Starting phenix.real_space_refine on Wed Jul 30 06:14:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqg_23485/07_2025/7lqg_23485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqg_23485/07_2025/7lqg_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_23485/07_2025/7lqg_23485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqg_23485/07_2025/7lqg_23485.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqg_23485/07_2025/7lqg_23485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqg_23485/07_2025/7lqg_23485.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.030 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 144 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "UA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "VA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "WA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "XA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "aA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "cA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "dA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "eA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "fA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "gA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "hA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "iA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "jA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "kA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "lA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "mA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "nA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "oA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "pA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "qA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "rA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "sA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "tA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "uA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "vA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "wA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "xA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "yA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "zA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.73, per 1000 atoms: 0.64 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: 2.85 Conformation dependent library (CDL) restraints added in 588.1 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 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: 3.12 Time building geometry restraints manager: 3.30 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: 2.970 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 27.070 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.210 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 31.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEUA 205 Details of bonding type rmsd hydrogen bonds : bond 0.31156 ( 278) hydrogen bonds : angle 15.44566 ( 786) covalent geometry : bond 0.01603 (12528) covalent geometry : angle 1.41747 (16272) Misc. bond : bond 0.38093 ( 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 : 1.167 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: 0.6990 (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: 0.7387 (mp0) cc_final: 0.6353 (pm20) REVERT: T 1004 GLU cc_start: 0.7416 (mp0) cc_final: 0.6368 (pm20) REVERT: W 1302 LYS cc_start: 0.8672 (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: 0.8389 (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: 0.8400 (tttt) REVERT: n 104 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6300 (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: 0.6343 (mm-30) REVERT: t 1306 LYS cc_start: 0.8723 (tttt) cc_final: 0.8465 (tttt) REVERT: E 4 GLU cc_start: 0.7451 (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: 0.8440 (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: 0.8359 (tttt) REVERT: x 1004 GLU cc_start: 0.7477 (mp0) cc_final: 0.7137 (mp0) REVERT: x 1006 LYS cc_start: 0.8388 (mtmt) cc_final: 0.8120 (mtmt) REVERT: y 1102 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8447 (mtpp) REVERT: y 1104 GLU cc_start: 0.7536 (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: 0.7496 (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: 0.7394 (mp0) cc_final: 0.6855 (pm20) REVERT: 2 206 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8190 (ttmm) REVERT: 3 306 LYS cc_start: 0.8751 (tttt) cc_final: 0.8443 (tttt) REVERT: 4 1004 GLU cc_start: 0.7422 (mp0) cc_final: 0.6862 (pm20) REVERT: 6 1206 LYS cc_start: 0.8447 (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: 0.7500 (mp0) cc_final: 0.6448 (mp0) REVERT: 9 202 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8271 (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: 0.7518 (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: 0.6823 (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: 0.7418 (mp0) REVERT: OA 306 LYS cc_start: 0.8620 (tttt) cc_final: 0.8202 (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: 0.8225 (tttt) REVERT: a 3 PHE cc_start: 0.9235 (t80) cc_final: 0.9009 (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: 0.9235 (t80) cc_final: 0.9018 (t80) REVERT: WA 1005 PHE cc_start: 0.9054 (t80) cc_final: 0.8645 (t80) REVERT: WA 1007 PHE cc_start: 0.9255 (t80) cc_final: 0.8980 (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: 0.8423 (tttm) REVERT: YA 1206 LYS cc_start: 0.8893 (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: 0.8364 (tttm) REVERT: hA 103 PHE cc_start: 0.8994 (t80) cc_final: 0.8567 (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: 0.8388 (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: 0.7272 (tm-30) cc_final: 0.6925 (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: 0.8378 (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: 0.8262 (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: 0.8278 (t80) REVERT: 3A 202 LYS cc_start: 0.8895 (tttm) cc_final: 0.8665 (tttm) REVERT: 3A 206 LYS cc_start: 0.8908 (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: 0.9117 (t80) cc_final: 0.8615 (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: 0.8771 (tm-30) cc_final: 0.8244 (tm-30) REVERT: g 7 PHE cc_start: 0.9090 (t80) cc_final: 0.8841 (t80) REVERT: 9A 102 LYS cc_start: 0.8870 (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: 0.8841 (t80) REVERT: CB 1007 PHE cc_start: 0.9095 (t80) cc_final: 0.8865 (t80) REVERT: DB 1106 LYS cc_start: 0.8873 (tttp) cc_final: 0.8662 (tttp) REVERT: DB 1107 PHE cc_start: 0.8889 (t80) cc_final: 0.8278 (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: 0.8280 (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: 0.8274 (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: 0.8770 (tptp) cc_final: 0.8563 (tptp) REVERT: KB 1102 LYS cc_start: 0.8919 (tptm) cc_final: 0.8618 (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: 0.7337 (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: 0.8157 (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: 0.8487 (tttt) REVERT: TB 1305 PHE cc_start: 0.8512 (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: 0.4392 time to fit residues: 283.9845 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 : 1.170 ------------------------------------------------------------------------------- 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: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.056794 restraints weight = 34505.965| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.14 r_work: 0.2589 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.317 12564 Z= 4.871 Angle : 3.952 31.986 16272 Z= 1.756 Chirality : 0.299 0.846 1152 Planarity : 0.018 0.055 2160 Dihedral : 21.237 78.266 1786 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 102.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.72 % Favored : 86.28 % Rotamer: Outliers : 13.66 % Allowed : 20.25 % Favored : 66.09 % Cbeta Deviations : 12.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.15 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.117 0.018 PHE G 7 Details of bonding type rmsd hydrogen bonds : bond 0.18865 ( 278) hydrogen bonds : angle 9.26061 ( 786) covalent geometry : bond 0.10912 (12528) covalent geometry : angle 3.95178 (16272) Misc. bond : bond 0.01102 ( 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: 118 poor density : 447 time to evaluate : 1.260 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: J 106 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8898 (mmmm) REVERT: L 304 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8582 (mm-30) REVERT: N 1106 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8861 (mmmm) REVERT: O 1204 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8645 (mt-10) REVERT: P 1304 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8573 (mm-30) REVERT: B 6 LYS cc_start: 0.9306 (mtmt) cc_final: 0.8964 (mtmt) REVERT: Q 106 LYS cc_start: 0.9104 (tptm) cc_final: 0.8815 (tptm) REVERT: R 202 LYS cc_start: 0.9423 (mtpt) cc_final: 0.9185 (mtpt) REVERT: R 204 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8222 (mt-10) REVERT: T 1006 LYS cc_start: 0.9292 (mtmt) cc_final: 0.8916 (mtmt) REVERT: U 1106 LYS cc_start: 0.9098 (tptm) cc_final: 0.8736 (tptm) REVERT: V 1202 LYS cc_start: 0.9366 (mtpt) cc_final: 0.9116 (mtpt) REVERT: V 1204 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8206 (mt-10) REVERT: W 1302 LYS cc_start: 0.9436 (ttpt) cc_final: 0.9064 (ttmm) REVERT: C 6 LYS cc_start: 0.9299 (mtmt) cc_final: 0.8947 (mtmt) REVERT: X 106 LYS cc_start: 0.9143 (mmmm) cc_final: 0.8839 (mmmm) REVERT: j 1006 LYS cc_start: 0.9279 (mtmt) cc_final: 0.8943 (mtmt) REVERT: k 1106 LYS cc_start: 0.9161 (mmmm) cc_final: 0.8814 (mmmm) REVERT: l 1202 LYS cc_start: 0.9331 (mtpt) cc_final: 0.9077 (mmmm) REVERT: m 1302 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9095 (ttpt) REVERT: n 106 LYS cc_start: 0.9332 (mmmm) cc_final: 0.8989 (mmmm) REVERT: o 202 LYS cc_start: 0.9301 (mtpt) cc_final: 0.8862 (mmmm) REVERT: p 302 LYS cc_start: 0.9412 (ttpt) cc_final: 0.8889 (ttpp) REVERT: p 304 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8006 (mm-30) REVERT: r 1106 LYS cc_start: 0.9308 (mmmm) cc_final: 0.8960 (mmmm) REVERT: t 1302 LYS cc_start: 0.9387 (ttpt) cc_final: 0.9118 (ttpp) REVERT: t 1304 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8034 (mm-30) REVERT: u 102 LYS cc_start: 0.9262 (ttpt) cc_final: 0.8744 (ttmm) REVERT: u 104 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8127 (mm-30) REVERT: u 106 LYS cc_start: 0.9314 (tptm) cc_final: 0.8959 (tptm) REVERT: w 302 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9061 (ttmm) REVERT: x 1006 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8573 (mtmt) REVERT: y 1102 LYS cc_start: 0.9255 (ttpt) cc_final: 0.8711 (ttmm) REVERT: y 1104 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8134 (mm-30) REVERT: y 1106 LYS cc_start: 0.9251 (tptm) cc_final: 0.8873 (tptm) REVERT: 0 1302 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9105 (ttmm) REVERT: F 4 GLU cc_start: 0.8370 (mp0) cc_final: 0.7585 (mp0) REVERT: F 6 LYS cc_start: 0.9205 (mtmt) cc_final: 0.8971 (mtmt) REVERT: 2 202 LYS cc_start: 0.9421 (mtpt) cc_final: 0.9135 (mtpt) REVERT: 2 204 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8181 (mt-10) REVERT: 4 1004 GLU cc_start: 0.8362 (mp0) cc_final: 0.7575 (mp0) REVERT: 4 1006 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8972 (mtmt) REVERT: 6 1202 LYS cc_start: 0.9414 (mtpt) cc_final: 0.9117 (mtpt) REVERT: G 6 LYS cc_start: 0.9179 (mtmt) cc_final: 0.8844 (mtmt) REVERT: 8 106 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8724 (mmmm) REVERT: BA 1006 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8736 (mtmt) REVERT: CA 1106 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8731 (mmmm) REVERT: EA 1304 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8399 (mm-30) REVERT: FA 104 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8058 (mm-30) REVERT: FA 106 LYS cc_start: 0.9306 (mmmm) cc_final: 0.9062 (mmmm) REVERT: HA 304 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8044 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8082 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9304 (mmmm) cc_final: 0.9056 (mmmm) REVERT: I 6 LYS cc_start: 0.9227 (mtmt) cc_final: 0.8541 (mtmt) REVERT: MA 102 LYS cc_start: 0.9256 (ttpt) cc_final: 0.8823 (mmtt) REVERT: OA 302 LYS cc_start: 0.9459 (ttpt) cc_final: 0.9016 (tptt) REVERT: OA 304 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8545 (mm-30) REVERT: PA 1006 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8423 (mtmt) REVERT: QA 1102 LYS cc_start: 0.9275 (ttpt) cc_final: 0.8785 (tptt) REVERT: SA 1302 LYS cc_start: 0.9467 (ttpt) cc_final: 0.8901 (mmmt) REVERT: SA 1304 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8532 (mm-30) REVERT: a 4 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8640 (tp30) REVERT: TA 104 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8525 (tm-30) REVERT: UA 204 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8050 (tp30) REVERT: WA 1004 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8631 (tp30) REVERT: XA 1104 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8478 (tm-30) REVERT: YA 1204 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7783 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8349 (tm-30) REVERT: ZA 1307 PHE cc_start: 0.9327 (t80) cc_final: 0.9111 (t80) REVERT: bA 202 LYS cc_start: 0.9347 (tttm) cc_final: 0.9073 (ttmm) REVERT: bA 204 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8012 (tm-30) REVERT: cA 304 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8353 (tm-30) REVERT: fA 1204 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7971 (tm-30) REVERT: gA 1304 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8283 (tm-30) REVERT: hA 102 LYS cc_start: 0.9449 (tptm) cc_final: 0.9227 (tptm) REVERT: hA 103 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.9196 (t80) REVERT: iA 202 LYS cc_start: 0.9368 (tttm) cc_final: 0.8942 (ttmm) REVERT: iA 204 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7906 (tm-30) REVERT: iA 206 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9023 (tttt) REVERT: jA 306 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8641 (ttpp) REVERT: kA 1002 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8967 (ttpt) REVERT: lA 1102 LYS cc_start: 0.9441 (tptm) cc_final: 0.9219 (tptm) REVERT: lA 1103 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9179 (t80) REVERT: mA 1204 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7798 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8866 (tttm) REVERT: nA 1306 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8637 (ttpp) REVERT: pA 204 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8466 (tp30) REVERT: qA 304 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8305 (tm-30) REVERT: sA 1103 PHE cc_start: 0.9301 (t80) cc_final: 0.8942 (t80) REVERT: tA 1204 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8302 (tp30) REVERT: uA 1304 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8315 (tm-30) REVERT: e 4 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: vA 104 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8024 (tm-30) REVERT: wA 202 LYS cc_start: 0.9310 (tttm) cc_final: 0.8775 (ttmm) REVERT: wA 204 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8089 (tm-30) REVERT: xA 302 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8845 (tptp) REVERT: xA 304 GLU cc_start: 0.9253 (tm-30) cc_final: 0.7985 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8289 (tp30) REVERT: zA 1102 LYS cc_start: 0.9373 (tptm) cc_final: 0.9141 (tptm) REVERT: 0A 1202 LYS cc_start: 0.9243 (tttm) cc_final: 0.8730 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7562 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8679 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9256 (tm-30) cc_final: 0.7978 (tm-30) REVERT: f 2 LYS cc_start: 0.9257 (ptpt) cc_final: 0.9029 (ptpt) REVERT: 8A 1304 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8600 (tm-30) REVERT: g 4 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8333 (tp30) REVERT: g 6 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8869 (ttpt) REVERT: 9A 102 LYS cc_start: 0.9366 (tptm) cc_final: 0.9099 (tptm) REVERT: 9A 106 LYS cc_start: 0.9166 (tttp) cc_final: 0.8886 (tttm) REVERT: AB 202 LYS cc_start: 0.9298 (tttm) cc_final: 0.8947 (ttmm) REVERT: AB 204 GLU cc_start: 0.8582 (tm-30) cc_final: 0.7995 (tm-30) REVERT: BB 306 LYS cc_start: 0.9212 (tptp) cc_final: 0.8960 (tptp) REVERT: CB 1004 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8517 (tp30) REVERT: DB 1102 LYS cc_start: 0.9361 (tptm) cc_final: 0.9117 (tptm) REVERT: EB 1204 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7959 (tm-30) REVERT: FB 1306 LYS cc_start: 0.9200 (tptp) cc_final: 0.8991 (tptp) REVERT: h 4 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: GB 102 LYS cc_start: 0.9310 (tptm) cc_final: 0.8977 (tptm) REVERT: HB 202 LYS cc_start: 0.9358 (tttm) cc_final: 0.8997 (ttmm) REVERT: JB 1004 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: KB 1102 LYS cc_start: 0.9290 (tptm) cc_final: 0.8950 (tptm) REVERT: i 4 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: i 5 PHE cc_start: 0.9307 (t80) cc_final: 0.8669 (t80) REVERT: OB 204 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8226 (tm-30) REVERT: OB 206 LYS cc_start: 0.9353 (tttt) cc_final: 0.9109 (tttm) REVERT: PB 307 PHE cc_start: 0.9474 (t80) cc_final: 0.9241 (t80) REVERT: QB 1002 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9043 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9290 (t80) cc_final: 0.8921 (t80) REVERT: SB 1204 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8172 (tm-30) REVERT: TB 1307 PHE cc_start: 0.9471 (t80) cc_final: 0.9250 (t80) outliers start: 118 outliers final: 67 residues processed: 490 average time/residue: 0.5864 time to fit residues: 349.2339 Evaluate side-chains 540 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 447 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain m residue 1302 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1306 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.059920 restraints weight = 33927.509| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.10 r_work: 0.2663 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.312 12564 Z= 4.873 Angle : 4.147 65.849 16272 Z= 1.829 Chirality : 0.298 0.861 1152 Planarity : 0.017 0.052 2160 Dihedral : 20.551 89.025 1530 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 106.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Rotamer: Outliers : 18.40 % Allowed : 22.69 % Favored : 58.91 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.97 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.54 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.105 0.018 PHE9A 103 Details of bonding type rmsd hydrogen bonds : bond 0.19338 ( 278) hydrogen bonds : angle 9.07390 ( 786) covalent geometry : bond 0.10946 (12528) covalent geometry : angle 4.14724 (16272) Misc. bond : bond 0.01037 ( 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 597 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 438 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8151 (mm-30) REVERT: J 106 LYS cc_start: 0.9303 (mmmm) cc_final: 0.8882 (mmmm) REVERT: L 304 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8633 (mm-30) REVERT: N 1106 LYS cc_start: 0.9272 (mmmm) cc_final: 0.8873 (mmmm) REVERT: O 1204 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8618 (mt-10) REVERT: P 1304 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8643 (mm-30) REVERT: B 4 GLU cc_start: 0.8504 (mp0) cc_final: 0.7951 (mp0) REVERT: B 6 LYS cc_start: 0.9263 (mtmt) cc_final: 0.8985 (mtmt) REVERT: Q 106 LYS cc_start: 0.9196 (tptm) cc_final: 0.8702 (tptm) REVERT: R 202 LYS cc_start: 0.9401 (mtpt) cc_final: 0.9089 (mtpt) REVERT: S 302 LYS cc_start: 0.9487 (ttpt) cc_final: 0.9143 (ttmm) REVERT: T 1004 GLU cc_start: 0.8618 (mp0) cc_final: 0.7954 (mp0) REVERT: T 1006 LYS cc_start: 0.9249 (mtmt) cc_final: 0.8967 (mtmt) REVERT: U 1106 LYS cc_start: 0.9183 (tptm) cc_final: 0.8687 (tptm) REVERT: V 1202 LYS cc_start: 0.9370 (mtpt) cc_final: 0.9123 (mtpt) REVERT: W 1302 LYS cc_start: 0.9480 (ttpt) cc_final: 0.9133 (ttmm) REVERT: C 4 GLU cc_start: 0.7933 (mp0) cc_final: 0.7357 (mp0) REVERT: C 6 LYS cc_start: 0.9242 (mtmt) cc_final: 0.8857 (mtmt) REVERT: X 106 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8963 (mmmm) REVERT: Z 302 LYS cc_start: 0.9482 (ttpt) cc_final: 0.9076 (ttmm) REVERT: j 1004 GLU cc_start: 0.7807 (mp0) cc_final: 0.7564 (mp0) REVERT: j 1006 LYS cc_start: 0.9223 (mtmt) cc_final: 0.8908 (mtmt) REVERT: k 1106 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8965 (mmmm) REVERT: D 4 GLU cc_start: 0.8521 (mp0) cc_final: 0.7563 (mp0) REVERT: n 104 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8039 (mm-30) REVERT: n 106 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8912 (mmmm) REVERT: r 1104 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7947 (mm-30) REVERT: r 1106 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8891 (mmmm) REVERT: t 1302 LYS cc_start: 0.9402 (ttpt) cc_final: 0.9104 (ttpp) REVERT: E 6 LYS cc_start: 0.9086 (mtmt) cc_final: 0.8840 (mtmt) REVERT: u 102 LYS cc_start: 0.9239 (ttpt) cc_final: 0.8689 (ttmm) REVERT: u 104 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7909 (mm-30) REVERT: u 106 LYS cc_start: 0.9301 (tptm) cc_final: 0.8911 (tptm) REVERT: w 302 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9053 (ttmm) REVERT: x 1006 LYS cc_start: 0.9121 (mtmt) cc_final: 0.8829 (mtmt) REVERT: y 1104 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7955 (mm-30) REVERT: y 1106 LYS cc_start: 0.9259 (tptm) cc_final: 0.8866 (tptm) REVERT: 0 1302 LYS cc_start: 0.9404 (mtmt) cc_final: 0.9115 (ttmm) REVERT: F 4 GLU cc_start: 0.8359 (mp0) cc_final: 0.7811 (mp0) REVERT: F 6 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8997 (mtmt) REVERT: 1 104 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7889 (mm-30) REVERT: 1 106 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8978 (mmmm) REVERT: 2 202 LYS cc_start: 0.9399 (mtpt) cc_final: 0.9067 (mtpt) REVERT: 4 1004 GLU cc_start: 0.8400 (mp0) cc_final: 0.7707 (mp0) REVERT: 5 1106 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8948 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9379 (mtpt) cc_final: 0.9042 (mtpt) REVERT: G 4 GLU cc_start: 0.8295 (mp0) cc_final: 0.7075 (mp0) REVERT: G 6 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8798 (mtmt) REVERT: 8 106 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8698 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8320 (mp0) cc_final: 0.7187 (mp0) REVERT: BA 1006 LYS cc_start: 0.9114 (mtmt) cc_final: 0.8772 (mtmt) REVERT: CA 1106 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8681 (mmmm) REVERT: FA 104 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8105 (mm-30) REVERT: FA 106 LYS cc_start: 0.9269 (mmmm) cc_final: 0.9014 (mmmm) REVERT: GA 202 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8876 (mtpt) REVERT: JA 1104 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7954 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9004 (mmmm) REVERT: I 6 LYS cc_start: 0.9224 (mtmt) cc_final: 0.8616 (mtmt) REVERT: OA 302 LYS cc_start: 0.9420 (ttpt) cc_final: 0.9011 (tptt) REVERT: OA 304 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8546 (mm-30) REVERT: PA 1006 LYS cc_start: 0.9192 (mtmt) cc_final: 0.8529 (mtmt) REVERT: SA 1302 LYS cc_start: 0.9432 (ttpt) cc_final: 0.8874 (mmmt) REVERT: a 4 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8660 (tp30) REVERT: UA 202 LYS cc_start: 0.9432 (tttm) cc_final: 0.9217 (tttm) REVERT: UA 204 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8021 (tp30) REVERT: VA 304 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8719 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8583 (tp30) REVERT: YA 1204 GLU cc_start: 0.8242 (tm-30) cc_final: 0.8013 (tp30) REVERT: ZA 1304 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8498 (tm-30) REVERT: aA 105 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9048 (t80) REVERT: bA 202 LYS cc_start: 0.9318 (tttm) cc_final: 0.9024 (ttmm) REVERT: cA 304 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8521 (tm-30) REVERT: cA 305 PHE cc_start: 0.9285 (t80) cc_final: 0.9035 (t80) REVERT: eA 1105 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.9091 (t80) REVERT: eA 1106 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8813 (ptmm) REVERT: fA 1204 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7797 (tp30) REVERT: gA 1304 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8683 (tm-30) REVERT: hA 102 LYS cc_start: 0.9413 (tptm) cc_final: 0.9208 (tptm) REVERT: iA 202 LYS cc_start: 0.9349 (tttm) cc_final: 0.9121 (tttm) REVERT: iA 204 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8108 (tp30) REVERT: iA 206 LYS cc_start: 0.9311 (tttt) cc_final: 0.9073 (tttm) REVERT: jA 306 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8554 (ttpp) REVERT: jA 307 PHE cc_start: 0.9532 (OUTLIER) cc_final: 0.9048 (t80) REVERT: lA 1102 LYS cc_start: 0.9413 (tptm) cc_final: 0.9188 (tptm) REVERT: mA 1204 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7796 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9282 (tttt) cc_final: 0.8982 (tttm) REVERT: nA 1306 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8535 (ttpp) REVERT: oA 103 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.9003 (t80) REVERT: qA 304 GLU cc_start: 0.9314 (tm-30) cc_final: 0.8571 (tm-30) REVERT: rA 1002 LYS cc_start: 0.9178 (ptpt) cc_final: 0.8949 (ptpt) REVERT: uA 1304 GLU cc_start: 0.9339 (tm-30) cc_final: 0.8655 (tm-30) REVERT: wA 202 LYS cc_start: 0.9281 (tttm) cc_final: 0.8741 (ttmm) REVERT: wA 204 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7962 (tm-30) REVERT: xA 302 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8962 (tptp) REVERT: xA 304 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8258 (tm-30) REVERT: zA 1102 LYS cc_start: 0.9363 (tptm) cc_final: 0.9106 (tptm) REVERT: zA 1105 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.9018 (t80) REVERT: 0A 1202 LYS cc_start: 0.9223 (tttm) cc_final: 0.8817 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7481 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8594 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8292 (tm-30) REVERT: f 2 LYS cc_start: 0.9263 (ptpt) cc_final: 0.9028 (ptpt) REVERT: 4A 304 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8672 (tm-30) REVERT: 5A 1004 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8201 (tp30) REVERT: 8A 1304 GLU cc_start: 0.9281 (tm-30) cc_final: 0.8663 (tm-30) REVERT: g 4 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: AB 202 LYS cc_start: 0.9296 (tttm) cc_final: 0.8910 (ttmm) REVERT: AB 204 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8033 (tm-30) REVERT: BB 302 LYS cc_start: 0.9100 (tptp) cc_final: 0.8886 (tptp) REVERT: CB 1004 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8461 (tp30) REVERT: DB 1102 LYS cc_start: 0.9388 (tptm) cc_final: 0.9145 (tptm) REVERT: EB 1204 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7978 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9092 (tptp) cc_final: 0.8877 (tptp) REVERT: i 4 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7786 (tp30) REVERT: i 5 PHE cc_start: 0.9285 (t80) cc_final: 0.8819 (t80) REVERT: OB 206 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8705 (ttpp) REVERT: QB 1004 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9276 (t80) cc_final: 0.9044 (t80) REVERT: SB 1206 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9055 (pttt) outliers start: 159 outliers final: 104 residues processed: 498 average time/residue: 0.6079 time to fit residues: 367.2263 Evaluate side-chains 568 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 440 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain NA residue 202 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain SB residue 1206 LYS Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.069661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.060168 restraints weight = 33606.535| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.05 r_work: 0.2663 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.324 12564 Z= 4.870 Angle : 4.175 53.550 16272 Z= 1.848 Chirality : 0.297 0.806 1152 Planarity : 0.017 0.052 2160 Dihedral : 20.529 78.267 1518 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 107.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.15 % Favored : 83.68 % Rotamer: Outliers : 21.30 % Allowed : 22.80 % Favored : 55.90 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.04 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.111 0.017 PHEPB 303 Details of bonding type rmsd hydrogen bonds : bond 0.19445 ( 278) hydrogen bonds : angle 8.98346 ( 786) covalent geometry : bond 0.10945 (12528) covalent geometry : angle 4.17521 (16272) Misc. bond : bond 0.01108 ( 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 620 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 436 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8545 (mp0) cc_final: 0.8228 (mp0) REVERT: A 6 LYS cc_start: 0.9249 (mtmt) cc_final: 0.8998 (mmmt) REVERT: J 106 LYS cc_start: 0.9317 (mmmm) cc_final: 0.8919 (mmmm) REVERT: L 304 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8667 (mm-30) REVERT: M 1004 GLU cc_start: 0.8553 (mp0) cc_final: 0.8197 (mp0) REVERT: M 1006 LYS cc_start: 0.9275 (mtmt) cc_final: 0.8992 (mmmt) REVERT: N 1106 LYS cc_start: 0.9307 (mmmm) cc_final: 0.8889 (mmmm) REVERT: O 1204 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8606 (mt-10) REVERT: B 4 GLU cc_start: 0.8546 (mp0) cc_final: 0.8049 (mp0) REVERT: B 6 LYS cc_start: 0.9285 (mtmt) cc_final: 0.8965 (mtmt) REVERT: Q 106 LYS cc_start: 0.9194 (tptm) cc_final: 0.8600 (tptm) REVERT: R 202 LYS cc_start: 0.9456 (mtpt) cc_final: 0.9163 (mtpt) REVERT: S 302 LYS cc_start: 0.9457 (ttpt) cc_final: 0.9113 (mtpp) REVERT: T 1004 GLU cc_start: 0.8564 (mp0) cc_final: 0.8016 (mp0) REVERT: T 1006 LYS cc_start: 0.9250 (mtmt) cc_final: 0.8981 (mtmt) REVERT: U 1106 LYS cc_start: 0.9201 (tptm) cc_final: 0.8588 (tptm) REVERT: V 1202 LYS cc_start: 0.9380 (mtpt) cc_final: 0.9154 (mtpt) REVERT: W 1302 LYS cc_start: 0.9481 (ttpt) cc_final: 0.9181 (mtpp) REVERT: C 6 LYS cc_start: 0.9265 (mtmt) cc_final: 0.8933 (mtmt) REVERT: X 106 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8977 (mmmm) REVERT: Z 302 LYS cc_start: 0.9475 (ttpt) cc_final: 0.9132 (ttmm) REVERT: j 1006 LYS cc_start: 0.9254 (mtmt) cc_final: 0.8952 (mtmt) REVERT: k 1106 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8953 (mmmm) REVERT: m 1302 LYS cc_start: 0.9420 (ttpt) cc_final: 0.8839 (ttpp) REVERT: D 4 GLU cc_start: 0.8367 (mp0) cc_final: 0.7965 (mp0) REVERT: n 104 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8105 (mm-30) REVERT: n 106 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8928 (mmmm) REVERT: o 202 LYS cc_start: 0.9345 (mtpt) cc_final: 0.9069 (mtpp) REVERT: p 302 LYS cc_start: 0.9397 (ttpt) cc_final: 0.9068 (ttpp) REVERT: q 1002 LYS cc_start: 0.8256 (tttt) cc_final: 0.7909 (tptm) REVERT: q 1004 GLU cc_start: 0.8531 (mp0) cc_final: 0.7558 (mp0) REVERT: r 1104 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8080 (mm-30) REVERT: r 1106 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8907 (mmmm) REVERT: t 1302 LYS cc_start: 0.9389 (ttpt) cc_final: 0.9102 (ttpp) REVERT: E 6 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8858 (mtmt) REVERT: u 102 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8815 (ttpt) REVERT: u 104 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8190 (mm-30) REVERT: u 106 LYS cc_start: 0.9286 (tptm) cc_final: 0.8896 (tptm) REVERT: w 302 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9034 (ttmm) REVERT: x 1002 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6659 (mmtp) REVERT: x 1006 LYS cc_start: 0.9067 (mtmt) cc_final: 0.8798 (mtmt) REVERT: y 1104 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8134 (mm-30) REVERT: y 1106 LYS cc_start: 0.9284 (tptm) cc_final: 0.8880 (tptm) REVERT: 0 1302 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9087 (ttmm) REVERT: F 4 GLU cc_start: 0.8325 (mp0) cc_final: 0.7828 (mp0) REVERT: 1 104 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7839 (mm-30) REVERT: 1 106 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8895 (mmmm) REVERT: 2 206 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8942 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8331 (mp0) cc_final: 0.7538 (mp0) REVERT: 5 1104 GLU cc_start: 0.8676 (mm-30) cc_final: 0.7443 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8859 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9378 (mtpt) cc_final: 0.9054 (mtpt) REVERT: G 4 GLU cc_start: 0.8322 (mp0) cc_final: 0.7322 (mp0) REVERT: G 6 LYS cc_start: 0.9185 (mtmt) cc_final: 0.8839 (mtmt) REVERT: BA 1004 GLU cc_start: 0.8327 (mp0) cc_final: 0.7389 (mp0) REVERT: BA 1006 LYS cc_start: 0.9143 (mtmt) cc_final: 0.8823 (mtmt) REVERT: CA 1106 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8823 (mmmm) REVERT: FA 106 LYS cc_start: 0.9303 (mmmm) cc_final: 0.9054 (mmmm) REVERT: GA 202 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8886 (mtpt) REVERT: HA 304 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8676 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8030 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9300 (mmmm) cc_final: 0.9051 (mmmm) REVERT: LA 1304 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8457 (mm-30) REVERT: MA 106 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.5760 (tptp) REVERT: OA 302 LYS cc_start: 0.9433 (ttpt) cc_final: 0.9017 (tptt) REVERT: PA 1006 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8858 (mtmt) REVERT: SA 1302 LYS cc_start: 0.9402 (ttpt) cc_final: 0.8858 (mmmt) REVERT: SA 1306 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6804 (mmmt) REVERT: a 4 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8658 (tp30) REVERT: UA 204 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7810 (tm-30) REVERT: VA 304 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8742 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8626 (tp30) REVERT: YA 1204 GLU cc_start: 0.8259 (tm-30) cc_final: 0.8059 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9279 (tptp) cc_final: 0.9053 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8483 (tm-30) REVERT: aA 105 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.9040 (t80) REVERT: bA 202 LYS cc_start: 0.9307 (tttm) cc_final: 0.9012 (ttmm) REVERT: bA 204 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8141 (tp30) REVERT: cA 304 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8369 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.9005 (t80) REVERT: eA 1106 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8330 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8150 (tm-30) REVERT: gA 1304 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8676 (tm-30) REVERT: iA 202 LYS cc_start: 0.9374 (tttm) cc_final: 0.9135 (tttm) REVERT: iA 204 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8239 (tp30) REVERT: iA 206 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8654 (ttpp) REVERT: jA 306 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8430 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7929 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8547 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8466 (ttpp) REVERT: nA 1307 PHE cc_start: 0.9531 (OUTLIER) cc_final: 0.9108 (t80) REVERT: oA 103 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.9041 (t80) REVERT: qA 304 GLU cc_start: 0.9349 (tm-30) cc_final: 0.8705 (tm-30) REVERT: rA 1002 LYS cc_start: 0.9228 (ptpt) cc_final: 0.9017 (ptpt) REVERT: uA 1304 GLU cc_start: 0.9353 (tm-30) cc_final: 0.8556 (tm-30) REVERT: e 2 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8942 (ttpt) REVERT: e 4 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: vA 104 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8098 (tm-30) REVERT: wA 202 LYS cc_start: 0.9290 (tttm) cc_final: 0.8785 (ttmm) REVERT: wA 204 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7531 (tm-30) REVERT: xA 302 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8714 (tptp) REVERT: xA 304 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8372 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8983 (tppt) REVERT: yA 1004 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8423 (tp30) REVERT: 0A 1202 LYS cc_start: 0.9210 (tttm) cc_final: 0.8808 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7486 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8599 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8400 (tm-30) REVERT: f 2 LYS cc_start: 0.9251 (ptpt) cc_final: 0.9024 (ptpt) REVERT: 4A 304 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8686 (tm-30) REVERT: 4A 306 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8887 (ttpp) REVERT: 5A 1004 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: 6A 1102 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8997 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8665 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9153 (tptp) cc_final: 0.8881 (tptp) REVERT: g 4 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8331 (tp30) REVERT: AB 202 LYS cc_start: 0.9324 (tttm) cc_final: 0.8948 (ttmm) REVERT: AB 204 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8508 (tp30) REVERT: EB 1204 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: h 2 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8973 (pptt) REVERT: i 4 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: i 5 PHE cc_start: 0.9299 (t80) cc_final: 0.8827 (t80) REVERT: i 6 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8948 (ttpt) REVERT: OB 206 LYS cc_start: 0.9361 (tttt) cc_final: 0.9137 (tttm) REVERT: QB 1004 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9283 (t80) cc_final: 0.9061 (t80) REVERT: QB 1006 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8949 (ttpt) outliers start: 184 outliers final: 125 residues processed: 503 average time/residue: 0.4821 time to fit residues: 294.0002 Evaluate side-chains 599 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 437 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 202 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.060027 restraints weight = 33778.799| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.03 r_work: 0.2662 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.310 12564 Z= 4.873 Angle : 4.209 51.182 16272 Z= 1.859 Chirality : 0.298 0.785 1152 Planarity : 0.017 0.052 2160 Dihedral : 20.570 88.112 1510 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 110.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.01 % Favored : 82.99 % Rotamer: Outliers : 24.19 % Allowed : 24.31 % Favored : 51.50 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.04 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.017 PHE V1207 Details of bonding type rmsd hydrogen bonds : bond 0.19596 ( 278) hydrogen bonds : angle 9.07122 ( 786) covalent geometry : bond 0.10954 (12528) covalent geometry : angle 4.20944 (16272) Misc. bond : bond 0.01130 ( 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 643 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 434 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9252 (mtmt) cc_final: 0.9029 (mmmt) REVERT: J 106 LYS cc_start: 0.9318 (mmmm) cc_final: 0.8900 (mmmm) REVERT: N 1106 LYS cc_start: 0.9282 (mmmm) cc_final: 0.8864 (mmmm) REVERT: B 4 GLU cc_start: 0.8563 (mp0) cc_final: 0.8121 (mp0) REVERT: B 6 LYS cc_start: 0.9280 (mtmt) cc_final: 0.8993 (mtmt) REVERT: Q 106 LYS cc_start: 0.9223 (tptm) cc_final: 0.8656 (tptm) REVERT: R 202 LYS cc_start: 0.9442 (mtpt) cc_final: 0.9193 (mtpt) REVERT: S 302 LYS cc_start: 0.9445 (ttpt) cc_final: 0.9109 (mtpp) REVERT: T 1004 GLU cc_start: 0.8546 (mp0) cc_final: 0.8069 (mp0) REVERT: T 1006 LYS cc_start: 0.9257 (mtmt) cc_final: 0.8986 (mtmt) REVERT: V 1202 LYS cc_start: 0.9374 (mtpt) cc_final: 0.9158 (mtpt) REVERT: W 1302 LYS cc_start: 0.9478 (ttpt) cc_final: 0.9143 (mtpp) REVERT: C 6 LYS cc_start: 0.9206 (mtmt) cc_final: 0.8874 (mtmt) REVERT: X 106 LYS cc_start: 0.9225 (mmmm) cc_final: 0.8981 (mmmm) REVERT: Z 302 LYS cc_start: 0.9517 (ttpt) cc_final: 0.9198 (ttpp) REVERT: j 1006 LYS cc_start: 0.9244 (mtmt) cc_final: 0.8949 (mtmt) REVERT: k 1106 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8908 (mmmm) REVERT: m 1302 LYS cc_start: 0.9450 (ttpt) cc_final: 0.9098 (ttmm) REVERT: D 4 GLU cc_start: 0.8425 (mp0) cc_final: 0.8012 (mp0) REVERT: n 104 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8103 (mm-30) REVERT: n 106 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8928 (mmmm) REVERT: o 202 LYS cc_start: 0.9358 (mtpt) cc_final: 0.9077 (mtpp) REVERT: p 302 LYS cc_start: 0.9394 (ttpt) cc_final: 0.9054 (ttpp) REVERT: q 1002 LYS cc_start: 0.8346 (tttt) cc_final: 0.8066 (tptm) REVERT: q 1004 GLU cc_start: 0.8601 (mp0) cc_final: 0.7932 (mp0) REVERT: r 1104 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8123 (mm-30) REVERT: r 1106 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8937 (mmmm) REVERT: t 1302 LYS cc_start: 0.9397 (ttpt) cc_final: 0.9100 (ttpp) REVERT: u 102 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8982 (ttpt) REVERT: u 104 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8246 (mm-30) REVERT: u 106 LYS cc_start: 0.9283 (tptm) cc_final: 0.8896 (tptm) REVERT: w 302 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9020 (ttmm) REVERT: x 1002 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6685 (mmtp) REVERT: x 1006 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8740 (mtmt) REVERT: y 1104 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8205 (mm-30) REVERT: y 1106 LYS cc_start: 0.9281 (tptm) cc_final: 0.8901 (tptm) REVERT: 0 1302 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9097 (ttmm) REVERT: 1 106 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8883 (mmmm) REVERT: 4 1004 GLU cc_start: 0.8380 (mp0) cc_final: 0.7595 (mp0) REVERT: 5 1104 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8129 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8900 (mmmm) REVERT: G 4 GLU cc_start: 0.8341 (mp0) cc_final: 0.7430 (mp0) REVERT: G 6 LYS cc_start: 0.9169 (mtmt) cc_final: 0.8834 (mtmt) REVERT: BA 1004 GLU cc_start: 0.8341 (mp0) cc_final: 0.7489 (mp0) REVERT: BA 1006 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8807 (mtmt) REVERT: CA 1106 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8831 (mmmm) REVERT: GA 202 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8875 (mtpt) REVERT: GA 204 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.4888 (pm20) REVERT: JA 1104 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7940 (mm-30) REVERT: LA 1304 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8474 (mm-30) REVERT: MA 106 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6034 (tptp) REVERT: OA 302 LYS cc_start: 0.9415 (ttpt) cc_final: 0.9011 (tptt) REVERT: PA 1006 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8830 (mtmt) REVERT: SA 1302 LYS cc_start: 0.9395 (ttpt) cc_final: 0.8845 (mmmt) REVERT: SA 1306 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6398 (mmmt) REVERT: a 4 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8675 (tp30) REVERT: TA 107 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8047 (t80) REVERT: VA 304 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8756 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8648 (tp30) REVERT: YA 1204 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7872 (tm-30) REVERT: ZA 1302 LYS cc_start: 0.9289 (tptp) cc_final: 0.8940 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8667 (tm-30) REVERT: b 2 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8940 (ttmt) REVERT: aA 105 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.9049 (t80) REVERT: bA 202 LYS cc_start: 0.9326 (tttm) cc_final: 0.9026 (ttmm) REVERT: bA 204 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8176 (tp30) REVERT: cA 304 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8663 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.9079 (t80) REVERT: eA 1106 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8349 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8057 (tp30) REVERT: gA 1304 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8514 (tm-30) REVERT: iA 202 LYS cc_start: 0.9337 (tttm) cc_final: 0.9100 (tttm) REVERT: iA 204 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8292 (tp30) REVERT: iA 206 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8702 (ttpp) REVERT: jA 306 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8495 (ttpp) REVERT: mA 1206 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8469 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8470 (ttpp) REVERT: oA 103 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.9007 (t80) REVERT: qA 304 GLU cc_start: 0.9363 (tm-30) cc_final: 0.8746 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9003 (pttt) REVERT: uA 1304 GLU cc_start: 0.9375 (tm-30) cc_final: 0.8790 (tm-30) REVERT: vA 104 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8138 (tm-30) REVERT: wA 202 LYS cc_start: 0.9296 (tttm) cc_final: 0.8814 (ttmm) REVERT: wA 204 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7498 (tm-30) REVERT: xA 302 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8687 (tptp) REVERT: xA 304 GLU cc_start: 0.9280 (tm-30) cc_final: 0.8462 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8924 (tppt) REVERT: 0A 1202 LYS cc_start: 0.9223 (tttm) cc_final: 0.8834 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7468 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8597 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8462 (tm-30) REVERT: f 2 LYS cc_start: 0.9265 (ptpt) cc_final: 0.9038 (ptpt) REVERT: 4A 304 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8723 (tm-30) REVERT: 4A 306 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8910 (ttpp) REVERT: 5A 1004 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: 6A 1102 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9008 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8677 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8920 (ttpp) REVERT: g 4 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: 9A 102 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9106 (tptm) REVERT: AB 202 LYS cc_start: 0.9328 (tttm) cc_final: 0.8952 (ttmm) REVERT: AB 204 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8516 (tp30) REVERT: EB 1204 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: h 2 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8965 (pptt) REVERT: i 4 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8030 (tp30) REVERT: i 5 PHE cc_start: 0.9281 (t80) cc_final: 0.8805 (t80) REVERT: i 6 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8943 (ttpt) REVERT: OB 206 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8720 (ttpp) REVERT: QB 1004 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9293 (t80) cc_final: 0.9068 (t80) REVERT: QB 1006 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8927 (ttpt) outliers start: 209 outliers final: 150 residues processed: 513 average time/residue: 0.5440 time to fit residues: 340.1306 Evaluate side-chains 624 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 434 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 202 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 203 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.070194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.060643 restraints weight = 34239.814| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.08 r_work: 0.2668 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.307 12564 Z= 4.873 Angle : 4.222 53.970 16272 Z= 1.864 Chirality : 0.298 0.771 1152 Planarity : 0.017 0.053 2160 Dihedral : 20.701 82.624 1510 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 111.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.49 % Favored : 83.51 % Rotamer: Outliers : 25.58 % Allowed : 25.23 % Favored : 49.19 % Cbeta Deviations : 14.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.04 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.017 PHE R 207 Details of bonding type rmsd hydrogen bonds : bond 0.19630 ( 278) hydrogen bonds : angle 9.09041 ( 786) covalent geometry : bond 0.10956 (12528) covalent geometry : angle 4.22158 (16272) Misc. bond : bond 0.01205 ( 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 652 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 431 time to evaluate : 1.181 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 4 GLU cc_start: 0.8632 (mp0) cc_final: 0.8353 (mp0) REVERT: A 6 LYS cc_start: 0.9250 (mtmt) cc_final: 0.9047 (mmmt) REVERT: J 106 LYS cc_start: 0.9310 (mmmm) cc_final: 0.8886 (mmmm) REVERT: L 304 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8608 (mm-30) REVERT: M 1004 GLU cc_start: 0.8567 (mp0) cc_final: 0.8208 (mp0) REVERT: N 1106 LYS cc_start: 0.9301 (mmmm) cc_final: 0.8880 (mmmm) REVERT: B 4 GLU cc_start: 0.8586 (mp0) cc_final: 0.8137 (mp0) REVERT: B 6 LYS cc_start: 0.9289 (mtmt) cc_final: 0.8990 (mtmt) REVERT: Q 106 LYS cc_start: 0.9187 (tptm) cc_final: 0.8660 (tptm) REVERT: R 202 LYS cc_start: 0.9434 (mtpt) cc_final: 0.9203 (mtpt) REVERT: S 302 LYS cc_start: 0.9438 (ttpt) cc_final: 0.9100 (mtpp) REVERT: T 1004 GLU cc_start: 0.8543 (mp0) cc_final: 0.8083 (mp0) REVERT: T 1006 LYS cc_start: 0.9286 (mtmt) cc_final: 0.9007 (mtmt) REVERT: V 1202 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9169 (mtpt) REVERT: W 1302 LYS cc_start: 0.9479 (ttpt) cc_final: 0.9132 (mtpp) REVERT: C 6 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8913 (mtmt) REVERT: X 106 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8969 (mmmm) REVERT: Z 302 LYS cc_start: 0.9492 (ttpt) cc_final: 0.9176 (ttpp) REVERT: j 1006 LYS cc_start: 0.9242 (mtmt) cc_final: 0.8931 (mtmt) REVERT: k 1106 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8900 (mmmm) REVERT: m 1302 LYS cc_start: 0.9460 (ttpt) cc_final: 0.9158 (ttpp) REVERT: D 4 GLU cc_start: 0.8500 (mp0) cc_final: 0.8146 (mp0) REVERT: n 104 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8088 (mm-30) REVERT: n 106 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8898 (mmmm) REVERT: o 202 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9076 (mtpp) REVERT: p 302 LYS cc_start: 0.9380 (ttpt) cc_final: 0.9026 (ttpp) REVERT: q 1002 LYS cc_start: 0.8402 (tttt) cc_final: 0.8154 (tptm) REVERT: q 1004 GLU cc_start: 0.8567 (mp0) cc_final: 0.8083 (mp0) REVERT: r 1104 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8084 (mm-30) REVERT: r 1106 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8907 (mmmm) REVERT: t 1302 LYS cc_start: 0.9395 (ttpt) cc_final: 0.9088 (ttpp) REVERT: u 102 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8938 (mtpp) REVERT: u 106 LYS cc_start: 0.9291 (tptm) cc_final: 0.8885 (tptm) REVERT: w 302 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9026 (ttmm) REVERT: x 1002 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6710 (mmtp) REVERT: x 1006 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8755 (mtmt) REVERT: y 1106 LYS cc_start: 0.9289 (tptm) cc_final: 0.8899 (tptm) REVERT: 0 1302 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9099 (ttmm) REVERT: 1 104 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8232 (mm-30) REVERT: 1 106 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8890 (mmmm) REVERT: 2 206 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8927 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8395 (mp0) cc_final: 0.7591 (mp0) REVERT: 5 1104 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8195 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8859 (mmmm) REVERT: G 4 GLU cc_start: 0.8346 (mp0) cc_final: 0.7539 (mp0) REVERT: G 6 LYS cc_start: 0.9178 (mtmt) cc_final: 0.8834 (mtmt) REVERT: BA 1004 GLU cc_start: 0.8382 (mp0) cc_final: 0.7588 (mp0) REVERT: BA 1006 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8825 (mtmt) REVERT: GA 202 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8846 (mtpt) REVERT: GA 204 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.4912 (pm20) REVERT: HA 304 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8498 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7919 (mm-30) REVERT: KA 1204 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5324 (pm20) REVERT: LA 1304 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8527 (mm-30) REVERT: MA 106 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.5979 (tptp) REVERT: OA 302 LYS cc_start: 0.9430 (ttpt) cc_final: 0.8990 (tptt) REVERT: SA 1302 LYS cc_start: 0.9394 (ttpt) cc_final: 0.8828 (mmmt) REVERT: SA 1306 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5912 (mmmt) REVERT: a 4 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8701 (tp30) REVERT: UA 204 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8046 (tp30) REVERT: VA 304 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8576 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8633 (tp30) REVERT: YA 1204 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7885 (tm-30) REVERT: ZA 1302 LYS cc_start: 0.9278 (tptp) cc_final: 0.8924 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8665 (tm-30) REVERT: b 2 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8929 (ttmt) REVERT: bA 202 LYS cc_start: 0.9333 (tttm) cc_final: 0.9028 (ttmm) REVERT: bA 204 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8189 (tp30) REVERT: cA 304 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8638 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.9071 (t80) REVERT: eA 1106 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8340 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7991 (tp30) REVERT: gA 1304 GLU cc_start: 0.9210 (tm-30) cc_final: 0.8534 (tm-30) REVERT: iA 204 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8111 (tm-30) REVERT: iA 206 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8670 (ttpp) REVERT: jA 306 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8466 (ttpp) REVERT: mA 1206 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8471 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8469 (ttpp) REVERT: oA 103 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.9033 (t80) REVERT: qA 304 GLU cc_start: 0.9364 (tm-30) cc_final: 0.8735 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8971 (pttt) REVERT: uA 1304 GLU cc_start: 0.9361 (tm-30) cc_final: 0.8802 (tm-30) REVERT: vA 104 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8140 (tm-30) REVERT: wA 202 LYS cc_start: 0.9298 (tttm) cc_final: 0.8818 (ttmm) REVERT: wA 204 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7405 (tm-30) REVERT: xA 302 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8658 (tptp) REVERT: xA 304 GLU cc_start: 0.9283 (tm-30) cc_final: 0.8450 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8895 (tppt) REVERT: 0A 1202 LYS cc_start: 0.9226 (tttm) cc_final: 0.8758 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7402 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8612 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8479 (tm-30) REVERT: 4A 304 GLU cc_start: 0.9281 (tm-30) cc_final: 0.8700 (tm-30) REVERT: 4A 306 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8898 (ttpp) REVERT: 6A 1102 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9141 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8646 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8914 (ttpp) REVERT: g 4 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8340 (tp30) REVERT: 9A 102 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9145 (tptm) REVERT: AB 204 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8462 (tp30) REVERT: EB 1204 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: i 4 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: i 5 PHE cc_start: 0.9272 (t80) cc_final: 0.8798 (t80) REVERT: i 6 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8933 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9292 (t80) cc_final: 0.9064 (t80) REVERT: QB 1006 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8928 (ttpt) REVERT: SB 1206 LYS cc_start: 0.9320 (pttt) cc_final: 0.8587 (ttpp) outliers start: 221 outliers final: 161 residues processed: 520 average time/residue: 0.4678 time to fit residues: 295.2862 Evaluate side-chains 629 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 433 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 202 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain XA residue 1107 PHE Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.070028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.060480 restraints weight = 34064.435| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.05 r_work: 0.2667 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.7406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.372 12564 Z= 4.873 Angle : 4.236 54.735 16272 Z= 1.868 Chirality : 0.299 0.779 1152 Planarity : 0.017 0.056 2160 Dihedral : 20.772 93.051 1510 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 112.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.49 % Favored : 83.51 % Rotamer: Outliers : 26.62 % Allowed : 24.42 % Favored : 48.96 % Cbeta Deviations : 14.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.12 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.66 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.119 0.017 PHE V1207 Details of bonding type rmsd hydrogen bonds : bond 0.19684 ( 278) hydrogen bonds : angle 9.10252 ( 786) covalent geometry : bond 0.10954 (12528) covalent geometry : angle 4.23552 (16272) Misc. bond : bond 0.01226 ( 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 664 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 434 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 106 LYS cc_start: 0.9312 (mmmm) cc_final: 0.8882 (mmmm) REVERT: M 1004 GLU cc_start: 0.8570 (mp0) cc_final: 0.8350 (mp0) REVERT: N 1106 LYS cc_start: 0.9298 (mmmm) cc_final: 0.8867 (mmmm) REVERT: P 1304 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: B 4 GLU cc_start: 0.8563 (mp0) cc_final: 0.8137 (mp0) REVERT: B 6 LYS cc_start: 0.9276 (mtmt) cc_final: 0.8954 (mtmt) REVERT: Q 106 LYS cc_start: 0.9199 (tptm) cc_final: 0.8680 (tptm) REVERT: R 202 LYS cc_start: 0.9444 (mtpt) cc_final: 0.9234 (mtpt) REVERT: S 302 LYS cc_start: 0.9436 (ttpt) cc_final: 0.9102 (mtpp) REVERT: T 1004 GLU cc_start: 0.8555 (mp0) cc_final: 0.8098 (mp0) REVERT: T 1006 LYS cc_start: 0.9267 (mtmt) cc_final: 0.8934 (mtmt) REVERT: W 1302 LYS cc_start: 0.9457 (ttpt) cc_final: 0.9105 (mtpp) REVERT: C 6 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8921 (mtmt) REVERT: X 106 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8975 (mmmm) REVERT: Z 302 LYS cc_start: 0.9478 (ttpt) cc_final: 0.9207 (ttpp) REVERT: j 1006 LYS cc_start: 0.9227 (mtmt) cc_final: 0.8911 (mtmt) REVERT: k 1106 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8900 (mmmm) REVERT: m 1302 LYS cc_start: 0.9463 (ttpt) cc_final: 0.9149 (ttpp) REVERT: D 4 GLU cc_start: 0.8418 (mp0) cc_final: 0.8015 (mm-30) REVERT: n 104 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8088 (mm-30) REVERT: n 106 LYS cc_start: 0.9241 (mmmm) cc_final: 0.8911 (mmmm) REVERT: o 202 LYS cc_start: 0.9375 (mtpt) cc_final: 0.9078 (mtpp) REVERT: p 302 LYS cc_start: 0.9384 (ttpt) cc_final: 0.9030 (ttpp) REVERT: q 1002 LYS cc_start: 0.8407 (tttt) cc_final: 0.8152 (tptm) REVERT: q 1004 GLU cc_start: 0.8535 (mp0) cc_final: 0.8093 (mp0) REVERT: r 1104 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8088 (mm-30) REVERT: r 1106 LYS cc_start: 0.9207 (mmmm) cc_final: 0.8894 (mmmm) REVERT: t 1302 LYS cc_start: 0.9389 (ttpt) cc_final: 0.9077 (ttpp) REVERT: u 102 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8847 (mtpp) REVERT: u 106 LYS cc_start: 0.9285 (tptm) cc_final: 0.8889 (tptm) REVERT: w 302 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9040 (ttmm) REVERT: x 1002 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6817 (mmtp) REVERT: x 1006 LYS cc_start: 0.9086 (mtmt) cc_final: 0.8755 (mtmt) REVERT: y 1106 LYS cc_start: 0.9282 (tptm) cc_final: 0.8884 (tptm) REVERT: 0 1302 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9102 (ttmm) REVERT: F 4 GLU cc_start: 0.8622 (mp0) cc_final: 0.8292 (mp0) REVERT: 1 104 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7985 (mm-30) REVERT: 1 106 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8881 (mmmm) REVERT: 2 206 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8928 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8426 (mp0) cc_final: 0.7739 (mp0) REVERT: 5 1104 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8194 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9223 (mmmm) cc_final: 0.8783 (mmmm) REVERT: 6 1206 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8950 (ptmm) REVERT: G 4 GLU cc_start: 0.8594 (mp0) cc_final: 0.8220 (mp0) REVERT: G 6 LYS cc_start: 0.9185 (mtmt) cc_final: 0.8834 (mtmt) REVERT: BA 1004 GLU cc_start: 0.8588 (mp0) cc_final: 0.8214 (mp0) REVERT: BA 1006 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8814 (mtmt) REVERT: EA 1302 LYS cc_start: 0.9384 (ttpt) cc_final: 0.8988 (ttmm) REVERT: FA 104 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8355 (mm-30) REVERT: GA 202 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8845 (mtpt) REVERT: GA 204 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5226 (pm20) REVERT: HA 304 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8590 (mm-30) REVERT: LA 1304 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8508 (mm-30) REVERT: I 2 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8838 (tttt) REVERT: MA 106 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.5893 (tptp) REVERT: OA 302 LYS cc_start: 0.9432 (ttpt) cc_final: 0.8974 (tptt) REVERT: OA 306 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.4108 (mmmt) REVERT: SA 1302 LYS cc_start: 0.9402 (ttpt) cc_final: 0.8801 (mmmt) REVERT: SA 1306 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.5743 (mmmt) REVERT: a 4 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8685 (tp30) REVERT: UA 204 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8055 (tp30) REVERT: VA 304 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8571 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8655 (tp30) REVERT: YA 1204 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7858 (tm-30) REVERT: ZA 1302 LYS cc_start: 0.9273 (tptp) cc_final: 0.8903 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8643 (tm-30) REVERT: b 2 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8945 (ttmt) REVERT: aA 105 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9048 (t80) REVERT: bA 202 LYS cc_start: 0.9329 (tttm) cc_final: 0.9032 (ttmm) REVERT: bA 204 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8194 (tp30) REVERT: cA 304 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8655 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8944 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.9072 (t80) REVERT: eA 1106 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8342 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8104 (tp30) REVERT: gA 1304 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8490 (tm-30) REVERT: iA 204 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8131 (tm-30) REVERT: iA 206 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8683 (ttpp) REVERT: jA 306 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8495 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8146 (tp30) REVERT: mA 1206 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8519 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8366 (ttpp) REVERT: oA 103 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.9029 (t80) REVERT: pA 206 LYS cc_start: 0.9266 (pttt) cc_final: 0.8790 (ptmm) REVERT: qA 304 GLU cc_start: 0.9362 (tm-30) cc_final: 0.8733 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8969 (pttt) REVERT: uA 1304 GLU cc_start: 0.9373 (tm-30) cc_final: 0.8831 (tm-30) REVERT: vA 104 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8157 (tm-30) REVERT: wA 202 LYS cc_start: 0.9292 (tttm) cc_final: 0.8816 (ttmm) REVERT: wA 204 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7443 (tm-30) REVERT: xA 302 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8666 (tptp) REVERT: xA 304 GLU cc_start: 0.9282 (tm-30) cc_final: 0.8472 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8896 (tppt) REVERT: zA 1105 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8890 (t80) REVERT: 0A 1202 LYS cc_start: 0.9234 (tttm) cc_final: 0.8775 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7332 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8605 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8489 (tm-30) REVERT: 3A 202 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9190 (tppp) REVERT: 4A 306 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8897 (ttpp) REVERT: 6A 1102 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9131 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8669 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8923 (ttpp) REVERT: g 4 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8347 (tp30) REVERT: 9A 102 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9143 (tptm) REVERT: AB 204 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8452 (tp30) REVERT: DB 1102 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9170 (tptm) REVERT: EB 1204 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: i 4 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8087 (tp30) REVERT: i 5 PHE cc_start: 0.9264 (t80) cc_final: 0.8795 (t80) REVERT: i 6 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8923 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9293 (t80) cc_final: 0.9065 (t80) REVERT: QB 1006 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8945 (ttpt) outliers start: 230 outliers final: 168 residues processed: 521 average time/residue: 0.4550 time to fit residues: 288.8292 Evaluate side-chains 646 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 434 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain M residue 1006 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain P residue 1304 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 202 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1002 LYS Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 202 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain XA residue 1107 PHE Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 202 LYS Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 303 PHE Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.070535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.060990 restraints weight = 34065.553| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.03 r_work: 0.2678 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.7445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.328 12564 Z= 4.870 Angle : 4.235 53.753 16272 Z= 1.871 Chirality : 0.299 0.776 1152 Planarity : 0.017 0.052 2160 Dihedral : 20.824 105.344 1510 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 111.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.36 % Favored : 82.64 % Rotamer: Outliers : 26.74 % Allowed : 25.00 % Favored : 48.26 % Cbeta Deviations : 14.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.08 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.115 0.017 PHE R 207 Details of bonding type rmsd hydrogen bonds : bond 0.19651 ( 278) hydrogen bonds : angle 9.10195 ( 786) covalent geometry : bond 0.10947 (12528) covalent geometry : angle 4.23518 (16272) Misc. bond : bond 0.01205 ( 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 663 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 432 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 106 LYS cc_start: 0.9306 (mmmm) cc_final: 0.8885 (mmmm) REVERT: N 1106 LYS cc_start: 0.9302 (mmmm) cc_final: 0.8870 (mmmm) REVERT: B 4 GLU cc_start: 0.8583 (mp0) cc_final: 0.8173 (mp0) REVERT: B 6 LYS cc_start: 0.9293 (mtmt) cc_final: 0.8969 (mtmt) REVERT: Q 106 LYS cc_start: 0.9224 (tptm) cc_final: 0.8693 (tptm) REVERT: S 302 LYS cc_start: 0.9436 (ttpt) cc_final: 0.9092 (mtpp) REVERT: T 1006 LYS cc_start: 0.9270 (mtmt) cc_final: 0.8938 (mtmt) REVERT: W 1302 LYS cc_start: 0.9448 (ttpt) cc_final: 0.9111 (mtpp) REVERT: C 6 LYS cc_start: 0.9193 (mtmt) cc_final: 0.8858 (mtmt) REVERT: X 106 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8979 (mmmm) REVERT: Z 302 LYS cc_start: 0.9483 (ttpt) cc_final: 0.9208 (ttpp) REVERT: j 1006 LYS cc_start: 0.9234 (mtmt) cc_final: 0.8923 (mtmt) REVERT: k 1106 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8909 (mmmm) REVERT: m 1302 LYS cc_start: 0.9457 (ttpt) cc_final: 0.9139 (ttpp) REVERT: D 4 GLU cc_start: 0.8467 (mp0) cc_final: 0.8097 (mp0) REVERT: n 104 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8127 (mm-30) REVERT: n 106 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8904 (mmmm) REVERT: o 202 LYS cc_start: 0.9389 (mtpt) cc_final: 0.9082 (mtpp) REVERT: p 302 LYS cc_start: 0.9374 (ttpt) cc_final: 0.9019 (ttpp) REVERT: q 1002 LYS cc_start: 0.8415 (tttt) cc_final: 0.8157 (tptm) REVERT: q 1004 GLU cc_start: 0.8540 (mp0) cc_final: 0.8023 (mp0) REVERT: r 1104 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8087 (mp0) REVERT: r 1106 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8904 (mmmm) REVERT: t 1302 LYS cc_start: 0.9379 (ttpt) cc_final: 0.9057 (ttpp) REVERT: u 102 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8898 (mtpp) REVERT: u 106 LYS cc_start: 0.9293 (tptm) cc_final: 0.8906 (tptm) REVERT: w 302 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9036 (ttmm) REVERT: x 1002 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6751 (mmtp) REVERT: x 1006 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8757 (mtmt) REVERT: y 1106 LYS cc_start: 0.9273 (tptm) cc_final: 0.8894 (tptm) REVERT: 0 1302 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9107 (ttmm) REVERT: F 4 GLU cc_start: 0.8615 (mp0) cc_final: 0.8377 (mp0) REVERT: 1 104 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8210 (mm-30) REVERT: 1 106 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8872 (mmmm) REVERT: 2 206 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8950 (ptmm) REVERT: 5 1104 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8174 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8792 (mmmm) REVERT: 6 1206 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8934 (ptmm) REVERT: G 4 GLU cc_start: 0.8468 (mp0) cc_final: 0.7991 (mp0) REVERT: G 6 LYS cc_start: 0.9211 (mtmt) cc_final: 0.8869 (mtmt) REVERT: BA 1004 GLU cc_start: 0.8432 (mp0) cc_final: 0.7957 (mp0) REVERT: BA 1006 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8862 (mtmt) REVERT: FA 104 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8373 (mm-30) REVERT: GA 202 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8827 (mtpt) REVERT: GA 204 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5399 (pm20) REVERT: HA 304 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8539 (mm-30) REVERT: I 2 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8825 (tttt) REVERT: MA 106 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5667 (tptp) REVERT: OA 302 LYS cc_start: 0.9426 (ttpt) cc_final: 0.8980 (tptt) REVERT: RA 1202 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8803 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9391 (ttpt) cc_final: 0.8954 (tptt) REVERT: a 4 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8721 (tp30) REVERT: UA 202 LYS cc_start: 0.9418 (mttm) cc_final: 0.9146 (mmmm) REVERT: UA 204 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8098 (tp30) REVERT: VA 304 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8599 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8658 (tp30) REVERT: YA 1204 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7863 (tm-30) REVERT: ZA 1302 LYS cc_start: 0.9278 (tptp) cc_final: 0.8932 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8654 (tm-30) REVERT: b 2 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8952 (ttmt) REVERT: bA 202 LYS cc_start: 0.9338 (tttm) cc_final: 0.9044 (ttmm) REVERT: bA 204 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8202 (tp30) REVERT: cA 304 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8663 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8939 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9080 (t80) REVERT: eA 1106 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8348 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8044 (tp30) REVERT: gA 1304 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8527 (tm-30) REVERT: iA 204 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8139 (tm-30) REVERT: iA 206 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8683 (ttpp) REVERT: jA 306 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8477 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8149 (tp30) REVERT: mA 1206 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8523 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8417 (ttpp) REVERT: oA 103 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.9032 (t80) REVERT: pA 206 LYS cc_start: 0.9291 (pttt) cc_final: 0.8856 (ptmm) REVERT: qA 304 GLU cc_start: 0.9366 (tm-30) cc_final: 0.8744 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8979 (pttt) REVERT: uA 1304 GLU cc_start: 0.9376 (tm-30) cc_final: 0.8853 (tm-30) REVERT: vA 104 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8186 (tm-30) REVERT: wA 202 LYS cc_start: 0.9283 (tttm) cc_final: 0.8818 (ttmm) REVERT: wA 204 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7481 (tm-30) REVERT: xA 302 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8660 (tptp) REVERT: xA 304 GLU cc_start: 0.9285 (tm-30) cc_final: 0.8483 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8921 (tppt) REVERT: zA 1105 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8932 (t80) REVERT: 0A 1202 LYS cc_start: 0.9225 (tttm) cc_final: 0.8861 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7427 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8612 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8511 (tm-30) REVERT: 3A 202 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9206 (tppp) REVERT: 4A 306 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8892 (ttpp) REVERT: 5A 1004 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: 6A 1102 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8999 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8671 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8918 (ttpp) REVERT: g 4 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: 9A 102 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9140 (tptm) REVERT: AB 204 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8458 (tp30) REVERT: DB 1102 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9180 (tptm) REVERT: EB 1204 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: i 4 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8292 (tp30) REVERT: i 5 PHE cc_start: 0.9291 (t80) cc_final: 0.8849 (t80) REVERT: i 6 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8941 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9297 (t80) cc_final: 0.9056 (t80) REVERT: QB 1006 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8944 (ttpt) outliers start: 231 outliers final: 172 residues processed: 521 average time/residue: 0.5058 time to fit residues: 325.7466 Evaluate side-chains 645 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 432 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain M residue 1006 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 202 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1002 LYS Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 202 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain XA residue 1107 PHE Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 202 LYS Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 303 PHE Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.061130 restraints weight = 33620.957| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.01 r_work: 0.2689 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.7478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.347 12564 Z= 4.873 Angle : 4.242 52.868 16272 Z= 1.874 Chirality : 0.299 0.775 1152 Planarity : 0.017 0.054 2160 Dihedral : 20.869 119.509 1510 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 111.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.36 % Favored : 82.64 % Rotamer: Outliers : 26.97 % Allowed : 26.16 % Favored : 46.88 % Cbeta Deviations : 14.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.08 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.119 0.017 PHE Q 105 Details of bonding type rmsd hydrogen bonds : bond 0.19669 ( 278) hydrogen bonds : angle 9.10767 ( 786) covalent geometry : bond 0.10955 (12528) covalent geometry : angle 4.24156 (16272) Misc. bond : bond 0.01186 ( 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 663 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 430 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 106 LYS cc_start: 0.9302 (mmmm) cc_final: 0.8880 (mmmm) REVERT: N 1106 LYS cc_start: 0.9300 (mmmm) cc_final: 0.8865 (mmmm) REVERT: B 4 GLU cc_start: 0.8582 (mp0) cc_final: 0.8155 (mp0) REVERT: B 6 LYS cc_start: 0.9292 (mtmt) cc_final: 0.8962 (mtmt) REVERT: Q 106 LYS cc_start: 0.9188 (tptm) cc_final: 0.8686 (tptm) REVERT: S 302 LYS cc_start: 0.9426 (ttpt) cc_final: 0.9095 (mtpp) REVERT: T 1006 LYS cc_start: 0.9266 (mtmt) cc_final: 0.8948 (mtmt) REVERT: W 1302 LYS cc_start: 0.9448 (ttpt) cc_final: 0.9107 (mtpp) REVERT: C 6 LYS cc_start: 0.9233 (mtmt) cc_final: 0.8905 (mtmt) REVERT: X 106 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8985 (mmmm) REVERT: Z 302 LYS cc_start: 0.9480 (ttpt) cc_final: 0.9202 (ttpp) REVERT: j 1006 LYS cc_start: 0.9229 (mtmt) cc_final: 0.8916 (mtmt) REVERT: k 1106 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8915 (mmmm) REVERT: m 1302 LYS cc_start: 0.9462 (ttpt) cc_final: 0.9136 (ttpp) REVERT: D 4 GLU cc_start: 0.8432 (mp0) cc_final: 0.8009 (mm-30) REVERT: n 104 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8099 (mm-30) REVERT: n 106 LYS cc_start: 0.9225 (mmmm) cc_final: 0.8888 (mmmm) REVERT: o 202 LYS cc_start: 0.9382 (mtpt) cc_final: 0.9064 (mtpp) REVERT: p 302 LYS cc_start: 0.9378 (ttpt) cc_final: 0.9010 (ttpp) REVERT: q 1002 LYS cc_start: 0.8407 (tttt) cc_final: 0.8151 (tptm) REVERT: q 1004 GLU cc_start: 0.8524 (mp0) cc_final: 0.7983 (mp0) REVERT: r 1104 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8086 (mp0) REVERT: r 1106 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8883 (mmmm) REVERT: t 1302 LYS cc_start: 0.9383 (ttpt) cc_final: 0.9053 (ttpp) REVERT: u 102 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8890 (mtpp) REVERT: u 106 LYS cc_start: 0.9289 (tptm) cc_final: 0.8901 (tptm) REVERT: w 302 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9036 (ttmm) REVERT: x 1002 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6693 (mmtp) REVERT: x 1006 LYS cc_start: 0.9101 (mtmt) cc_final: 0.8787 (mtmt) REVERT: y 1106 LYS cc_start: 0.9286 (tptm) cc_final: 0.8902 (tptm) REVERT: 0 1302 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9107 (ttmm) REVERT: F 4 GLU cc_start: 0.8650 (mp0) cc_final: 0.8433 (mp0) REVERT: 1 104 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8093 (mm-30) REVERT: 1 106 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8880 (mmmm) REVERT: 2 206 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8939 (ptmm) REVERT: 5 1106 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8793 (mmmm) REVERT: 6 1206 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8935 (ptmm) REVERT: G 4 GLU cc_start: 0.8541 (mp0) cc_final: 0.8199 (mp0) REVERT: G 6 LYS cc_start: 0.9200 (mtmt) cc_final: 0.8850 (mtmt) REVERT: BA 1004 GLU cc_start: 0.8565 (mp0) cc_final: 0.8223 (mp0) REVERT: BA 1006 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8838 (mtmt) REVERT: FA 104 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8436 (tm-30) REVERT: GA 202 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8823 (mtpt) REVERT: GA 204 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5537 (pm20) REVERT: HA 304 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8545 (mm-30) REVERT: I 2 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8822 (tttt) REVERT: MA 106 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.5632 (tptp) REVERT: OA 302 LYS cc_start: 0.9415 (ttpt) cc_final: 0.8966 (tptt) REVERT: RA 1202 LYS cc_start: 0.9214 (ttpt) cc_final: 0.8819 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9395 (ttpt) cc_final: 0.8938 (tptt) REVERT: a 4 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8717 (tp30) REVERT: UA 202 LYS cc_start: 0.9443 (mttm) cc_final: 0.9199 (mmmm) REVERT: UA 204 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8044 (tp30) REVERT: VA 304 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8600 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8654 (tp30) REVERT: YA 1204 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7856 (tm-30) REVERT: ZA 1302 LYS cc_start: 0.9279 (tptp) cc_final: 0.8933 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8508 (tm-30) REVERT: b 2 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8944 (ttmt) REVERT: bA 202 LYS cc_start: 0.9338 (tttm) cc_final: 0.9049 (ttmm) REVERT: bA 204 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8196 (tp30) REVERT: cA 304 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8683 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8928 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9078 (t80) REVERT: eA 1106 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8356 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8041 (tp30) REVERT: gA 1304 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8532 (tm-30) REVERT: iA 204 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8138 (tm-30) REVERT: iA 206 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8684 (ttpp) REVERT: jA 306 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8490 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7990 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8490 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8426 (ttpp) REVERT: oA 103 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.9035 (t80) REVERT: pA 206 LYS cc_start: 0.9292 (pttt) cc_final: 0.8846 (ptmm) REVERT: qA 304 GLU cc_start: 0.9358 (tm-30) cc_final: 0.8736 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8975 (pttt) REVERT: uA 1304 GLU cc_start: 0.9361 (tm-30) cc_final: 0.8862 (tm-30) REVERT: vA 104 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8196 (tm-30) REVERT: wA 202 LYS cc_start: 0.9302 (tttm) cc_final: 0.8837 (ttmm) REVERT: wA 204 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7549 (tm-30) REVERT: xA 302 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8656 (tptp) REVERT: xA 304 GLU cc_start: 0.9289 (tm-30) cc_final: 0.8494 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8908 (tppt) REVERT: zA 1102 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9144 (tptm) REVERT: zA 1105 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8991 (t80) REVERT: 0A 1202 LYS cc_start: 0.9234 (tttm) cc_final: 0.8871 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7386 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8605 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8518 (tm-30) REVERT: 3A 202 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9190 (tppp) REVERT: 4A 306 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8889 (ttpp) REVERT: 6A 1102 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9123 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8663 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8924 (ttpp) REVERT: g 4 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8361 (tp30) REVERT: 9A 102 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9151 (tptm) REVERT: AB 204 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: DB 1102 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9194 (tptm) REVERT: EB 1204 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: i 5 PHE cc_start: 0.9325 (t80) cc_final: 0.9007 (t80) REVERT: i 6 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8942 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8339 (tm-30) REVERT: QB 1006 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8910 (ttpt) outliers start: 233 outliers final: 177 residues processed: 518 average time/residue: 0.5597 time to fit residues: 355.2913 Evaluate side-chains 649 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 431 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain M residue 1006 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain P residue 1304 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 202 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 202 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 204 GLU Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain XA residue 1107 PHE Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 202 LYS Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1102 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 303 PHE Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.061149 restraints weight = 33508.986| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.02 r_work: 0.2689 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.7490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.331 12564 Z= 4.874 Angle : 4.249 53.822 16272 Z= 1.878 Chirality : 0.299 0.781 1152 Planarity : 0.017 0.053 2160 Dihedral : 20.868 125.399 1510 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 112.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.53 % Favored : 82.47 % Rotamer: Outliers : 26.39 % Allowed : 26.74 % Favored : 46.88 % Cbeta Deviations : 15.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.13 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.67 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.119 0.017 PHE U1105 Details of bonding type rmsd hydrogen bonds : bond 0.19612 ( 278) hydrogen bonds : angle 9.10050 ( 786) covalent geometry : bond 0.10959 (12528) covalent geometry : angle 4.24882 (16272) Misc. bond : bond 0.01181 ( 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 658 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 430 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 106 LYS cc_start: 0.9305 (mmmm) cc_final: 0.8884 (mmmm) REVERT: N 1106 LYS cc_start: 0.9304 (mmmm) cc_final: 0.8870 (mmmm) REVERT: B 4 GLU cc_start: 0.8572 (mp0) cc_final: 0.8149 (mp0) REVERT: B 6 LYS cc_start: 0.9309 (mtmt) cc_final: 0.8969 (mtmt) REVERT: Q 106 LYS cc_start: 0.9188 (tptm) cc_final: 0.8680 (tptm) REVERT: S 302 LYS cc_start: 0.9424 (ttpt) cc_final: 0.9089 (mtpp) REVERT: T 1006 LYS cc_start: 0.9273 (mtmt) cc_final: 0.8945 (mtmt) REVERT: W 1302 LYS cc_start: 0.9448 (ttpt) cc_final: 0.9110 (mtpp) REVERT: C 6 LYS cc_start: 0.9192 (mtmt) cc_final: 0.8852 (mtmt) REVERT: X 106 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8991 (mmmm) REVERT: Z 302 LYS cc_start: 0.9481 (ttpt) cc_final: 0.9206 (ttpp) REVERT: j 1006 LYS cc_start: 0.9232 (mtmt) cc_final: 0.8920 (mtmt) REVERT: k 1106 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8921 (mmmm) REVERT: m 1302 LYS cc_start: 0.9462 (ttpt) cc_final: 0.9136 (ttpp) REVERT: D 4 GLU cc_start: 0.8448 (mp0) cc_final: 0.8014 (mm-30) REVERT: n 104 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8105 (mm-30) REVERT: n 106 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8894 (mmmm) REVERT: o 202 LYS cc_start: 0.9381 (mtpt) cc_final: 0.9055 (mtpp) REVERT: p 302 LYS cc_start: 0.9384 (ttpt) cc_final: 0.9015 (ttpp) REVERT: q 1002 LYS cc_start: 0.8421 (tttt) cc_final: 0.8166 (tptm) REVERT: q 1004 GLU cc_start: 0.8483 (mp0) cc_final: 0.8060 (mp0) REVERT: r 1104 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8075 (mp0) REVERT: r 1106 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8884 (mmmm) REVERT: t 1302 LYS cc_start: 0.9373 (ttpt) cc_final: 0.9039 (ttpp) REVERT: E 3 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8807 (m-80) REVERT: u 102 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8891 (mtpp) REVERT: u 106 LYS cc_start: 0.9292 (tptm) cc_final: 0.8910 (tptm) REVERT: w 302 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9046 (ttmm) REVERT: x 1002 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6703 (mmtp) REVERT: x 1006 LYS cc_start: 0.9099 (mtmt) cc_final: 0.8782 (mtmt) REVERT: y 1106 LYS cc_start: 0.9273 (tptm) cc_final: 0.8895 (tptm) REVERT: 0 1302 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9109 (ttmm) REVERT: F 4 GLU cc_start: 0.8658 (mp0) cc_final: 0.8439 (mp0) REVERT: 1 104 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8056 (mm-30) REVERT: 1 106 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8863 (mmmm) REVERT: 2 206 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8948 (ptmm) REVERT: 5 1106 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8792 (mmmm) REVERT: 6 1206 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9005 (ptmm) REVERT: G 4 GLU cc_start: 0.8483 (mp0) cc_final: 0.8117 (mp0) REVERT: G 6 LYS cc_start: 0.9214 (mtmt) cc_final: 0.8752 (mtmt) REVERT: 8 106 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8765 (tmmm) REVERT: BA 1004 GLU cc_start: 0.8504 (mp0) cc_final: 0.8115 (mp0) REVERT: BA 1006 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8854 (mtmt) REVERT: FA 104 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8466 (tm-30) REVERT: GA 202 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8804 (mtpt) REVERT: HA 304 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8534 (mm-30) REVERT: LA 1304 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8463 (mm-30) REVERT: MA 106 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.5613 (tptp) REVERT: OA 302 LYS cc_start: 0.9385 (ttpt) cc_final: 0.8951 (tptt) REVERT: RA 1202 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8811 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9383 (ttpt) cc_final: 0.8926 (tptt) REVERT: a 4 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8717 (tp30) REVERT: UA 202 LYS cc_start: 0.9451 (mttm) cc_final: 0.9180 (mmmm) REVERT: UA 204 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: VA 304 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8601 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8657 (tp30) REVERT: YA 1204 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7896 (tm-30) REVERT: ZA 1302 LYS cc_start: 0.9283 (tptp) cc_final: 0.8954 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8505 (tm-30) REVERT: b 2 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8934 (ttmt) REVERT: bA 202 LYS cc_start: 0.9332 (tttm) cc_final: 0.9040 (ttmm) REVERT: bA 204 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8239 (tp30) REVERT: cA 304 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8684 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8926 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.9080 (t80) REVERT: eA 1106 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8354 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8016 (tp30) REVERT: gA 1304 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8545 (tm-30) REVERT: iA 204 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8156 (tm-30) REVERT: iA 206 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8688 (ttpp) REVERT: jA 306 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8498 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7987 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8481 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8423 (ttpp) REVERT: oA 103 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.9033 (t80) REVERT: pA 206 LYS cc_start: 0.9295 (pttt) cc_final: 0.8847 (ptmm) REVERT: qA 304 GLU cc_start: 0.9372 (tm-30) cc_final: 0.8768 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9000 (pttt) REVERT: uA 1304 GLU cc_start: 0.9361 (tm-30) cc_final: 0.8870 (tm-30) REVERT: vA 104 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8185 (tm-30) REVERT: wA 202 LYS cc_start: 0.9308 (tttm) cc_final: 0.8847 (ttmm) REVERT: wA 204 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7544 (tm-30) REVERT: xA 302 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8655 (tptp) REVERT: xA 304 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8493 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8909 (tppt) REVERT: zA 1102 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9143 (tptm) REVERT: zA 1105 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8973 (t80) REVERT: 0A 1202 LYS cc_start: 0.9241 (tttm) cc_final: 0.8877 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7413 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8598 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8533 (tm-30) REVERT: 3A 202 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9191 (tppp) REVERT: 4A 306 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8916 (ttpp) REVERT: 6A 1102 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9126 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8663 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8921 (ttpp) REVERT: g 4 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8357 (tp30) REVERT: 9A 102 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9145 (tptm) REVERT: AB 204 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8476 (tp30) REVERT: DB 1102 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9194 (tptm) REVERT: EB 1204 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: i 5 PHE cc_start: 0.9343 (t80) cc_final: 0.8989 (t80) REVERT: i 6 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8940 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: QB 1006 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8887 (ttpt) REVERT: SB 1206 LYS cc_start: 0.9302 (pttt) cc_final: 0.8586 (ttpp) outliers start: 228 outliers final: 178 residues processed: 517 average time/residue: 0.5888 time to fit residues: 369.6388 Evaluate side-chains 649 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 430 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain M residue 1006 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 202 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 202 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 204 GLU Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain XA residue 1107 PHE Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 202 LYS Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1102 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 303 PHE Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.061270 restraints weight = 33573.009| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.02 r_work: 0.2694 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.7502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.340 12564 Z= 4.875 Angle : 4.250 52.424 16272 Z= 1.879 Chirality : 0.299 0.777 1152 Planarity : 0.017 0.052 2160 Dihedral : 20.883 128.519 1510 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 112.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.06 % Favored : 81.94 % Rotamer: Outliers : 26.97 % Allowed : 26.04 % Favored : 46.99 % Cbeta Deviations : 14.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.15 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.110 0.017 PHE U1105 Details of bonding type rmsd hydrogen bonds : bond 0.19609 ( 278) hydrogen bonds : angle 9.10304 ( 786) covalent geometry : bond 0.10962 (12528) covalent geometry : angle 4.25022 (16272) Misc. bond : bond 0.01202 ( 36) =============================================================================== Job complete usr+sys time: 6852.24 seconds wall clock time: 123 minutes 49.50 seconds (7429.50 seconds total)