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8246 (mtpt) REVERT: E 6 LYS cc_start: 0.8663 (mtmt) cc_final: 0.7949 (mtmt) REVERT: v 204 GLU cc_start: 0.7754 (tm-30) cc_final: 0.6982 (tm-30) REVERT: v 206 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8548 (ttmm) REVERT: w 304 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7652 (mm-30) REVERT: w 306 LYS cc_start: 0.8769 (tttt) cc_final: 0.8405 (tttt) REVERT: y 1102 LYS cc_start: 0.8922 (ttpt) cc_final: 0.7966 (ttmm) REVERT: z 1206 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8346 (ttmm) REVERT: 0 1302 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8410 (ttmm) REVERT: 0 1306 LYS cc_start: 0.8774 (tttt) cc_final: 0.7993 (tttt) REVERT: 2 206 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8600 (ttmm) REVERT: 3 302 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8809 (ttmm) REVERT: 3 304 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7850 (mm-30) REVERT: 3 306 LYS cc_start: 0.8899 (tttt) cc_final: 0.8586 (mttt) REVERT: 5 1106 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8557 (tmtm) REVERT: 6 1206 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8633 (ttmm) REVERT: 7 1302 LYS cc_start: 0.9193 (mtpp) cc_final: 0.8761 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8953 (tttt) cc_final: 0.8726 (tttt) REVERT: G 4 GLU cc_start: 0.8057 (mp0) cc_final: 0.7294 (mp0) REVERT: 9 204 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7575 (mt-10) REVERT: AA 306 LYS cc_start: 0.8886 (tttt) cc_final: 0.8587 (tttt) REVERT: BA 1004 GLU cc_start: 0.7984 (mp0) cc_final: 0.7219 (mp0) REVERT: CA 1102 LYS cc_start: 0.9110 (ttpt) cc_final: 0.8767 (mtpt) REVERT: DA 1202 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8712 (mtpt) REVERT: DA 1204 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7537 (mt-10) REVERT: EA 1306 LYS cc_start: 0.8891 (tttt) cc_final: 0.8562 (tttt) REVERT: FA 106 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8687 (mmmt) REVERT: JA 1106 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8687 (mmmt) REVERT: KA 1206 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8663 (pptt) REVERT: MA 102 LYS cc_start: 0.9196 (ttpt) cc_final: 0.8851 (ttpt) REVERT: MA 106 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8359 (mmmm) REVERT: NA 206 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8595 (ttmm) REVERT: OA 302 LYS cc_start: 0.9055 (ttpt) cc_final: 0.8480 (ttmm) REVERT: OA 304 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7795 (mm-30) REVERT: PA 1004 GLU cc_start: 0.8262 (mp0) cc_final: 0.7879 (mp0) REVERT: QA 1102 LYS cc_start: 0.9206 (ttpt) cc_final: 0.8883 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8302 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8604 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8399 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7988 (mm-30) REVERT: a 3 PHE cc_start: 0.9095 (t80) cc_final: 0.8688 (t80) REVERT: a 7 PHE cc_start: 0.9190 (t80) cc_final: 0.8606 (t80) REVERT: UA 202 LYS cc_start: 0.8717 (tttm) cc_final: 0.8237 (mtpp) REVERT: UA 204 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7128 (tm-30) REVERT: VA 303 PHE cc_start: 0.8424 (t80) cc_final: 0.7956 (t80) REVERT: VA 304 GLU cc_start: 0.8849 (tm-30) cc_final: 0.7723 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8156 (ttpt) REVERT: WA 1003 PHE cc_start: 0.9101 (t80) cc_final: 0.8699 (t80) REVERT: YA 1202 LYS cc_start: 0.8702 (tttm) cc_final: 0.8375 (tttm) REVERT: YA 1204 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7035 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8287 (tm-30) REVERT: b 2 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8306 (tppt) REVERT: b 3 PHE cc_start: 0.9201 (t80) cc_final: 0.8968 (t80) REVERT: aA 102 LYS cc_start: 0.8647 (tptm) cc_final: 0.8064 (tptm) REVERT: aA 103 PHE cc_start: 0.8393 (t80) cc_final: 0.8108 (t80) REVERT: aA 107 PHE cc_start: 0.9002 (t80) cc_final: 0.8775 (t80) REVERT: dA 1002 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8402 (ttpt) REVERT: dA 1003 PHE cc_start: 0.9135 (t80) cc_final: 0.8922 (t80) REVERT: eA 1107 PHE cc_start: 0.9007 (t80) cc_final: 0.8789 (t80) REVERT: fA 1205 PHE cc_start: 0.8310 (t80) cc_final: 0.8100 (t80) REVERT: hA 102 LYS cc_start: 0.8575 (tptm) cc_final: 0.7880 (tptm) REVERT: hA 103 PHE cc_start: 0.8633 (t80) cc_final: 0.8069 (t80) REVERT: iA 202 LYS cc_start: 0.8602 (tttm) cc_final: 0.8188 (mtpp) REVERT: iA 204 GLU cc_start: 0.7630 (tm-30) cc_final: 0.6797 (tm-30) REVERT: iA 206 LYS cc_start: 0.8585 (tttt) cc_final: 0.8306 (tttt) REVERT: jA 306 LYS cc_start: 0.8668 (tptp) cc_final: 0.8104 (tptp) REVERT: kA 1002 LYS cc_start: 0.8524 (ttpt) cc_final: 0.7979 (tppt) REVERT: lA 1103 PHE cc_start: 0.8541 (t80) cc_final: 0.8158 (t80) REVERT: mA 1203 PHE cc_start: 0.8827 (t80) cc_final: 0.8621 (t80) REVERT: mA 1204 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7147 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8596 (tttt) cc_final: 0.8293 (tptt) REVERT: d 2 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8293 (tppt) REVERT: oA 102 LYS cc_start: 0.8527 (tptm) cc_final: 0.8254 (tptm) REVERT: oA 103 PHE cc_start: 0.8485 (t80) cc_final: 0.8079 (t80) REVERT: pA 202 LYS cc_start: 0.8551 (tttm) cc_final: 0.8237 (ttmm) REVERT: pA 204 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7083 (tm-30) REVERT: pA 206 LYS cc_start: 0.8820 (tttt) cc_final: 0.8493 (tptt) REVERT: qA 306 LYS cc_start: 0.8643 (tptp) cc_final: 0.8299 (tptp) REVERT: rA 1002 LYS cc_start: 0.8547 (ttpt) cc_final: 0.8233 (tppt) REVERT: sA 1102 LYS cc_start: 0.8551 (tptm) cc_final: 0.8245 (tptm) REVERT: sA 1103 PHE cc_start: 0.8466 (t80) cc_final: 0.8069 (t80) REVERT: tA 1202 LYS cc_start: 0.8548 (tttm) cc_final: 0.8215 (ttmm) REVERT: e 2 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8302 (tppt) REVERT: wA 202 LYS cc_start: 0.8683 (tttm) cc_final: 0.8294 (ttmm) REVERT: wA 204 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7400 (tm-30) REVERT: wA 206 LYS cc_start: 0.8556 (tttt) cc_final: 0.8252 (tttm) REVERT: xA 307 PHE cc_start: 0.8919 (t80) cc_final: 0.8454 (t80) REVERT: yA 1002 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8189 (tppt) REVERT: yA 1005 PHE cc_start: 0.8828 (t80) cc_final: 0.8437 (t80) REVERT: 1A 1307 PHE cc_start: 0.8993 (t80) cc_final: 0.8730 (t80) REVERT: f 7 PHE cc_start: 0.9189 (t80) cc_final: 0.8618 (t80) REVERT: 2A 102 LYS cc_start: 0.8419 (tptm) cc_final: 0.7960 (tptm) REVERT: 5A 1002 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8143 (ttpt) REVERT: 5A 1003 PHE cc_start: 0.9028 (t80) cc_final: 0.8827 (t80) REVERT: 5A 1007 PHE cc_start: 0.9151 (t80) cc_final: 0.8669 (t80) REVERT: 6A 1102 LYS cc_start: 0.8482 (tptm) cc_final: 0.8014 (tptm) REVERT: g 5 PHE cc_start: 0.8929 (t80) cc_final: 0.8534 (t80) REVERT: g 7 PHE cc_start: 0.9238 (t80) cc_final: 0.8837 (t80) REVERT: 9A 102 LYS cc_start: 0.8721 (tptm) cc_final: 0.8239 (tptm) REVERT: AB 202 LYS cc_start: 0.8677 (tttm) cc_final: 0.8225 (mmmm) REVERT: AB 203 PHE cc_start: 0.8873 (t80) cc_final: 0.8514 (t80) REVERT: AB 204 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7207 (tm-30) REVERT: BB 304 GLU cc_start: 0.8793 (tm-30) cc_final: 0.7997 (tm-30) REVERT: BB 305 PHE cc_start: 0.8521 (t80) cc_final: 0.8192 (t80) REVERT: CB 1003 PHE cc_start: 0.9126 (t80) cc_final: 0.8761 (t80) REVERT: CB 1005 PHE cc_start: 0.8976 (t80) cc_final: 0.8520 (t80) REVERT: CB 1007 PHE cc_start: 0.9228 (t80) cc_final: 0.8898 (t80) REVERT: DB 1102 LYS cc_start: 0.8674 (tptm) cc_final: 0.8199 (tptm) REVERT: EB 1202 LYS cc_start: 0.8651 (tttm) cc_final: 0.8321 (tttm) REVERT: EB 1203 PHE cc_start: 0.8849 (t80) cc_final: 0.8508 (t80) REVERT: EB 1204 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7183 (tm-30) REVERT: FB 1304 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8099 (tm-30) REVERT: GB 102 LYS cc_start: 0.8473 (tptm) cc_final: 0.8059 (tptm) REVERT: HB 202 LYS cc_start: 0.8727 (tttm) cc_final: 0.8395 (mmmm) REVERT: IB 304 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8378 (tm-30) REVERT: IB 307 PHE cc_start: 0.8954 (t80) cc_final: 0.8492 (t80) REVERT: JB 1003 PHE cc_start: 0.9094 (t80) cc_final: 0.8584 (t80) REVERT: MB 1307 PHE cc_start: 0.8936 (t80) cc_final: 0.8424 (t80) REVERT: i 6 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8420 (ttpt) REVERT: OB 202 LYS cc_start: 0.8738 (mttm) cc_final: 0.8305 (mmmm) REVERT: OB 204 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7050 (tm-30) REVERT: PB 302 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8180 (tptp) REVERT: PB 303 PHE cc_start: 0.7885 (t80) cc_final: 0.7368 (t80) REVERT: PB 304 GLU cc_start: 0.8657 (tm-30) cc_final: 0.7396 (pm20) REVERT: PB 305 PHE cc_start: 0.8514 (t80) cc_final: 0.7641 (t80) REVERT: PB 307 PHE cc_start: 0.8555 (t80) cc_final: 0.8327 (t80) REVERT: QB 1002 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8088 (tppt) REVERT: RB 1102 LYS cc_start: 0.8636 (tptm) cc_final: 0.8195 (tptm) REVERT: SB 1204 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7178 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8717 (tttt) cc_final: 0.8480 (tttt) REVERT: TB 1302 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8205 (tptp) REVERT: TB 1303 PHE cc_start: 0.7870 (t80) cc_final: 0.7389 (t80) REVERT: TB 1304 GLU cc_start: 0.8599 (tm-30) cc_final: 0.7405 (pm20) REVERT: TB 1305 PHE cc_start: 0.8517 (t80) cc_final: 0.7610 (t80) REVERT: TB 1307 PHE cc_start: 0.8554 (t80) cc_final: 0.8293 (t80) outliers start: 21 outliers final: 10 residues processed: 474 average time/residue: 0.1967 time to fit residues: 115.9708 Evaluate side-chains 477 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 460 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain T residue 1006 LYS Chi-restraints excluded: chain V residue 1202 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain PB residue 302 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: 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 = 0.3508 r_free = 0.3508 target = 0.089417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.078247 restraints weight = 25724.855| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.10 r_work: 0.3062 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.058 12564 Z= 0.708 Angle : 0.928 10.008 16272 Z= 0.428 Chirality : 0.047 0.165 1152 Planarity : 0.004 0.016 2160 Dihedral : 15.126 88.115 1456 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.98 % Allowed : 27.89 % 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: -5.35 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.12), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.004 PHEnA1303 Details of bonding type rmsd/Z covalent geometry : bond 0.01571 / 0.71 (12528) covalent geometry : angle 0.92829 / 0.43 (16272) hydrogen bonds : bond 0.04066 / 2.27 ( 278) hydrogen bonds : angle 6.58413 / 3.71 ( 786) Misc. bond : bond 0.00203 / 0.10 ( 36) *********************** 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 562 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 519 time to evaluate : 0.422 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: 0.8928 (OUTLIER) cc_final: 0.8589 (tmmm) REVERT: L 304 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8148 (mm-30) REVERT: M 1005 PHE cc_start: 0.8902 (m-80) cc_final: 0.8591 (m-10) REVERT: N 1104 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7893 (mm-30) REVERT: N 1106 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8513 (tmtm) REVERT: P 1302 LYS cc_start: 0.9213 (ttpt) cc_final: 0.8525 (ttmm) REVERT: P 1304 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7776 (mm-30) REVERT: Q 106 LYS cc_start: 0.8892 (tptm) cc_final: 0.8514 (tptm) REVERT: S 302 LYS cc_start: 0.9226 (mtpt) cc_final: 0.8706 (ttmm) REVERT: T 1006 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8477 (mtmt) REVERT: U 1106 LYS cc_start: 0.8884 (tptm) cc_final: 0.8595 (tptm) REVERT: W 1302 LYS cc_start: 0.9189 (mtpt) cc_final: 0.8557 (ttmm) REVERT: X 102 LYS cc_start: 0.8616 (ttpt) cc_final: 0.7767 (ttpp) REVERT: X 104 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7425 (mm-30) REVERT: X 106 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8577 (mmmt) REVERT: Z 302 LYS cc_start: 0.9232 (ttpt) cc_final: 0.8867 (ttmm) REVERT: Z 304 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8136 (mm-30) REVERT: Z 306 LYS cc_start: 0.9079 (tttt) cc_final: 0.8768 (mttt) REVERT: k 1102 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8126 (ttmm) REVERT: k 1104 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7228 (mm-30) REVERT: m 1302 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8918 (ttmm) REVERT: m 1306 LYS cc_start: 0.9080 (tttt) cc_final: 0.8819 (mttt) REVERT: D 2 LYS cc_start: 0.7594 (tttt) cc_final: 0.7310 (tttt) REVERT: n 104 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7880 (mm-30) REVERT: q 1002 LYS cc_start: 0.7563 (tttt) cc_final: 0.7262 (tttt) REVERT: r 1104 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7935 (mm-30) REVERT: r 1106 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8379 (mmmm) REVERT: t 1306 LYS cc_start: 0.9000 (tttt) cc_final: 0.8731 (tttm) REVERT: E 6 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8063 (mtmt) REVERT: u 102 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8180 (ttmm) REVERT: v 204 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7107 (tm-30) REVERT: w 304 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8036 (mm-30) REVERT: x 1006 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8550 (mtmt) REVERT: y 1102 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8165 (ttmm) REVERT: y 1104 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8198 (mm-30) REVERT: z 1206 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8462 (ttmm) REVERT: 0 1302 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8580 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8196 (mm-30) REVERT: 0 1306 LYS cc_start: 0.9067 (tttt) cc_final: 0.8700 (tttt) REVERT: 3 304 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7859 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8587 (tmtm) REVERT: 6 1206 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8679 (ttmm) REVERT: G 4 GLU cc_start: 0.7958 (mp0) cc_final: 0.7463 (mp0) REVERT: AA 306 LYS cc_start: 0.9005 (tttt) cc_final: 0.8752 (tttt) REVERT: BA 1004 GLU cc_start: 0.7964 (mp0) cc_final: 0.7369 (mp0) REVERT: CA 1102 LYS cc_start: 0.9138 (ttpt) cc_final: 0.8781 (mtpt) REVERT: CA 1104 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8157 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8893 (tptm) cc_final: 0.8440 (tptm) REVERT: EA 1306 LYS cc_start: 0.9084 (tttt) cc_final: 0.8817 (tttt) REVERT: FA 104 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8134 (mm-30) REVERT: FA 106 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8786 (mmmt) REVERT: GA 206 LYS cc_start: 0.6156 (pptt) cc_final: 0.5122 (pptt) REVERT: JA 1104 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8001 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8746 (mmmt) REVERT: I 2 LYS cc_start: 0.8984 (tttt) cc_final: 0.8627 (tttm) REVERT: MA 102 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8960 (ttpt) REVERT: MA 106 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8508 (mmmm) REVERT: NA 206 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8715 (ttmm) REVERT: OA 302 LYS cc_start: 0.9289 (ttpt) cc_final: 0.8574 (ttmm) REVERT: OA 304 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8069 (mm-30) REVERT: OA 306 LYS cc_start: 0.9091 (tttt) cc_final: 0.8849 (mmmt) REVERT: PA 1004 GLU cc_start: 0.8354 (mp0) cc_final: 0.7816 (mp0) REVERT: QA 1102 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8934 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8482 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8676 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9227 (ttpt) cc_final: 0.8570 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8192 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9060 (tttt) cc_final: 0.8851 (mmmt) REVERT: TA 102 LYS cc_start: 0.8898 (tptm) cc_final: 0.8458 (tptm) REVERT: TA 103 PHE cc_start: 0.8686 (t80) cc_final: 0.8412 (t80) REVERT: UA 202 LYS cc_start: 0.9036 (tttm) cc_final: 0.8656 (mmmm) REVERT: UA 204 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7028 (tm-30) REVERT: VA 302 LYS cc_start: 0.8803 (tptp) cc_final: 0.8465 (tptp) REVERT: VA 304 GLU cc_start: 0.8977 (tm-30) cc_final: 0.7665 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8531 (ttpt) REVERT: WA 1004 GLU cc_start: 0.8373 (tp30) cc_final: 0.7712 (tp30) REVERT: WA 1007 PHE cc_start: 0.9265 (t80) cc_final: 0.8887 (t80) REVERT: XA 1102 LYS cc_start: 0.8865 (tptm) cc_final: 0.8505 (tptm) REVERT: XA 1103 PHE cc_start: 0.8669 (t80) cc_final: 0.7699 (t80) REVERT: YA 1202 LYS cc_start: 0.9028 (tttm) cc_final: 0.8677 (tttm) REVERT: YA 1204 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7358 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8435 (tm-30) REVERT: b 2 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8620 (tppt) REVERT: b 4 GLU cc_start: 0.8038 (tp30) cc_final: 0.7706 (tp30) REVERT: b 5 PHE cc_start: 0.9014 (t80) cc_final: 0.8779 (t80) REVERT: aA 102 LYS cc_start: 0.8909 (tptm) cc_final: 0.8405 (tptm) REVERT: cA 304 GLU cc_start: 0.8905 (tm-30) cc_final: 0.7903 (tm-30) REVERT: dA 1002 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8461 (tppt) REVERT: dA 1006 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8533 (ttpp) REVERT: gA 1307 PHE cc_start: 0.8841 (t80) cc_final: 0.8614 (t80) REVERT: hA 103 PHE cc_start: 0.8878 (t80) cc_final: 0.8377 (t80) REVERT: iA 202 LYS cc_start: 0.8937 (tttm) cc_final: 0.8547 (mtpp) REVERT: iA 204 GLU cc_start: 0.7829 (tm-30) cc_final: 0.6879 (tm-30) REVERT: iA 206 LYS cc_start: 0.8838 (tttt) cc_final: 0.8420 (tttt) REVERT: jA 302 LYS cc_start: 0.8853 (tptp) cc_final: 0.8639 (tptp) REVERT: jA 303 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8324 (t80) REVERT: jA 304 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8685 (tm-30) REVERT: jA 306 LYS cc_start: 0.8768 (tptp) cc_final: 0.8301 (tptp) REVERT: kA 1002 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8486 (ttpt) REVERT: lA 1103 PHE cc_start: 0.8710 (t80) cc_final: 0.8332 (t80) REVERT: mA 1204 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7219 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8456 (tptt) REVERT: nA 1302 LYS cc_start: 0.8836 (tptp) cc_final: 0.8509 (tptp) REVERT: nA 1303 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8220 (t80) REVERT: nA 1306 LYS cc_start: 0.8811 (tptp) cc_final: 0.8334 (tptp) REVERT: d 2 LYS cc_start: 0.9216 (ttpt) cc_final: 0.8767 (tppt) REVERT: d 4 GLU cc_start: 0.8128 (tp30) cc_final: 0.7878 (tp30) REVERT: oA 102 LYS cc_start: 0.8892 (tptm) cc_final: 0.8618 (tptm) REVERT: pA 202 LYS cc_start: 0.8957 (tttm) cc_final: 0.8545 (mtpp) REVERT: pA 204 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7256 (tp30) REVERT: pA 206 LYS cc_start: 0.8933 (tttt) cc_final: 0.8530 (tttm) REVERT: qA 302 LYS cc_start: 0.8719 (tptp) cc_final: 0.8325 (tptp) REVERT: qA 303 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7142 (t80) REVERT: qA 304 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8795 (tm-30) REVERT: qA 306 LYS cc_start: 0.8758 (tptp) cc_final: 0.8536 (tptp) REVERT: sA 1102 LYS cc_start: 0.8836 (tptm) cc_final: 0.8585 (tptm) REVERT: tA 1204 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7225 (tp30) REVERT: uA 1302 LYS cc_start: 0.8743 (tptp) cc_final: 0.8337 (tptp) REVERT: uA 1303 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7090 (t80) REVERT: uA 1306 LYS cc_start: 0.8740 (tptp) cc_final: 0.8532 (tptp) REVERT: e 2 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8750 (tppt) REVERT: vA 102 LYS cc_start: 0.8830 (tptm) cc_final: 0.8352 (tptm) REVERT: wA 202 LYS cc_start: 0.8923 (tttm) cc_final: 0.8441 (ttmm) REVERT: wA 204 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7529 (tm-30) REVERT: wA 206 LYS cc_start: 0.8762 (tttt) cc_final: 0.8266 (tttm) REVERT: xA 304 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8525 (tm-30) REVERT: yA 1002 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8686 (ttpt) REVERT: 1A 1304 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8481 (tm-30) REVERT: f 2 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8756 (ttpt) REVERT: 2A 102 LYS cc_start: 0.8778 (tptm) cc_final: 0.8114 (tptm) REVERT: 4A 304 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8152 (tm-30) REVERT: 8A 1304 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8145 (tm-30) REVERT: g 2 LYS cc_start: 0.8933 (ttpt) cc_final: 0.8725 (ttpt) REVERT: g 4 GLU cc_start: 0.8313 (tp30) cc_final: 0.7952 (tp30) REVERT: 9A 102 LYS cc_start: 0.8956 (tptm) cc_final: 0.8573 (tptm) REVERT: AB 202 LYS cc_start: 0.8837 (tttm) cc_final: 0.8416 (mtpp) REVERT: AB 203 PHE cc_start: 0.8917 (t80) cc_final: 0.8555 (t80) REVERT: AB 204 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7560 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8411 (tp30) cc_final: 0.8000 (tp30) REVERT: DB 1102 LYS cc_start: 0.8931 (tptm) cc_final: 0.8555 (tptm) REVERT: EB 1202 LYS cc_start: 0.8810 (tttm) cc_final: 0.8554 (tttm) REVERT: EB 1203 PHE cc_start: 0.8877 (t80) cc_final: 0.8538 (t80) REVERT: EB 1204 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7518 (tm-30) REVERT: FB 1304 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8719 (tm-30) REVERT: h 4 GLU cc_start: 0.7593 (tp30) cc_final: 0.7364 (tp30) REVERT: GB 102 LYS cc_start: 0.8909 (tptm) cc_final: 0.8552 (tptm) REVERT: HB 202 LYS cc_start: 0.8871 (tttm) cc_final: 0.8514 (mtpp) REVERT: IB 302 LYS cc_start: 0.8905 (tptp) cc_final: 0.8610 (tptp) REVERT: IB 307 PHE cc_start: 0.9092 (t80) cc_final: 0.8779 (t80) REVERT: KB 1102 LYS cc_start: 0.8813 (tptm) cc_final: 0.8500 (tptm) REVERT: MB 1304 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8536 (tm-30) REVERT: MB 1307 PHE cc_start: 0.9071 (t80) cc_final: 0.8797 (t80) REVERT: i 6 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8565 (ttpt) REVERT: OB 202 LYS cc_start: 0.8783 (mttm) cc_final: 0.8445 (mmmm) REVERT: OB 204 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7343 (tm-30) REVERT: OB 206 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8635 (tptt) REVERT: PB 302 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8298 (tptp) REVERT: PB 303 PHE cc_start: 0.8144 (t80) cc_final: 0.7704 (t80) REVERT: PB 304 GLU cc_start: 0.8730 (tm-30) cc_final: 0.7435 (pm20) REVERT: PB 305 PHE cc_start: 0.8763 (t80) cc_final: 0.7930 (t80) REVERT: PB 307 PHE cc_start: 0.8909 (t80) cc_final: 0.8671 (t80) REVERT: QB 1005 PHE cc_start: 0.9145 (t80) cc_final: 0.8912 (t80) REVERT: RB 1102 LYS cc_start: 0.8849 (tptm) cc_final: 0.8462 (tptm) REVERT: SB 1204 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7273 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8906 (tttt) cc_final: 0.8676 (tttt) REVERT: TB 1302 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8305 (tptp) REVERT: TB 1304 GLU cc_start: 0.8703 (tm-30) cc_final: 0.7474 (pm20) REVERT: TB 1305 PHE cc_start: 0.8746 (t80) cc_final: 0.7882 (t80) REVERT: TB 1307 PHE cc_start: 0.8918 (t80) cc_final: 0.8668 (t80) outliers start: 43 outliers final: 23 residues processed: 521 average time/residue: 0.1961 time to fit residues: 126.9305 Evaluate side-chains 551 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 515 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain Q residue 102 LYS Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain T residue 1006 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain V residue 1202 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain HA residue 302 LYS Chi-restraints excluded: chain LA residue 1302 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain RB residue 1105 PHE 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: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.095810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083771 restraints weight = 24006.750| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.10 r_work: 0.3208 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12564 Z= 0.123 Angle : 0.655 9.476 16272 Z= 0.307 Chirality : 0.031 0.106 1152 Planarity : 0.002 0.015 2160 Dihedral : 14.258 89.108 1456 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.74 % Allowed : 31.94 % Favored : 66.32 % 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: -5.09 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.12), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.034 0.002 PHEzA1103 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (12528) covalent geometry : angle 0.65499 / 0.31 (16272) hydrogen bonds : bond 0.01872 / 1.05 ( 278) hydrogen bonds : angle 5.73089 / 3.22 ( 786) Misc. bond : bond 0.00110 / 0.05 ( 36) *********************** 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 493 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 478 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8476 (mtmt) REVERT: J 104 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7906 (mm-30) REVERT: J 106 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8461 (tmmm) REVERT: L 304 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7930 (mm-30) REVERT: N 1104 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7639 (mm-30) REVERT: N 1106 LYS cc_start: 0.9004 (tmtm) cc_final: 0.8369 (tmtm) REVERT: P 1302 LYS cc_start: 0.9125 (ttpt) cc_final: 0.8522 (ttmm) REVERT: Q 106 LYS cc_start: 0.8798 (tptm) cc_final: 0.8464 (tptm) REVERT: S 302 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8634 (ttmm) REVERT: T 1006 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8354 (mtmt) REVERT: U 1106 LYS cc_start: 0.8860 (tptm) cc_final: 0.8591 (tptm) REVERT: W 1302 LYS cc_start: 0.9106 (mtpt) cc_final: 0.8510 (ttmm) REVERT: W 1304 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7992 (mm-30) REVERT: X 102 LYS cc_start: 0.8510 (ttpt) cc_final: 0.7532 (ttpp) REVERT: X 104 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7266 (mm-30) REVERT: X 106 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8450 (mmmt) REVERT: Z 306 LYS cc_start: 0.8905 (tttt) cc_final: 0.8612 (mttt) REVERT: k 1102 LYS cc_start: 0.8448 (ttpt) cc_final: 0.7426 (ttpp) REVERT: k 1104 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7109 (mm-30) REVERT: k 1106 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8423 (mmmt) REVERT: l 1206 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8611 (ttmm) REVERT: m 1302 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8233 (ttmm) REVERT: m 1306 LYS cc_start: 0.8931 (tttt) cc_final: 0.8621 (mttt) REVERT: n 104 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7575 (mm-30) REVERT: r 1104 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7441 (mm-30) REVERT: r 1106 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8224 (mmmm) REVERT: s 1202 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8407 (mtpt) REVERT: E 6 LYS cc_start: 0.8675 (mtmt) cc_final: 0.7944 (mtmt) REVERT: v 206 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8493 (ttmm) REVERT: w 302 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8352 (ttmm) REVERT: w 304 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7639 (mm-30) REVERT: y 1102 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8387 (ttmm) REVERT: y 1104 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8119 (mm-30) REVERT: z 1206 LYS cc_start: 0.8834 (ttmm) cc_final: 0.8400 (ttmm) REVERT: 0 1302 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8458 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7543 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8902 (tttt) cc_final: 0.8405 (tttt) REVERT: 1 106 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8384 (tmmm) REVERT: 2 206 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8619 (ttmm) REVERT: 3 302 LYS cc_start: 0.9207 (mtpp) cc_final: 0.8704 (ttmm) REVERT: 3 304 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7728 (mm-30) REVERT: 3 306 LYS cc_start: 0.8988 (tttt) cc_final: 0.8704 (tttt) REVERT: 4 1004 GLU cc_start: 0.7873 (mp0) cc_final: 0.7601 (mp0) REVERT: 5 1106 LYS cc_start: 0.8940 (tmtm) cc_final: 0.8344 (tmtm) REVERT: 6 1206 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8587 (ttmm) REVERT: 7 1302 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8707 (ttmm) REVERT: G 4 GLU cc_start: 0.7839 (mp0) cc_final: 0.7553 (mp0) REVERT: 9 204 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7360 (mt-10) REVERT: AA 306 LYS cc_start: 0.8915 (tttt) cc_final: 0.8660 (tttt) REVERT: BA 1004 GLU cc_start: 0.7835 (mp0) cc_final: 0.7136 (mp0) REVERT: CA 1102 LYS cc_start: 0.9068 (ttpt) cc_final: 0.8699 (mtpt) REVERT: CA 1104 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8074 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8926 (tptm) cc_final: 0.8475 (tptm) REVERT: DA 1202 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8732 (mtpt) REVERT: DA 1204 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7286 (mt-10) REVERT: EA 1306 LYS cc_start: 0.8939 (tttt) cc_final: 0.8656 (tttt) REVERT: FA 106 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8664 (mmmt) REVERT: JA 1102 LYS cc_start: 0.8279 (ttpt) cc_final: 0.8067 (ttmm) REVERT: JA 1106 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8618 (mmmt) REVERT: KA 1202 LYS cc_start: 0.9004 (tttt) cc_final: 0.8612 (pptt) REVERT: LA 1302 LYS cc_start: 0.9229 (mtpt) cc_final: 0.8525 (ttmm) REVERT: MA 102 LYS cc_start: 0.9166 (ttpt) cc_final: 0.8836 (ttpt) REVERT: MA 106 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8456 (mmmm) REVERT: NA 206 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8582 (ttmm) REVERT: OA 302 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8404 (ttmm) REVERT: OA 304 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7940 (mm-30) REVERT: OA 306 LYS cc_start: 0.9011 (tttt) cc_final: 0.8743 (mmmt) REVERT: PA 1004 GLU cc_start: 0.8334 (mp0) cc_final: 0.7736 (mp0) REVERT: QA 1102 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8876 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8434 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8596 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8435 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7768 (mm-30) REVERT: a 3 PHE cc_start: 0.9116 (t80) cc_final: 0.8886 (t80) REVERT: UA 202 LYS cc_start: 0.8792 (tttm) cc_final: 0.8413 (mmmm) REVERT: UA 204 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7322 (tm-30) REVERT: VA 304 GLU cc_start: 0.8924 (tm-30) cc_final: 0.7697 (tm-30) REVERT: VA 305 PHE cc_start: 0.8572 (t80) cc_final: 0.8255 (t80) REVERT: WA 1002 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8202 (ttpt) REVERT: WA 1007 PHE cc_start: 0.9279 (t80) cc_final: 0.8954 (t80) REVERT: YA 1202 LYS cc_start: 0.8777 (tttm) cc_final: 0.8453 (tttm) REVERT: YA 1204 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7188 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.8867 (tm-30) cc_final: 0.7816 (tm-30) REVERT: b 2 LYS cc_start: 0.8820 (tppt) cc_final: 0.8338 (tppt) REVERT: b 4 GLU cc_start: 0.7979 (tp30) cc_final: 0.7702 (tp30) REVERT: aA 102 LYS cc_start: 0.8714 (tptm) cc_final: 0.8120 (tptm) REVERT: aA 103 PHE cc_start: 0.8442 (t80) cc_final: 0.8129 (t80) REVERT: eA 1107 PHE cc_start: 0.9079 (t80) cc_final: 0.8821 (t80) REVERT: gA 1307 PHE cc_start: 0.8790 (t80) cc_final: 0.8378 (t80) REVERT: c 2 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8234 (tppt) REVERT: hA 103 PHE cc_start: 0.8618 (t80) cc_final: 0.8231 (t80) REVERT: iA 202 LYS cc_start: 0.8736 (tttm) cc_final: 0.8313 (mtpp) REVERT: iA 204 GLU cc_start: 0.7703 (tm-30) cc_final: 0.6649 (tm-30) REVERT: iA 206 LYS cc_start: 0.8593 (tttt) cc_final: 0.8313 (tttt) REVERT: jA 302 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8237 (tptp) REVERT: jA 303 PHE cc_start: 0.8343 (t80) cc_final: 0.8068 (t80) REVERT: jA 306 LYS cc_start: 0.8707 (tptp) cc_final: 0.8209 (tptp) REVERT: kA 1002 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8046 (tppt) REVERT: lA 1103 PHE cc_start: 0.8618 (t80) cc_final: 0.8252 (t80) REVERT: mA 1204 GLU cc_start: 0.7626 (tm-30) cc_final: 0.6703 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8604 (tttt) cc_final: 0.8182 (tptt) REVERT: nA 1306 LYS cc_start: 0.8774 (tptp) cc_final: 0.8183 (tptp) REVERT: d 2 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8419 (tppt) REVERT: d 4 GLU cc_start: 0.8053 (tp30) cc_final: 0.7746 (tp30) REVERT: d 5 PHE cc_start: 0.8790 (t80) cc_final: 0.8174 (t80) REVERT: oA 102 LYS cc_start: 0.8686 (tptm) cc_final: 0.8345 (tptm) REVERT: oA 103 PHE cc_start: 0.8154 (t80) cc_final: 0.7442 (t80) REVERT: pA 202 LYS cc_start: 0.8673 (tttm) cc_final: 0.8345 (ttmm) REVERT: pA 204 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7457 (tp30) REVERT: pA 206 LYS cc_start: 0.8854 (tttt) cc_final: 0.8497 (tttm) REVERT: qA 306 LYS cc_start: 0.8658 (tptp) cc_final: 0.8354 (tptp) REVERT: rA 1002 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8271 (tppt) REVERT: sA 1102 LYS cc_start: 0.8659 (tptm) cc_final: 0.8328 (tptm) REVERT: sA 1103 PHE cc_start: 0.8040 (t80) cc_final: 0.7827 (t80) REVERT: tA 1202 LYS cc_start: 0.8643 (tttm) cc_final: 0.8307 (ttmm) REVERT: tA 1204 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7057 (tm-30) REVERT: uA 1306 LYS cc_start: 0.8667 (tptp) cc_final: 0.8406 (tptp) REVERT: e 2 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8394 (tppt) REVERT: wA 202 LYS cc_start: 0.8750 (tttm) cc_final: 0.8324 (ttmm) REVERT: wA 204 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7384 (tm-30) REVERT: wA 206 LYS cc_start: 0.8589 (tttt) cc_final: 0.8185 (tttm) REVERT: xA 304 GLU cc_start: 0.8822 (tm-30) cc_final: 0.7753 (tm-30) REVERT: yA 1002 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8306 (tppt) REVERT: 1A 1304 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8411 (tm-30) REVERT: f 7 PHE cc_start: 0.9242 (t80) cc_final: 0.8641 (t80) REVERT: 5A 1002 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8234 (ttpt) REVERT: 5A 1007 PHE cc_start: 0.9236 (t80) cc_final: 0.8720 (t80) REVERT: 6A 1102 LYS cc_start: 0.8522 (tptm) cc_final: 0.8067 (tptm) REVERT: 6A 1103 PHE cc_start: 0.8236 (t80) cc_final: 0.8011 (t80) REVERT: g 2 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8317 (ttpt) REVERT: g 4 GLU cc_start: 0.8141 (tp30) cc_final: 0.7721 (tp30) REVERT: 9A 102 LYS cc_start: 0.8842 (tptm) cc_final: 0.8434 (tptm) REVERT: 9A 107 PHE cc_start: 0.9020 (t80) cc_final: 0.8809 (t80) REVERT: AB 202 LYS cc_start: 0.8704 (tttm) cc_final: 0.8347 (mtpp) REVERT: AB 203 PHE cc_start: 0.8898 (t80) cc_final: 0.8590 (t80) REVERT: AB 204 GLU cc_start: 0.8018 (tm-30) cc_final: 0.6923 (tm-30) REVERT: CB 1002 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8386 (ttpt) REVERT: CB 1005 PHE cc_start: 0.8907 (t80) cc_final: 0.8502 (t80) REVERT: DB 1102 LYS cc_start: 0.8804 (tptm) cc_final: 0.8367 (tptm) REVERT: EB 1202 LYS cc_start: 0.8733 (tttm) cc_final: 0.8484 (tttm) REVERT: EB 1203 PHE cc_start: 0.8883 (t80) cc_final: 0.8617 (t80) REVERT: EB 1204 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7259 (tm-30) REVERT: FB 1304 GLU cc_start: 0.9050 (tm-30) cc_final: 0.7989 (tm-30) REVERT: h 3 PHE cc_start: 0.8936 (t80) cc_final: 0.8573 (t80) REVERT: GB 102 LYS cc_start: 0.8553 (tptm) cc_final: 0.8132 (tptm) REVERT: IB 304 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8466 (tm-30) REVERT: IB 307 PHE cc_start: 0.9004 (t80) cc_final: 0.8725 (t80) REVERT: KB 1102 LYS cc_start: 0.8543 (tptm) cc_final: 0.8187 (tptm) REVERT: MB 1304 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8702 (tm-30) REVERT: MB 1307 PHE cc_start: 0.8993 (t80) cc_final: 0.8712 (t80) REVERT: i 6 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8413 (ttpt) REVERT: NB 102 LYS cc_start: 0.8693 (tptm) cc_final: 0.8457 (tptm) REVERT: OB 204 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7348 (tm-30) REVERT: PB 302 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8122 (tptp) REVERT: PB 303 PHE cc_start: 0.8133 (t80) cc_final: 0.7656 (t80) REVERT: PB 304 GLU cc_start: 0.8657 (tm-30) cc_final: 0.7447 (pm20) REVERT: PB 305 PHE cc_start: 0.8470 (t80) cc_final: 0.7595 (t80) REVERT: PB 307 PHE cc_start: 0.8780 (t80) cc_final: 0.8471 (t80) REVERT: QB 1002 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8120 (tppt) REVERT: RB 1102 LYS cc_start: 0.8634 (tptm) cc_final: 0.8369 (tptm) REVERT: SB 1204 GLU cc_start: 0.7754 (tm-30) cc_final: 0.6815 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8736 (tttt) cc_final: 0.8445 (tttt) REVERT: TB 1302 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8220 (tptp) REVERT: TB 1303 PHE cc_start: 0.8095 (t80) cc_final: 0.7560 (t80) REVERT: TB 1304 GLU cc_start: 0.8607 (tm-30) cc_final: 0.7458 (pm20) REVERT: TB 1305 PHE cc_start: 0.8465 (t80) cc_final: 0.7583 (t80) REVERT: TB 1307 PHE cc_start: 0.8759 (t80) cc_final: 0.8488 (t80) outliers start: 15 outliers final: 8 residues processed: 481 average time/residue: 0.1976 time to fit residues: 117.8805 Evaluate side-chains 485 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 470 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain Q residue 102 LYS Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain T residue 1006 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain V residue 1202 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain PB residue 302 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: 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 = 0.3518 r_free = 0.3518 target = 0.089907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078695 restraints weight = 25595.676| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.08 r_work: 0.3067 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.074 12564 Z= 0.710 Angle : 0.949 10.492 16272 Z= 0.438 Chirality : 0.048 0.162 1152 Planarity : 0.004 0.015 2160 Dihedral : 14.353 88.773 1448 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.98 % Allowed : 29.86 % Favored : 65.16 % 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: -5.29 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.12), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.004 PHEgA1305 Details of bonding type rmsd/Z covalent geometry : bond 0.01574 / 0.71 (12528) covalent geometry : angle 0.94880 / 0.44 (16272) hydrogen bonds : bond 0.04172 / 2.35 ( 278) hydrogen bonds : angle 6.65058 / 3.74 ( 786) Misc. bond : bond 0.00207 / 0.11 ( 36) *********************** 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 551 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 508 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8244 (mtmt) REVERT: J 106 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8558 (tmmm) REVERT: K 206 LYS cc_start: 0.9001 (ttmm) cc_final: 0.8764 (ttmm) REVERT: L 304 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8066 (mm-30) REVERT: L 306 LYS cc_start: 0.9107 (ttpt) cc_final: 0.8808 (ttpt) REVERT: M 1005 PHE cc_start: 0.8934 (m-80) cc_final: 0.8706 (m-10) REVERT: N 1104 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7738 (mm-30) REVERT: N 1106 LYS cc_start: 0.9044 (tmtm) cc_final: 0.8470 (tmtm) REVERT: P 1302 LYS cc_start: 0.9210 (ttpt) cc_final: 0.8643 (ttmm) REVERT: Q 106 LYS cc_start: 0.8941 (tptm) cc_final: 0.8496 (tptm) REVERT: S 302 LYS cc_start: 0.9221 (mtpt) cc_final: 0.8712 (ttmm) REVERT: T 1006 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8535 (mtmt) REVERT: U 1106 LYS cc_start: 0.8978 (tptm) cc_final: 0.8679 (tptm) REVERT: W 1302 LYS cc_start: 0.9183 (mtpt) cc_final: 0.8591 (ttmm) REVERT: W 1304 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8156 (mm-30) REVERT: X 102 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8027 (ttmm) REVERT: X 104 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7442 (mm-30) REVERT: X 106 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8575 (mmmt) REVERT: Y 206 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8642 (ttmm) REVERT: Z 306 LYS cc_start: 0.9086 (tttt) cc_final: 0.8768 (mttt) REVERT: k 1102 LYS cc_start: 0.8625 (ttpt) cc_final: 0.7739 (ttpp) REVERT: k 1104 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7236 (mm-30) REVERT: k 1106 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8527 (mmmt) REVERT: m 1302 LYS cc_start: 0.9225 (mtpt) cc_final: 0.8925 (ttmm) REVERT: m 1306 LYS cc_start: 0.9065 (tttt) cc_final: 0.8807 (mttt) REVERT: n 104 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7628 (mm-30) REVERT: q 1002 LYS cc_start: 0.7408 (tttt) cc_final: 0.7101 (tttt) REVERT: r 1102 LYS cc_start: 0.8433 (ttpt) cc_final: 0.7980 (ttpp) REVERT: r 1104 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7687 (mm-30) REVERT: r 1106 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8385 (mmmm) REVERT: t 1306 LYS cc_start: 0.9022 (tttt) cc_final: 0.8734 (tttm) REVERT: E 6 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8071 (mtmt) REVERT: u 102 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8144 (ttmm) REVERT: u 104 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8161 (mm-30) REVERT: v 204 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7422 (tm-30) REVERT: v 206 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8448 (ttmm) REVERT: w 304 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8019 (mm-30) REVERT: x 1006 LYS cc_start: 0.8758 (mtmt) cc_final: 0.7915 (mtmt) REVERT: y 1102 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8161 (ttmm) REVERT: y 1104 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8153 (mm-30) REVERT: z 1206 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8650 (ttmm) REVERT: 0 1302 LYS cc_start: 0.9170 (mtpt) cc_final: 0.8591 (ttmm) REVERT: 0 1306 LYS cc_start: 0.9077 (tttt) cc_final: 0.8847 (tttt) REVERT: 1 106 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8416 (tmmm) REVERT: 4 1004 GLU cc_start: 0.7947 (mp0) cc_final: 0.7057 (mp0) REVERT: 5 1106 LYS cc_start: 0.8961 (tmtm) cc_final: 0.8365 (tmtm) REVERT: 7 1302 LYS cc_start: 0.9202 (mtpp) cc_final: 0.8923 (ttmm) REVERT: G 4 GLU cc_start: 0.7939 (mp0) cc_final: 0.7237 (mp0) REVERT: 8 106 LYS cc_start: 0.8888 (tptm) cc_final: 0.8421 (tptm) REVERT: BA 1004 GLU cc_start: 0.7971 (mp0) cc_final: 0.7243 (mp0) REVERT: CA 1102 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8800 (mtpt) REVERT: CA 1104 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8075 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8915 (tptm) cc_final: 0.8463 (tptm) REVERT: EA 1302 LYS cc_start: 0.9304 (ttpt) cc_final: 0.8862 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9105 (tttt) cc_final: 0.8857 (tttt) REVERT: FA 104 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8112 (mm-30) REVERT: FA 106 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8727 (mmmt) REVERT: HA 302 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8989 (mtpp) REVERT: HA 304 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8077 (mm-30) REVERT: JA 1102 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8321 (ttmm) REVERT: JA 1104 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7954 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8717 (mmmt) REVERT: LA 1302 LYS cc_start: 0.9339 (mtpt) cc_final: 0.8876 (ttmm) REVERT: I 2 LYS cc_start: 0.8969 (tttt) cc_final: 0.8659 (tttm) REVERT: MA 102 LYS cc_start: 0.9195 (ttpt) cc_final: 0.8916 (ttpt) REVERT: MA 106 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8530 (mmmm) REVERT: NA 206 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8739 (ttmm) REVERT: OA 302 LYS cc_start: 0.9303 (ttpt) cc_final: 0.8627 (ttmm) REVERT: OA 304 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8042 (mm-30) REVERT: OA 306 LYS cc_start: 0.9062 (tttt) cc_final: 0.8852 (mmmt) REVERT: PA 1004 GLU cc_start: 0.8339 (mp0) cc_final: 0.7753 (mp0) REVERT: QA 1102 LYS cc_start: 0.9199 (ttpt) cc_final: 0.8887 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8486 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8698 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9209 (ttpt) cc_final: 0.8569 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8071 (mm-30) REVERT: TA 102 LYS cc_start: 0.8927 (tptm) cc_final: 0.8528 (tptm) REVERT: UA 202 LYS cc_start: 0.9023 (tttm) cc_final: 0.8721 (tttm) REVERT: UA 204 GLU cc_start: 0.7949 (tm-30) cc_final: 0.6975 (tm-30) REVERT: VA 302 LYS cc_start: 0.8708 (tptp) cc_final: 0.8358 (tptp) REVERT: VA 304 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8112 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8532 (ttpt) REVERT: WA 1004 GLU cc_start: 0.8323 (tp30) cc_final: 0.7661 (tp30) REVERT: WA 1007 PHE cc_start: 0.9272 (t80) cc_final: 0.8908 (t80) REVERT: XA 1102 LYS cc_start: 0.8889 (tptm) cc_final: 0.8552 (tptm) REVERT: YA 1202 LYS cc_start: 0.9038 (tttm) cc_final: 0.8686 (tttm) REVERT: YA 1204 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7360 (tm-30) REVERT: ZA 1302 LYS cc_start: 0.8720 (tptp) cc_final: 0.8336 (tptp) REVERT: ZA 1304 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8315 (tm-30) REVERT: b 2 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8627 (tppt) REVERT: b 4 GLU cc_start: 0.8042 (tp30) cc_final: 0.7714 (tp30) REVERT: b 5 PHE cc_start: 0.9011 (t80) cc_final: 0.8757 (t80) REVERT: aA 102 LYS cc_start: 0.8974 (tptm) cc_final: 0.8449 (tptm) REVERT: cA 304 GLU cc_start: 0.8940 (tm-30) cc_final: 0.7962 (tm-30) REVERT: dA 1006 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8439 (ttpp) REVERT: gA 1302 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8375 (tptp) REVERT: gA 1307 PHE cc_start: 0.8875 (t80) cc_final: 0.8664 (t80) REVERT: hA 103 PHE cc_start: 0.8814 (t80) cc_final: 0.8350 (t80) REVERT: iA 202 LYS cc_start: 0.8900 (tttm) cc_final: 0.8506 (mtpp) REVERT: iA 204 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7262 (tp30) REVERT: iA 206 LYS cc_start: 0.8787 (tttt) cc_final: 0.8485 (tttt) REVERT: jA 302 LYS cc_start: 0.8849 (tptp) cc_final: 0.8443 (tptp) REVERT: jA 303 PHE cc_start: 0.8547 (t80) cc_final: 0.7447 (t80) REVERT: jA 306 LYS cc_start: 0.8775 (tptp) cc_final: 0.8288 (tptp) REVERT: kA 1002 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8492 (ttpt) REVERT: lA 1103 PHE cc_start: 0.8740 (t80) cc_final: 0.8424 (t80) REVERT: mA 1203 PHE cc_start: 0.8858 (t80) cc_final: 0.8640 (t80) REVERT: mA 1204 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7328 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8735 (tttt) cc_final: 0.8288 (tptt) REVERT: nA 1302 LYS cc_start: 0.8811 (tptp) cc_final: 0.8495 (tptp) REVERT: nA 1303 PHE cc_start: 0.8433 (t80) cc_final: 0.8204 (t80) REVERT: nA 1306 LYS cc_start: 0.8863 (tptp) cc_final: 0.8346 (tptp) REVERT: d 2 LYS cc_start: 0.9209 (ttpt) cc_final: 0.8872 (tppt) REVERT: d 4 GLU cc_start: 0.8140 (tp30) cc_final: 0.7897 (tp30) REVERT: oA 102 LYS cc_start: 0.8920 (tptm) cc_final: 0.8646 (tptm) REVERT: pA 202 LYS cc_start: 0.8882 (tttm) cc_final: 0.8462 (mtpp) REVERT: pA 204 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7281 (tp30) REVERT: pA 206 LYS cc_start: 0.8931 (tttt) cc_final: 0.8512 (tttm) REVERT: qA 302 LYS cc_start: 0.8631 (tptp) cc_final: 0.8239 (tptp) REVERT: qA 303 PHE cc_start: 0.8031 (t80) cc_final: 0.6939 (t80) REVERT: qA 304 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8403 (tm-30) REVERT: rA 1002 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8652 (tppt) REVERT: sA 1102 LYS cc_start: 0.8868 (tptm) cc_final: 0.8607 (tptm) REVERT: tA 1204 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7265 (tp30) REVERT: uA 1302 LYS cc_start: 0.8667 (tptp) cc_final: 0.8291 (tptp) REVERT: uA 1303 PHE cc_start: 0.7996 (t80) cc_final: 0.6983 (t80) REVERT: uA 1306 LYS cc_start: 0.8753 (tptp) cc_final: 0.8542 (tptp) REVERT: e 2 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8733 (tppt) REVERT: vA 102 LYS cc_start: 0.8833 (tptm) cc_final: 0.8403 (tptm) REVERT: wA 202 LYS cc_start: 0.8935 (tttm) cc_final: 0.8384 (ttmm) REVERT: wA 204 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7538 (tm-30) REVERT: wA 206 LYS cc_start: 0.8772 (tttt) cc_final: 0.8286 (tttt) REVERT: xA 304 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8507 (tm-30) REVERT: xA 307 PHE cc_start: 0.8951 (t80) cc_final: 0.8559 (t80) REVERT: 1A 1304 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8461 (tm-30) REVERT: 2A 102 LYS cc_start: 0.8844 (tptm) cc_final: 0.8231 (tptm) REVERT: 4A 304 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8121 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8748 (ttpt) REVERT: 6A 1107 PHE cc_start: 0.9152 (t80) cc_final: 0.8913 (t80) REVERT: 8A 1304 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8133 (tm-30) REVERT: g 2 LYS cc_start: 0.8922 (ttpt) cc_final: 0.8704 (ttpt) REVERT: g 4 GLU cc_start: 0.8302 (tp30) cc_final: 0.7886 (tp30) REVERT: 9A 102 LYS cc_start: 0.9005 (tptm) cc_final: 0.8629 (tptm) REVERT: AB 202 LYS cc_start: 0.8824 (tttm) cc_final: 0.8468 (mtpp) REVERT: AB 203 PHE cc_start: 0.8925 (t80) cc_final: 0.8577 (t80) REVERT: AB 204 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7576 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8312 (tp30) cc_final: 0.7997 (tp30) REVERT: DB 1102 LYS cc_start: 0.8900 (tptm) cc_final: 0.8442 (tptm) REVERT: EB 1202 LYS cc_start: 0.8820 (tttm) cc_final: 0.8600 (tttm) REVERT: EB 1203 PHE cc_start: 0.8930 (t80) cc_final: 0.8595 (t80) REVERT: EB 1204 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7541 (tm-30) REVERT: FB 1304 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8725 (tm-30) REVERT: GB 102 LYS cc_start: 0.8918 (tptm) cc_final: 0.8503 (tptm) REVERT: HB 202 LYS cc_start: 0.8922 (tttm) cc_final: 0.8571 (mtpp) REVERT: IB 302 LYS cc_start: 0.8979 (tptp) cc_final: 0.8696 (tptp) REVERT: KB 1102 LYS cc_start: 0.8867 (tptm) cc_final: 0.8541 (tptm) REVERT: MB 1302 LYS cc_start: 0.8898 (tptp) cc_final: 0.8605 (tptp) REVERT: MB 1304 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8069 (tm-30) REVERT: i 5 PHE cc_start: 0.9097 (t80) cc_final: 0.8841 (t80) REVERT: NB 102 LYS cc_start: 0.8868 (tptm) cc_final: 0.8594 (tptm) REVERT: OB 204 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7439 (tm-30) REVERT: PB 302 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8304 (tptp) REVERT: PB 303 PHE cc_start: 0.8043 (t80) cc_final: 0.7588 (t80) REVERT: PB 304 GLU cc_start: 0.8725 (tm-30) cc_final: 0.7412 (pm20) REVERT: PB 305 PHE cc_start: 0.8723 (t80) cc_final: 0.7790 (t80) REVERT: PB 307 PHE cc_start: 0.8963 (t80) cc_final: 0.8708 (t80) REVERT: RB 1102 LYS cc_start: 0.8836 (tptm) cc_final: 0.8576 (tptm) REVERT: SB 1204 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7284 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8912 (tttt) cc_final: 0.8644 (tttt) REVERT: TB 1302 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8345 (tptp) REVERT: TB 1304 GLU cc_start: 0.8710 (tm-30) cc_final: 0.7418 (pm20) REVERT: TB 1305 PHE cc_start: 0.8692 (t80) cc_final: 0.7789 (t80) REVERT: TB 1307 PHE cc_start: 0.8955 (t80) cc_final: 0.8707 (t80) outliers start: 43 outliers final: 21 residues processed: 511 average time/residue: 0.1987 time to fit residues: 126.0377 Evaluate side-chains 532 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 503 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain Q residue 102 LYS Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain T residue 1006 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain V residue 1202 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain HA residue 302 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain RB residue 1105 PHE 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: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.097377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085388 restraints weight = 23780.059| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.04 r_work: 0.3227 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12564 Z= 0.130 Angle : 0.693 9.746 16272 Z= 0.330 Chirality : 0.032 0.110 1152 Planarity : 0.002 0.015 2160 Dihedral : 13.702 88.326 1448 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.55 % Allowed : 33.10 % Favored : 64.35 % 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: -5.07 (0.17), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.13), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHEgA1305 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12528) covalent geometry : angle 0.69296 / 0.33 (16272) hydrogen bonds : bond 0.01911 / 1.10 ( 278) hydrogen bonds : angle 5.79484 / 3.24 ( 786) Misc. bond : bond 0.00117 / 0.06 ( 36) *********************** 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 493 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 471 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8500 (mtmt) REVERT: J 104 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7866 (mm-30) REVERT: J 106 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8521 (tmmm) REVERT: K 206 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8686 (ttmm) REVERT: L 302 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8421 (ttmm) REVERT: L 304 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7470 (mm-30) REVERT: L 306 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8575 (ttpt) REVERT: N 1103 PHE cc_start: 0.8914 (m-80) cc_final: 0.8601 (m-80) REVERT: N 1104 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7317 (mm-30) REVERT: N 1106 LYS cc_start: 0.9006 (tmtm) cc_final: 0.8384 (tmtm) REVERT: B 4 GLU cc_start: 0.7656 (mp0) cc_final: 0.6709 (mp0) REVERT: Q 106 LYS cc_start: 0.8852 (tptm) cc_final: 0.8541 (tptm) REVERT: S 302 LYS cc_start: 0.9137 (mtpt) cc_final: 0.8624 (ttmm) REVERT: T 1006 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8435 (mtmt) REVERT: U 1106 LYS cc_start: 0.8876 (tptm) cc_final: 0.8598 (tptm) REVERT: W 1302 LYS cc_start: 0.9075 (mtpt) cc_final: 0.8475 (ttmm) REVERT: X 102 LYS cc_start: 0.8513 (ttpt) cc_final: 0.7684 (ttpp) REVERT: X 104 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7098 (mm-30) REVERT: X 106 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8429 (mmmt) REVERT: Y 203 PHE cc_start: 0.8824 (m-80) cc_final: 0.8589 (m-80) REVERT: Y 206 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8605 (ttmm) REVERT: Z 302 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8483 (ttpp) REVERT: Z 306 LYS cc_start: 0.8878 (tttt) cc_final: 0.8554 (mttt) REVERT: k 1102 LYS cc_start: 0.8478 (ttpt) cc_final: 0.7466 (ttpp) REVERT: k 1104 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7099 (mm-30) REVERT: k 1106 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8365 (mmmt) REVERT: m 1302 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8214 (ttmm) REVERT: m 1306 LYS cc_start: 0.8890 (tttt) cc_final: 0.8578 (mttt) REVERT: n 104 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7121 (mm-30) REVERT: r 1103 PHE cc_start: 0.8924 (m-80) cc_final: 0.8359 (m-80) REVERT: r 1104 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7466 (mm-30) REVERT: r 1106 LYS cc_start: 0.8803 (mmmm) cc_final: 0.8222 (mmmm) REVERT: s 1202 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8330 (mtpt) REVERT: E 6 LYS cc_start: 0.8674 (mtmt) cc_final: 0.7959 (mtmt) REVERT: u 102 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8022 (ttmm) REVERT: v 204 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7188 (tm-30) REVERT: v 206 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8352 (ttmm) REVERT: w 302 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8428 (ttmm) REVERT: w 304 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7585 (mm-30) REVERT: x 1006 LYS cc_start: 0.8638 (mtmt) cc_final: 0.7767 (mtmt) REVERT: y 1102 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8390 (ttmm) REVERT: y 1104 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8093 (mm-30) REVERT: 0 1302 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8435 (ttmm) REVERT: 0 1304 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7871 (mm-30) REVERT: 1 106 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8298 (tmmm) REVERT: 3 302 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8724 (ttmm) REVERT: 4 1004 GLU cc_start: 0.7819 (mp0) cc_final: 0.6908 (mp0) REVERT: 5 1106 LYS cc_start: 0.8949 (tmtm) cc_final: 0.8279 (tmtm) REVERT: 7 1302 LYS cc_start: 0.9196 (mtpp) cc_final: 0.8706 (ttmm) REVERT: G 4 GLU cc_start: 0.7943 (mp0) cc_final: 0.7355 (mp0) REVERT: 8 106 LYS cc_start: 0.8900 (tptm) cc_final: 0.8555 (tptm) REVERT: 9 204 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7268 (mt-10) REVERT: BA 1004 GLU cc_start: 0.7855 (mp0) cc_final: 0.7174 (mp0) REVERT: CA 1102 LYS cc_start: 0.9016 (ttpt) cc_final: 0.8652 (mtpt) REVERT: CA 1104 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8021 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8933 (tptm) cc_final: 0.8517 (tptm) REVERT: DA 1202 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8616 (mtpt) REVERT: EA 1306 LYS cc_start: 0.8960 (tttt) cc_final: 0.8707 (tttt) REVERT: FA 106 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8618 (mmmt) REVERT: HA 302 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8574 (ttmm) REVERT: JA 1102 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7966 (ttmm) REVERT: JA 1104 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7695 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8633 (mmmt) REVERT: KA 1202 LYS cc_start: 0.8995 (tttt) cc_final: 0.8693 (pttt) REVERT: LA 1302 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8564 (ttmm) REVERT: MA 102 LYS cc_start: 0.9205 (ttpt) cc_final: 0.8846 (ttpt) REVERT: MA 106 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8406 (mmmm) REVERT: NA 206 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8539 (ttmm) REVERT: OA 302 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8407 (ttmm) REVERT: OA 304 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7816 (mm-30) REVERT: OA 306 LYS cc_start: 0.8949 (tttt) cc_final: 0.8698 (mmmt) REVERT: PA 1004 GLU cc_start: 0.8317 (mp0) cc_final: 0.7715 (mp0) REVERT: QA 1102 LYS cc_start: 0.9185 (ttpt) cc_final: 0.8859 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8409 (mmmm) REVERT: RA 1206 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8610 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9015 (ttpt) cc_final: 0.8431 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7675 (mm-30) REVERT: UA 204 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7346 (tm-30) REVERT: VA 304 GLU cc_start: 0.8782 (tm-30) cc_final: 0.7697 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8173 (ttpt) REVERT: WA 1007 PHE cc_start: 0.9307 (t80) cc_final: 0.9026 (t80) REVERT: YA 1202 LYS cc_start: 0.8809 (tttm) cc_final: 0.8459 (tttm) REVERT: YA 1204 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7212 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.8792 (tm-30) cc_final: 0.7747 (tm-30) REVERT: b 2 LYS cc_start: 0.8806 (tppt) cc_final: 0.8294 (tppt) REVERT: b 4 GLU cc_start: 0.7972 (tp30) cc_final: 0.7648 (tp30) REVERT: b 5 PHE cc_start: 0.9057 (t80) cc_final: 0.8625 (t80) REVERT: aA 102 LYS cc_start: 0.8697 (tptm) cc_final: 0.8165 (tptm) REVERT: aA 103 PHE cc_start: 0.8439 (t80) cc_final: 0.7936 (t80) REVERT: cA 302 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8300 (tptp) REVERT: eA 1107 PHE cc_start: 0.9074 (t80) cc_final: 0.8817 (t80) REVERT: gA 1302 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8155 (tptp) REVERT: gA 1307 PHE cc_start: 0.8804 (t80) cc_final: 0.8404 (t80) REVERT: c 2 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8242 (tppt) REVERT: hA 103 PHE cc_start: 0.8596 (t80) cc_final: 0.8387 (t80) REVERT: iA 202 LYS cc_start: 0.8673 (tttm) cc_final: 0.8244 (mtpp) REVERT: iA 204 GLU cc_start: 0.7780 (tm-30) cc_final: 0.6571 (tm-30) REVERT: iA 206 LYS cc_start: 0.8534 (tttt) cc_final: 0.8244 (tttt) REVERT: jA 303 PHE cc_start: 0.8302 (t80) cc_final: 0.8090 (t80) REVERT: jA 306 LYS cc_start: 0.8707 (tptp) cc_final: 0.8209 (tptp) REVERT: kA 1002 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8038 (tppt) REVERT: lA 1103 PHE cc_start: 0.8639 (t80) cc_final: 0.8289 (t80) REVERT: mA 1204 GLU cc_start: 0.7680 (tm-30) cc_final: 0.6686 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8595 (tttt) cc_final: 0.8153 (tptt) REVERT: nA 1306 LYS cc_start: 0.8800 (tptp) cc_final: 0.8210 (tptp) REVERT: d 2 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8457 (tppt) REVERT: d 4 GLU cc_start: 0.8042 (tp30) cc_final: 0.7738 (tp30) REVERT: d 5 PHE cc_start: 0.8776 (t80) cc_final: 0.8084 (t80) REVERT: oA 102 LYS cc_start: 0.8703 (tptm) cc_final: 0.8352 (tptm) REVERT: oA 103 PHE cc_start: 0.8065 (t80) cc_final: 0.7570 (t80) REVERT: pA 202 LYS cc_start: 0.8696 (tttm) cc_final: 0.8366 (ttmm) REVERT: pA 204 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7490 (tp30) REVERT: sA 1102 LYS cc_start: 0.8686 (tptm) cc_final: 0.8332 (tptm) REVERT: sA 1103 PHE cc_start: 0.7992 (t80) cc_final: 0.7739 (t80) REVERT: tA 1202 LYS cc_start: 0.8660 (tttm) cc_final: 0.8347 (ttmm) REVERT: uA 1306 LYS cc_start: 0.8675 (tptp) cc_final: 0.8421 (tptp) REVERT: e 2 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8359 (tppt) REVERT: wA 202 LYS cc_start: 0.8778 (tttm) cc_final: 0.8324 (ttmm) REVERT: wA 204 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7430 (tm-30) REVERT: wA 206 LYS cc_start: 0.8615 (tttt) cc_final: 0.8166 (tttm) REVERT: xA 304 GLU cc_start: 0.8787 (tm-30) cc_final: 0.7745 (tm-30) REVERT: yA 1002 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8324 (tppt) REVERT: 1A 1304 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8393 (tm-30) REVERT: f 3 PHE cc_start: 0.9020 (t80) cc_final: 0.8780 (t80) REVERT: f 7 PHE cc_start: 0.9250 (t80) cc_final: 0.8653 (t80) REVERT: 2A 102 LYS cc_start: 0.8537 (tptm) cc_final: 0.8176 (tptm) REVERT: 5A 1002 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8379 (ttpt) REVERT: 5A 1003 PHE cc_start: 0.8962 (t80) cc_final: 0.8751 (t80) REVERT: 5A 1007 PHE cc_start: 0.9224 (t80) cc_final: 0.8653 (t80) REVERT: 6A 1102 LYS cc_start: 0.8545 (tptm) cc_final: 0.8103 (tptm) REVERT: 7A 1203 PHE cc_start: 0.8864 (t80) cc_final: 0.8658 (t80) REVERT: g 2 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8340 (ttpt) REVERT: 9A 102 LYS cc_start: 0.8861 (tptm) cc_final: 0.8389 (tptm) REVERT: 9A 107 PHE cc_start: 0.9035 (t80) cc_final: 0.8799 (t80) REVERT: AB 202 LYS cc_start: 0.8717 (tttm) cc_final: 0.8352 (mtpp) REVERT: AB 203 PHE cc_start: 0.8889 (t80) cc_final: 0.8605 (t80) REVERT: AB 204 GLU cc_start: 0.8003 (tm-30) cc_final: 0.6930 (tm-30) REVERT: CB 1002 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8207 (ttpt) REVERT: CB 1003 PHE cc_start: 0.9071 (t80) cc_final: 0.8860 (t80) REVERT: DB 1102 LYS cc_start: 0.8792 (tptm) cc_final: 0.8355 (tptm) REVERT: DB 1107 PHE cc_start: 0.9029 (t80) cc_final: 0.8776 (t80) REVERT: EB 1202 LYS cc_start: 0.8667 (tttm) cc_final: 0.8425 (tttm) REVERT: EB 1203 PHE cc_start: 0.8876 (t80) cc_final: 0.8666 (t80) REVERT: EB 1204 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7280 (tm-30) REVERT: FB 1304 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8125 (tm-30) REVERT: KB 1102 LYS cc_start: 0.8525 (tptm) cc_final: 0.8153 (tptm) REVERT: i 6 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8289 (tppt) REVERT: NB 102 LYS cc_start: 0.8634 (tptm) cc_final: 0.8390 (tptm) REVERT: OB 204 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7376 (tm-30) REVERT: PB 302 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8247 (tptp) REVERT: PB 303 PHE cc_start: 0.8019 (t80) cc_final: 0.7546 (t80) REVERT: PB 304 GLU cc_start: 0.8648 (tm-30) cc_final: 0.7420 (pm20) REVERT: PB 305 PHE cc_start: 0.8439 (t80) cc_final: 0.7528 (t80) REVERT: PB 307 PHE cc_start: 0.8768 (t80) cc_final: 0.8503 (t80) REVERT: QB 1002 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8068 (tppt) REVERT: SB 1206 LYS cc_start: 0.8755 (tttt) cc_final: 0.8491 (tttt) REVERT: TB 1302 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8108 (tptp) REVERT: TB 1304 GLU cc_start: 0.8615 (tm-30) cc_final: 0.7357 (pm20) REVERT: TB 1305 PHE cc_start: 0.8402 (t80) cc_final: 0.7491 (t80) REVERT: TB 1307 PHE cc_start: 0.8699 (t80) cc_final: 0.8414 (t80) outliers start: 22 outliers final: 9 residues processed: 479 average time/residue: 0.1876 time to fit residues: 111.7070 Evaluate side-chains 480 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 464 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain Q residue 102 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain PB residue 302 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 = 0.3534 r_free = 0.3534 target = 0.090648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079304 restraints weight = 25518.899| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.11 r_work: 0.3078 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.071 12564 Z= 0.711 Angle : 0.991 10.655 16272 Z= 0.460 Chirality : 0.050 0.158 1152 Planarity : 0.004 0.023 2160 Dihedral : 14.075 89.205 1448 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.36 % Allowed : 34.03 % Favored : 62.62 % 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: -5.25 (0.17), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.13), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.004 PHE8A1303 Details of bonding type rmsd/Z covalent geometry : bond 0.01578 / 0.71 (12528) covalent geometry : angle 0.99087 / 0.46 (16272) hydrogen bonds : bond 0.04198 / 2.37 ( 278) hydrogen bonds : angle 6.67244 / 3.75 ( 786) Misc. bond : bond 0.00237 / 0.12 ( 36) ********************** 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 535 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 506 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8261 (mtmt) REVERT: J 106 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8581 (tmmm) REVERT: K 206 LYS cc_start: 0.8978 (ttmm) cc_final: 0.8720 (ttmm) REVERT: L 306 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8762 (ttpt) REVERT: N 1104 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7595 (mm-30) REVERT: N 1106 LYS cc_start: 0.9040 (tmtm) cc_final: 0.8457 (tmtm) REVERT: Q 106 LYS cc_start: 0.8958 (tptm) cc_final: 0.8490 (tptm) REVERT: S 302 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8712 (ttmm) REVERT: U 1106 LYS cc_start: 0.8975 (tptm) cc_final: 0.8692 (tptm) REVERT: W 1302 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8474 (ttmm) REVERT: X 102 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8211 (ttmm) REVERT: X 104 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7459 (mm-30) REVERT: X 106 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8577 (mmmt) REVERT: Y 206 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8659 (ttmm) REVERT: Z 306 LYS cc_start: 0.9040 (tttt) cc_final: 0.8765 (mttt) REVERT: k 1102 LYS cc_start: 0.8620 (ttpt) cc_final: 0.7750 (ttpp) REVERT: k 1104 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7252 (mm-30) REVERT: k 1106 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8518 (mmmt) REVERT: l 1206 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8677 (ttmm) REVERT: m 1302 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8908 (ttmm) REVERT: m 1306 LYS cc_start: 0.9040 (tttt) cc_final: 0.8730 (mttt) REVERT: n 104 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7724 (mm-30) REVERT: q 1002 LYS cc_start: 0.7155 (tttt) cc_final: 0.6871 (tttt) REVERT: r 1102 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7727 (ttpp) REVERT: r 1104 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7674 (mm-30) REVERT: r 1106 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8418 (mmmm) REVERT: t 1306 LYS cc_start: 0.9033 (tttt) cc_final: 0.8770 (tttm) REVERT: E 6 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8144 (mtmt) REVERT: u 102 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8541 (ttmm) REVERT: u 104 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8127 (mm-30) REVERT: v 204 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7392 (tm-30) REVERT: v 206 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8448 (ttmm) REVERT: w 302 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8672 (ttmm) REVERT: w 304 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8043 (mm-30) REVERT: x 1006 LYS cc_start: 0.8737 (mtmt) cc_final: 0.7865 (mtmt) REVERT: y 1102 LYS cc_start: 0.8968 (ttpt) cc_final: 0.8511 (ttmm) REVERT: y 1104 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8106 (mm-30) REVERT: z 1206 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8669 (ttmm) REVERT: 0 1302 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8645 (ttmm) REVERT: 1 106 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8400 (tmmm) REVERT: 4 1004 GLU cc_start: 0.7985 (mp0) cc_final: 0.7075 (mp0) REVERT: 5 1106 LYS cc_start: 0.8961 (tmtm) cc_final: 0.8300 (tmtm) REVERT: 7 1302 LYS cc_start: 0.9179 (mtpp) cc_final: 0.8896 (ttmm) REVERT: G 4 GLU cc_start: 0.7984 (mp0) cc_final: 0.7318 (mp0) REVERT: 8 106 LYS cc_start: 0.8933 (tptm) cc_final: 0.8603 (tptm) REVERT: BA 1004 GLU cc_start: 0.7926 (mp0) cc_final: 0.7232 (mp0) REVERT: CA 1102 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8769 (mtpt) REVERT: CA 1104 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8070 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8940 (tptm) cc_final: 0.8636 (tptm) REVERT: EA 1306 LYS cc_start: 0.9091 (tttt) cc_final: 0.8838 (tttt) REVERT: FA 106 LYS cc_start: 0.9109 (mmmt) cc_final: 0.8627 (mmmt) REVERT: HA 302 LYS cc_start: 0.9365 (mtpt) cc_final: 0.8763 (ttmm) REVERT: HA 304 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8162 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7949 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8717 (mmmt) REVERT: LA 1302 LYS cc_start: 0.9360 (mtpt) cc_final: 0.8897 (ttmm) REVERT: MA 102 LYS cc_start: 0.9220 (ttpt) cc_final: 0.8944 (ttpt) REVERT: MA 106 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8501 (mmmm) REVERT: NA 206 LYS cc_start: 0.8992 (ttmm) cc_final: 0.8729 (ttmm) REVERT: OA 302 LYS cc_start: 0.9257 (ttpt) cc_final: 0.8707 (ttmm) REVERT: OA 304 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7989 (mm-30) REVERT: OA 306 LYS cc_start: 0.9063 (tttt) cc_final: 0.8826 (mmmt) REVERT: PA 1004 GLU cc_start: 0.8375 (mp0) cc_final: 0.7759 (mp0) REVERT: QA 1102 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8901 (ttpt) REVERT: QA 1106 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8522 (mmmm) REVERT: SA 1302 LYS cc_start: 0.9189 (ttpt) cc_final: 0.8557 (ttmm) REVERT: SA 1304 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7841 (mm-30) REVERT: TA 102 LYS cc_start: 0.8951 (tptm) cc_final: 0.8539 (tptm) REVERT: TA 103 PHE cc_start: 0.8698 (t80) cc_final: 0.8490 (t80) REVERT: UA 202 LYS cc_start: 0.9030 (tttm) cc_final: 0.8521 (mtpp) REVERT: UA 204 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7020 (tm-30) REVERT: VA 302 LYS cc_start: 0.8652 (tptp) cc_final: 0.8310 (tptp) REVERT: VA 304 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8308 (tm-30) REVERT: WA 1002 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8519 (ttpt) REVERT: WA 1007 PHE cc_start: 0.9273 (t80) cc_final: 0.8927 (t80) REVERT: YA 1202 LYS cc_start: 0.9006 (tttm) cc_final: 0.8659 (tttm) REVERT: YA 1204 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7421 (tm-30) REVERT: ZA 1302 LYS cc_start: 0.8656 (tptp) cc_final: 0.8310 (tptp) REVERT: ZA 1304 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8444 (tm-30) REVERT: b 2 LYS cc_start: 0.9046 (tppt) cc_final: 0.8644 (tppt) REVERT: b 4 GLU cc_start: 0.8077 (tp30) cc_final: 0.7742 (tp30) REVERT: b 5 PHE cc_start: 0.9006 (t80) cc_final: 0.8663 (t80) REVERT: aA 102 LYS cc_start: 0.8935 (tptm) cc_final: 0.8391 (tptm) REVERT: cA 302 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8542 (tptp) REVERT: cA 304 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8058 (tm-30) REVERT: cA 306 LYS cc_start: 0.8533 (tptp) cc_final: 0.8300 (tptp) REVERT: gA 1302 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8432 (tptp) REVERT: hA 103 PHE cc_start: 0.8789 (t80) cc_final: 0.8324 (t80) REVERT: iA 202 LYS cc_start: 0.8864 (tttm) cc_final: 0.8478 (mtpp) REVERT: iA 204 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7213 (tm-30) REVERT: iA 206 LYS cc_start: 0.8844 (tttt) cc_final: 0.8510 (tttt) REVERT: jA 306 LYS cc_start: 0.8736 (tptp) cc_final: 0.8226 (tptp) REVERT: kA 1002 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8565 (ttpt) REVERT: lA 1103 PHE cc_start: 0.8713 (t80) cc_final: 0.8439 (t80) REVERT: mA 1204 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7221 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8763 (tttt) cc_final: 0.8327 (tptt) REVERT: nA 1306 LYS cc_start: 0.8841 (tptp) cc_final: 0.8339 (tptp) REVERT: d 2 LYS cc_start: 0.9225 (ttpt) cc_final: 0.8894 (tppt) REVERT: d 4 GLU cc_start: 0.8135 (tp30) cc_final: 0.7871 (tp30) REVERT: oA 102 LYS cc_start: 0.8962 (tptm) cc_final: 0.8722 (tptm) REVERT: oA 103 PHE cc_start: 0.8303 (t80) cc_final: 0.7264 (t80) REVERT: pA 202 LYS cc_start: 0.8866 (tttm) cc_final: 0.8471 (mtpp) REVERT: pA 204 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7236 (tp30) REVERT: qA 302 LYS cc_start: 0.8608 (tptp) cc_final: 0.8226 (tptp) REVERT: qA 303 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7044 (t80) REVERT: rA 1002 LYS cc_start: 0.9203 (ttpt) cc_final: 0.8693 (tppt) REVERT: sA 1102 LYS cc_start: 0.8942 (tptm) cc_final: 0.8679 (tptm) REVERT: sA 1103 PHE cc_start: 0.8302 (t80) cc_final: 0.7762 (t80) REVERT: tA 1204 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7449 (tp30) REVERT: uA 1302 LYS cc_start: 0.8612 (tptp) cc_final: 0.8214 (tptp) REVERT: uA 1303 PHE cc_start: 0.7925 (t80) cc_final: 0.6920 (t80) REVERT: uA 1306 LYS cc_start: 0.8762 (tptp) cc_final: 0.8543 (tptp) REVERT: e 2 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8741 (tppt) REVERT: vA 102 LYS cc_start: 0.8871 (tptm) cc_final: 0.8441 (tptm) REVERT: wA 202 LYS cc_start: 0.8906 (tttm) cc_final: 0.8374 (ttmm) REVERT: wA 204 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7568 (tm-30) REVERT: wA 206 LYS cc_start: 0.8747 (tttt) cc_final: 0.8314 (tttm) REVERT: xA 304 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8439 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8519 (tm-30) REVERT: 2A 102 LYS cc_start: 0.8876 (tptm) cc_final: 0.8260 (tptm) REVERT: 4A 304 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8157 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8575 (ttpt) REVERT: 6A 1103 PHE cc_start: 0.8259 (t80) cc_final: 0.7989 (t80) REVERT: g 4 GLU cc_start: 0.8375 (tp30) cc_final: 0.7920 (tp30) REVERT: g 5 PHE cc_start: 0.8875 (t80) cc_final: 0.8398 (t80) REVERT: 9A 102 LYS cc_start: 0.9048 (tptm) cc_final: 0.8670 (tptm) REVERT: AB 202 LYS cc_start: 0.8834 (tttm) cc_final: 0.8491 (mtpp) REVERT: AB 203 PHE cc_start: 0.8941 (t80) cc_final: 0.8594 (t80) REVERT: AB 204 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7585 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8317 (tp30) cc_final: 0.7777 (tp30) REVERT: DB 1102 LYS cc_start: 0.8999 (tptm) cc_final: 0.8590 (tptm) REVERT: DB 1103 PHE cc_start: 0.8495 (t80) cc_final: 0.7965 (t80) REVERT: EB 1202 LYS cc_start: 0.8801 (tttm) cc_final: 0.8575 (tttm) REVERT: EB 1203 PHE cc_start: 0.8918 (t80) cc_final: 0.8600 (t80) REVERT: EB 1204 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7648 (tm-30) REVERT: FB 1304 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8709 (tm-30) REVERT: GB 102 LYS cc_start: 0.8937 (tptm) cc_final: 0.8511 (tptm) REVERT: HB 202 LYS cc_start: 0.8920 (tttm) cc_final: 0.8642 (mmmm) REVERT: IB 302 LYS cc_start: 0.8925 (tptp) cc_final: 0.8674 (tptp) REVERT: KB 1102 LYS cc_start: 0.8895 (tptm) cc_final: 0.8562 (tptm) REVERT: MB 1302 LYS cc_start: 0.8880 (tptp) cc_final: 0.8628 (tptp) REVERT: MB 1304 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8872 (tm-30) REVERT: NB 102 LYS cc_start: 0.8860 (tptm) cc_final: 0.8607 (tptm) REVERT: OB 204 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7208 (tm-30) REVERT: PB 302 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8297 (tptp) REVERT: PB 303 PHE cc_start: 0.8068 (t80) cc_final: 0.7526 (t80) REVERT: PB 304 GLU cc_start: 0.8751 (tm-30) cc_final: 0.7425 (pm20) REVERT: PB 305 PHE cc_start: 0.8749 (t80) cc_final: 0.7766 (t80) REVERT: PB 307 PHE cc_start: 0.8954 (t80) cc_final: 0.8696 (t80) REVERT: SB 1204 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7251 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8909 (tttt) cc_final: 0.8653 (tttt) REVERT: TB 1302 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8315 (tptp) REVERT: TB 1304 GLU cc_start: 0.8668 (tm-30) cc_final: 0.7478 (pm20) REVERT: TB 1305 PHE cc_start: 0.8699 (t80) cc_final: 0.7817 (t80) REVERT: TB 1307 PHE cc_start: 0.8938 (t80) cc_final: 0.8679 (t80) outliers start: 29 outliers final: 15 residues processed: 509 average time/residue: 0.2013 time to fit residues: 126.7726 Evaluate side-chains 527 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 504 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain Q residue 102 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain v residue 202 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain PB residue 302 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: 0.8980 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 = 0.3668 r_free = 0.3668 target = 0.097378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085267 restraints weight = 24047.080| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.10 r_work: 0.3216 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12564 Z= 0.146 Angle : 0.735 9.893 16272 Z= 0.350 Chirality : 0.033 0.117 1152 Planarity : 0.002 0.016 2160 Dihedral : 13.593 86.781 1448 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.85 % Allowed : 35.76 % Favored : 62.38 % 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: -5.00 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.13), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.002 PHEIB 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (12528) covalent geometry : angle 0.73484 / 0.35 (16272) hydrogen bonds : bond 0.01996 / 1.13 ( 278) hydrogen bonds : angle 5.89629 / 3.30 ( 786) Misc. bond : bond 0.00154 / 0.08 ( 36) =============================================================================== Job complete usr+sys time: 2688.09 seconds wall clock time: 47 minutes 0.41 seconds (2820.41 seconds total)