Starting phenix.real_space_refine on Wed Sep 17 05:40:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqf_23484/09_2025/7lqf_23484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqf_23484/09_2025/7lqf_23484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqf_23484/09_2025/7lqf_23484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqf_23484/09_2025/7lqf_23484.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqf_23484/09_2025/7lqf_23484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqf_23484/09_2025/7lqf_23484.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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 3840 2.51 5 N 704 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5376 Number of models: 1 Model: "" Number of chains: 64 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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 Time building chain proxies: 1.23, per 1000 atoms: 0.23 Number of scatterers: 5376 At special positions: 0 Unit cell: (70.2, 87.48, 101.52, 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 832 8.00 N 704 7.00 C 3840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 91.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 106 through 107 removed outlier: 6.813A pdb=" N LYS A 6 " --> pdb=" O PHE L 107 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS B 6 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS D 6 " --> pdb=" O PHE X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'k' and resid 305 through 306 removed outlier: 6.248A pdb=" N PHE j 205 " --> pdb=" O LYS k 306 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE W 305 " --> pdb=" O LYS j 206 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE V 205 " --> pdb=" O LYS W 306 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE Q 305 " --> pdb=" O LYS V 206 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE P 205 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE K 305 " --> pdb=" O LYS P 206 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE J 205 " --> pdb=" O LYS K 306 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE M 205 " --> pdb=" O LYS N 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE S 205 " --> pdb=" O LYS T 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE Y 205 " --> pdb=" O LYS Z 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE m 205 " --> pdb=" O LYS n 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'a' and resid 4 through 6 removed outlier: 3.879A pdb=" N GLU a 4 " --> pdb=" O LYS r 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS r 106 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU r 104 " --> pdb=" O LYS a 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'o' and resid 104 through 106 removed outlier: 3.582A pdb=" N GLU o 104 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS o 106 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU c 4 " --> pdb=" O LYS o 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'y' and resid 202 through 205 removed outlier: 3.692A pdb=" N PHE z 305 " --> pdb=" O PHE y 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE y 205 " --> pdb=" O PHE z 303 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU s 204 " --> pdb=" O LYS z 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GMA z 308 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS s 202 " --> pdb=" O GMA z 308 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE t 305 " --> pdb=" O PHE s 203 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE s 205 " --> pdb=" O PHE t 303 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS p 206 " --> pdb=" O GLU t 304 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU p 204 " --> pdb=" O LYS t 306 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE q 305 " --> pdb=" O PHE p 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE p 205 " --> pdb=" O PHE q 303 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU v 204 " --> pdb=" O LYS q 306 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GMA q 308 " --> pdb=" O LYS v 202 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS v 202 " --> pdb=" O GMA q 308 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE w 305 " --> pdb=" O PHE v 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE v 205 " --> pdb=" O PHE w 303 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS 1 206 " --> pdb=" O GLU w 304 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU 1 204 " --> pdb=" O LYS w 306 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GMA w 308 " --> pdb=" O LYS 1 202 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS 1 202 " --> pdb=" O GMA w 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE 2 305 " --> pdb=" O PHE 1 203 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE 1 205 " --> pdb=" O PHE 2 303 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS 7 206 " --> pdb=" O GLU 2 304 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU 7 204 " --> pdb=" O LYS 2 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GMA 2 308 " --> pdb=" O LYS 7 202 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS 7 202 " --> pdb=" O GMA 2 308 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE 8 305 " --> pdb=" O PHE 7 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 7 205 " --> pdb=" O PHE 8 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 4 through 6 removed outlier: 3.815A pdb=" N GLU b 4 " --> pdb=" O LYS x 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'u' and resid 104 through 106 removed outlier: 3.578A pdb=" N GLU u 104 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS u 106 " --> pdb=" O GLU e 4 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU e 4 " --> pdb=" O LYS u 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 4 through 6 removed outlier: 3.865A pdb=" N GLU d 4 " --> pdb=" O LYS 3 106 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS 3 106 " --> pdb=" O GLU d 4 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU 3 104 " --> pdb=" O LYS d 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '0' and resid 104 through 106 removed outlier: 3.619A pdb=" N GLU 0 104 " --> pdb=" O LYS g 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS 0 106 " --> pdb=" O GLU g 4 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU g 4 " --> pdb=" O LYS 0 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 4 through 6 removed outlier: 3.795A pdb=" N GLU f 4 " --> pdb=" O LYS 9 106 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU 9 104 " --> pdb=" O LYS f 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 202 through 205 removed outlier: 3.693A pdb=" N PHE 5 305 " --> pdb=" O PHE 4 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 4 205 " --> pdb=" O PHE 5 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'AA' and resid 202 through 205 removed outlier: 3.692A pdb=" N PHEBA 305 " --> pdb=" O PHEAA 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHEAA 205 " --> pdb=" O PHEBA 303 " (cutoff:3.500A) 52 hydrogen bonds defined for protein. 126 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: 0.71 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 649 1.25 - 1.33: 411 1.33 - 1.40: 1820 1.40 - 1.47: 576 1.47 - 1.54: 2112 Bond restraints: 5568 Sorted by residual: bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.32e+01 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 6235 1.90 - 3.80: 717 3.80 - 5.70: 192 5.70 - 7.60: 80 7.60 - 9.50: 8 Bond angle restraints: 7232 Sorted by residual: angle pdb=" C 5CR q 301 " pdb=" CA 5CR q 301 " pdb=" CB 5CR q 301 " ideal model delta sigma weight residual 110.10 116.12 -6.02 1.90e+00 2.77e-01 1.00e+01 angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.41 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C 5CR t 301 " pdb=" CA 5CR t 301 " pdb=" CB 5CR t 301 " ideal model delta sigma weight residual 110.10 116.11 -6.01 1.90e+00 2.77e-01 1.00e+01 angle pdb=" C 5CR 5 301 " pdb=" CA 5CR 5 301 " pdb=" CB 5CR 5 301 " ideal model delta sigma weight residual 110.10 116.10 -6.00 1.90e+00 2.77e-01 9.99e+00 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.39 -9.48 3.00e+00 1.11e-01 9.99e+00 ... (remaining 7227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.80: 1977 10.80 - 21.61: 416 21.61 - 32.41: 159 32.41 - 43.21: 144 43.21 - 54.01: 56 Dihedral angle restraints: 2752 sinusoidal: 1280 harmonic: 1472 Sorted by residual: dihedral pdb=" CA LYS r 106 " pdb=" CB LYS r 106 " pdb=" CG LYS r 106 " pdb=" CD LYS r 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS 9 106 " pdb=" CB LYS 9 106 " pdb=" CG LYS 9 106 " pdb=" CD LYS 9 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS u 106 " pdb=" CB LYS u 106 " pdb=" CG LYS u 106 " pdb=" CD LYS u 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.00 54.00 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.017: 172 0.017 - 0.034: 140 0.034 - 0.051: 124 0.051 - 0.067: 60 0.067 - 0.084: 16 Chirality restraints: 512 Sorted by residual: chirality pdb=" CA PHE j 203 " pdb=" N PHE j 203 " pdb=" C PHE j 203 " pdb=" CB PHE j 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.76e-01 chirality pdb=" CA PHE Y 203 " pdb=" N PHE Y 203 " pdb=" C PHE Y 203 " pdb=" CB PHE Y 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.73e-01 chirality pdb=" CA PHE m 203 " pdb=" N PHE m 203 " pdb=" C PHE m 203 " pdb=" CB PHE m 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.71e-01 ... (remaining 509 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE p 203 " 0.009 2.00e-02 2.50e+03 6.10e-03 6.51e-01 pdb=" CG PHE p 203 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE p 203 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE p 203 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE p 203 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE p 203 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE p 203 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEBA 303 " 0.005 2.00e-02 2.50e+03 5.92e-03 6.14e-01 pdb=" CG PHEBA 303 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHEBA 303 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEBA 303 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEBA 303 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHEBA 303 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHEBA 303 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 4 203 " -0.009 2.00e-02 2.50e+03 5.91e-03 6.11e-01 pdb=" CG PHE 4 203 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE 4 203 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE 4 203 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE 4 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 4 203 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE 4 203 " -0.004 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1729 2.79 - 3.31: 4534 3.31 - 3.84: 8714 3.84 - 4.37: 11165 4.37 - 4.90: 19430 Nonbonded interactions: 45572 Sorted by model distance: nonbonded pdb=" O GMA I 108 " pdb=" N 5CR J 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA i 108 " pdb=" N 5CR j 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA X 108 " pdb=" N 5CR Y 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA l 108 " pdb=" N 5CR m 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA R 108 " pdb=" N 5CR S 201 " model vdw 2.258 3.120 ... (remaining 45567 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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 group one per residue 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.940 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.016 0.116 5568 Z= 0.776 Angle : 1.461 9.501 7232 Z= 0.602 Chirality : 0.035 0.084 512 Planarity : 0.002 0.007 960 Dihedral : 18.365 54.014 1728 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.77 (0.32), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.24), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE 5 303 Details of bonding type rmsd covalent geometry : bond 0.01575 ( 5568) covalent geometry : angle 1.46064 ( 7232) hydrogen bonds : bond 0.29011 ( 52) hydrogen bonds : angle 10.62446 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.188 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: A 2 LYS cc_start: 0.9136 (tttt) cc_final: 0.8811 (tptm) REVERT: A 7 PHE cc_start: 0.8216 (m-10) cc_final: 0.7886 (m-10) REVERT: J 202 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7898 (ttmm) REVERT: K 306 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7586 (mmmm) REVERT: B 2 LYS cc_start: 0.9157 (tttt) cc_final: 0.8892 (tptm) REVERT: B 6 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7432 (mmmm) REVERT: L 102 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8600 (mmtt) REVERT: M 204 GLU cc_start: 0.8113 (pt0) cc_final: 0.7204 (pm20) REVERT: N 306 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7691 (mmmm) REVERT: Q 306 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7608 (mmmm) REVERT: D 2 LYS cc_start: 0.9124 (tttt) cc_final: 0.8722 (tptm) REVERT: D 3 PHE cc_start: 0.8401 (m-80) cc_final: 0.8172 (m-80) REVERT: D 6 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7546 (mmmm) REVERT: R 104 GLU cc_start: 0.7921 (tm-30) cc_final: 0.6923 (tm-30) REVERT: S 204 GLU cc_start: 0.8108 (pt0) cc_final: 0.7535 (pm20) REVERT: T 305 PHE cc_start: 0.8456 (m-80) cc_final: 0.8254 (m-10) REVERT: T 306 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7671 (mmmm) REVERT: E 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8717 (tptm) REVERT: U 104 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7072 (tm-30) REVERT: V 204 GLU cc_start: 0.8325 (pt0) cc_final: 0.7746 (pm20) REVERT: W 302 LYS cc_start: 0.8301 (tppp) cc_final: 0.7719 (tppp) REVERT: W 306 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7862 (mmmm) REVERT: F 2 LYS cc_start: 0.9090 (tttt) cc_final: 0.8422 (tmtt) REVERT: X 104 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7017 (tm-30) REVERT: X 106 LYS cc_start: 0.7894 (tppt) cc_final: 0.7561 (tppt) REVERT: Y 204 GLU cc_start: 0.8371 (pt0) cc_final: 0.7350 (pp20) REVERT: Z 306 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7335 (mmmm) REVERT: G 6 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7868 (ttmm) REVERT: i 102 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8357 (mmtt) REVERT: i 104 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7020 (tm-30) REVERT: i 106 LYS cc_start: 0.7678 (tppt) cc_final: 0.7407 (tppt) REVERT: j 204 GLU cc_start: 0.8071 (pt0) cc_final: 0.7744 (pm20) REVERT: k 304 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6755 (tm-30) REVERT: H 3 PHE cc_start: 0.8404 (m-80) cc_final: 0.8026 (m-80) REVERT: l 102 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8558 (mmtt) REVERT: m 204 GLU cc_start: 0.7905 (pt0) cc_final: 0.7370 (pm20) REVERT: m 205 PHE cc_start: 0.8286 (m-80) cc_final: 0.8052 (m-80) REVERT: n 306 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7577 (mmmm) REVERT: p 203 PHE cc_start: 0.7511 (t80) cc_final: 0.7309 (t80) REVERT: q 303 PHE cc_start: 0.8252 (t80) cc_final: 0.7808 (t80) REVERT: q 307 PHE cc_start: 0.7542 (t80) cc_final: 0.7293 (t80) REVERT: r 105 PHE cc_start: 0.9015 (p90) cc_final: 0.8791 (p90) REVERT: t 303 PHE cc_start: 0.8188 (t80) cc_final: 0.7770 (t80) REVERT: t 305 PHE cc_start: 0.7586 (t80) cc_final: 0.7183 (t80) REVERT: v 204 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7051 (tm-30) REVERT: w 302 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8490 (tmtt) REVERT: x 105 PHE cc_start: 0.8978 (p90) cc_final: 0.8358 (p90) REVERT: x 107 PHE cc_start: 0.8027 (t80) cc_final: 0.7191 (t80) REVERT: z 305 PHE cc_start: 0.7904 (t80) cc_final: 0.7476 (t80) REVERT: e 6 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8167 (ttmm) REVERT: e 7 PHE cc_start: 0.9053 (t80) cc_final: 0.8752 (t80) REVERT: 1 202 LYS cc_start: 0.8057 (tptp) cc_final: 0.7783 (tptp) REVERT: 2 305 PHE cc_start: 0.7995 (t80) cc_final: 0.7673 (t80) REVERT: f 7 PHE cc_start: 0.8908 (t80) cc_final: 0.8382 (t80) REVERT: 3 105 PHE cc_start: 0.8867 (p90) cc_final: 0.8660 (p90) REVERT: 3 106 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8356 (ttpp) REVERT: 4 204 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7088 (tm-30) REVERT: 5 303 PHE cc_start: 0.8146 (t80) cc_final: 0.7910 (t80) REVERT: g 2 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8492 (mmtt) REVERT: 6 106 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8435 (ttpp) REVERT: 7 204 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7069 (tm-30) REVERT: 8 302 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8593 (tmtt) REVERT: 8 307 PHE cc_start: 0.7753 (t80) cc_final: 0.7394 (t80) REVERT: 9 107 PHE cc_start: 0.7939 (t80) cc_final: 0.7557 (t80) outliers start: 8 outliers final: 0 residues processed: 164 average time/residue: 0.1505 time to fit residues: 28.1670 Evaluate side-chains 161 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain G residue 6 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 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 = 0.2805 r_free = 0.2805 target = 0.053727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.046084 restraints weight = 20345.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.047947 restraints weight = 11023.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.049250 restraints weight = 6925.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.050133 restraints weight = 4713.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.050800 restraints weight = 3411.947| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.153 0.471 5568 Z= 6.696 Angle : 6.008 58.256 7232 Z= 2.679 Chirality : 0.409 1.111 512 Planarity : 0.029 0.097 960 Dihedral : 25.177 84.646 652 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 194.17 Ramachandran Plot: Outliers : 7.42 % Allowed : 33.59 % Favored : 58.98 % Rotamer: Outliers : 15.89 % Allowed : 27.08 % Favored : 57.03 % Cbeta Deviations : 47.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -8.46 (0.26), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.44 (0.20), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.199 0.029 PHE 3 107 Details of bonding type rmsd covalent geometry : bond 0.15309 ( 5568) covalent geometry : angle 6.00772 ( 7232) hydrogen bonds : bond 0.27896 ( 52) hydrogen bonds : angle 14.35482 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 0.141 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: A 7 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.9018 (m-10) REVERT: I 107 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8568 (m-10) REVERT: J 206 LYS cc_start: 0.9058 (tttm) cc_final: 0.7857 (ttpp) REVERT: K 306 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8283 (mmmm) REVERT: M 202 LYS cc_start: 0.9402 (ttmm) cc_final: 0.9152 (ttmm) REVERT: M 206 LYS cc_start: 0.8838 (tttm) cc_final: 0.8200 (tttm) REVERT: N 304 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7969 (tm-30) REVERT: N 306 LYS cc_start: 0.8789 (mmmm) cc_final: 0.8077 (mmmm) REVERT: N 307 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8442 (t80) REVERT: Q 303 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: S 202 LYS cc_start: 0.9483 (ttmm) cc_final: 0.9149 (ttpp) REVERT: S 206 LYS cc_start: 0.9017 (tttm) cc_final: 0.7914 (ttpp) REVERT: T 306 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8061 (mmmm) REVERT: E 6 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8724 (ttmm) REVERT: U 103 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8172 (m-80) REVERT: W 304 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7319 (tm-30) REVERT: W 306 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8305 (mmmm) REVERT: Y 206 LYS cc_start: 0.8746 (tttm) cc_final: 0.8397 (tttm) REVERT: Z 304 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8239 (tm-30) REVERT: Z 306 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8036 (mmmm) REVERT: Z 307 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: G 2 LYS cc_start: 0.9436 (tptt) cc_final: 0.9147 (tptm) REVERT: G 6 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8546 (ttmm) REVERT: G 7 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: i 106 LYS cc_start: 0.5475 (tppt) cc_final: 0.4700 (tptt) REVERT: i 107 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8610 (m-10) REVERT: l 103 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: l 106 LYS cc_start: 0.9046 (tppt) cc_final: 0.8684 (tppt) REVERT: m 202 LYS cc_start: 0.9319 (ttmm) cc_final: 0.8948 (ttmm) REVERT: m 204 GLU cc_start: 0.9022 (pt0) cc_final: 0.8641 (pt0) REVERT: n 302 LYS cc_start: 0.9031 (tppp) cc_final: 0.8830 (tppp) REVERT: n 304 GLU cc_start: 0.8508 (tm-30) cc_final: 0.7909 (tm-30) REVERT: n 306 LYS cc_start: 0.8820 (mmmm) cc_final: 0.8377 (mmmm) REVERT: n 307 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8840 (t80) REVERT: a 2 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8534 (mmtt) REVERT: p 204 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8074 (tm-30) REVERT: r 104 GLU cc_start: 0.9100 (pp20) cc_final: 0.8856 (pp20) REVERT: s 206 LYS cc_start: 0.8784 (tptp) cc_final: 0.8410 (tptp) REVERT: t 306 LYS cc_start: 0.9265 (tmtt) cc_final: 0.8438 (tmtt) REVERT: u 104 GLU cc_start: 0.8985 (pp20) cc_final: 0.8746 (pp20) REVERT: v 204 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7876 (tm-30) REVERT: d 7 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8976 (t80) REVERT: y 204 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7771 (tm-30) REVERT: z 306 LYS cc_start: 0.9214 (tttt) cc_final: 0.8229 (tmtt) REVERT: z 307 PHE cc_start: 0.8870 (t80) cc_final: 0.8645 (t80) REVERT: 0 106 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9003 (ttpp) REVERT: 2 302 LYS cc_start: 0.9375 (tmtt) cc_final: 0.8894 (tmtt) REVERT: 3 102 LYS cc_start: 0.9129 (tptp) cc_final: 0.8906 (tptp) REVERT: 3 103 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8292 (p90) REVERT: 3 107 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8617 (t80) REVERT: 4 204 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8049 (tm-30) REVERT: g 2 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8653 (mmtt) REVERT: 7 202 LYS cc_start: 0.9204 (tptp) cc_final: 0.8865 (tptp) REVERT: 7 204 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7888 (tm-30) REVERT: 8 306 LYS cc_start: 0.8692 (tttt) cc_final: 0.7972 (tmtt) REVERT: 8 307 PHE cc_start: 0.8689 (t80) cc_final: 0.8368 (t80) REVERT: AA 206 LYS cc_start: 0.8811 (tptp) cc_final: 0.8402 (tptp) REVERT: BA 307 PHE cc_start: 0.8802 (t80) cc_final: 0.8534 (t80) outliers start: 61 outliers final: 29 residues processed: 210 average time/residue: 0.1570 time to fit residues: 37.3098 Evaluate side-chains 206 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 107 PHE Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.2825 r_free = 0.2825 target = 0.054595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.047190 restraints weight = 20470.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.048985 restraints weight = 11236.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.050236 restraints weight = 7131.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.051118 restraints weight = 4863.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.051759 restraints weight = 3509.398| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.9554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.559 5568 Z= 6.730 Angle : 6.182 59.043 7232 Z= 2.745 Chirality : 0.414 1.063 512 Planarity : 0.028 0.091 960 Dihedral : 25.365 89.291 648 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 192.77 Ramachandran Plot: Outliers : 2.73 % Allowed : 55.08 % Favored : 42.19 % Rotamer: Outliers : 20.83 % Allowed : 31.51 % Favored : 47.66 % Cbeta Deviations : 47.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.90 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -9.08 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.92 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.186 0.027 PHE 5 303 Details of bonding type rmsd covalent geometry : bond 0.15381 ( 5568) covalent geometry : angle 6.18194 ( 7232) hydrogen bonds : bond 0.30459 ( 52) hydrogen bonds : angle 15.53797 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 161 time to evaluate : 0.226 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: A 2 LYS cc_start: 0.9425 (tptt) cc_final: 0.9154 (tptt) REVERT: A 5 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8454 (m-10) REVERT: A 7 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8993 (m-10) REVERT: I 107 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8652 (m-10) REVERT: J 206 LYS cc_start: 0.9055 (tttm) cc_final: 0.8494 (ttpp) REVERT: K 306 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8275 (mmmm) REVERT: M 202 LYS cc_start: 0.9384 (ttmm) cc_final: 0.9125 (ttmm) REVERT: N 302 LYS cc_start: 0.9155 (tppp) cc_final: 0.8934 (tppp) REVERT: N 304 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8081 (tm-30) REVERT: N 306 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8247 (mmmm) REVERT: N 307 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8397 (t80) REVERT: P 202 LYS cc_start: 0.9339 (ttmm) cc_final: 0.9114 (ttmm) REVERT: P 206 LYS cc_start: 0.8787 (tttm) cc_final: 0.8487 (tttm) REVERT: Q 302 LYS cc_start: 0.8943 (tppp) cc_final: 0.8724 (mmmm) REVERT: S 202 LYS cc_start: 0.9443 (ttmm) cc_final: 0.8425 (ttpp) REVERT: S 206 LYS cc_start: 0.9027 (tttm) cc_final: 0.8150 (ttpp) REVERT: T 304 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8034 (tm-30) REVERT: E 6 LYS cc_start: 0.9270 (mmmm) cc_final: 0.8839 (ttmm) REVERT: U 103 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: W 302 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8710 (ttpp) REVERT: W 304 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7269 (tm-30) REVERT: X 103 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8799 (m-10) REVERT: X 106 LYS cc_start: 0.9005 (tppt) cc_final: 0.8499 (ttpt) REVERT: Y 206 LYS cc_start: 0.8735 (tttm) cc_final: 0.8474 (tttm) REVERT: Z 302 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8422 (tppp) REVERT: Z 304 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8364 (tm-30) REVERT: Z 306 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8126 (mmmm) REVERT: Z 307 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: G 5 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: G 6 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.9013 (ttmm) REVERT: G 7 PHE cc_start: 0.9487 (OUTLIER) cc_final: 0.8851 (m-80) REVERT: j 206 LYS cc_start: 0.9109 (tttm) cc_final: 0.8724 (ttpp) REVERT: k 304 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7328 (tm-30) REVERT: l 102 LYS cc_start: 0.9483 (mmtt) cc_final: 0.9185 (mmtt) REVERT: l 103 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: m 202 LYS cc_start: 0.9361 (ttmm) cc_final: 0.9085 (ttmm) REVERT: m 204 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8651 (pt0) REVERT: m 206 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8279 (pttm) REVERT: n 304 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8024 (tm-30) REVERT: n 306 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8520 (mmmm) REVERT: n 307 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8842 (t80) REVERT: a 2 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8566 (mmtt) REVERT: p 203 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8518 (t80) REVERT: q 306 LYS cc_start: 0.9111 (tttt) cc_final: 0.8783 (tttp) REVERT: q 307 PHE cc_start: 0.8722 (t80) cc_final: 0.8170 (t80) REVERT: s 202 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8866 (tppp) REVERT: t 303 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7466 (t80) REVERT: v 204 GLU cc_start: 0.8661 (tm-30) cc_final: 0.7965 (tm-30) REVERT: v 207 PHE cc_start: 0.8863 (t80) cc_final: 0.7901 (t80) REVERT: y 202 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8724 (ttmm) REVERT: y 204 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8001 (tm-30) REVERT: z 302 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8685 (tmtt) REVERT: 1 203 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8457 (t80) REVERT: 2 302 LYS cc_start: 0.9354 (tmtt) cc_final: 0.8889 (tmtt) REVERT: 3 102 LYS cc_start: 0.9192 (tptp) cc_final: 0.8950 (tptp) REVERT: 3 103 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8652 (p90) REVERT: 3 107 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8751 (t80) REVERT: 5 306 LYS cc_start: 0.8947 (tttt) cc_final: 0.8685 (tttp) REVERT: g 2 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8683 (mmtt) REVERT: 7 204 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8084 (tm-30) REVERT: 8 307 PHE cc_start: 0.8588 (t80) cc_final: 0.8305 (t80) REVERT: AA 206 LYS cc_start: 0.8725 (tptp) cc_final: 0.8326 (tptp) REVERT: BA 302 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8855 (tmtt) REVERT: BA 307 PHE cc_start: 0.8745 (t80) cc_final: 0.8439 (t80) outliers start: 80 outliers final: 41 residues processed: 212 average time/residue: 0.1637 time to fit residues: 39.6632 Evaluate side-chains 221 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.2822 r_free = 0.2822 target = 0.054346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.047005 restraints weight = 20454.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.048788 restraints weight = 11100.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.050044 restraints weight = 7045.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.050924 restraints weight = 4779.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.051569 restraints weight = 3417.708| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.9763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.482 5568 Z= 6.727 Angle : 6.224 59.426 7232 Z= 2.761 Chirality : 0.415 1.044 512 Planarity : 0.028 0.090 960 Dihedral : 25.159 89.962 648 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 195.66 Ramachandran Plot: Outliers : 1.95 % Allowed : 55.47 % Favored : 42.58 % Rotamer: Outliers : 25.00 % Allowed : 33.59 % Favored : 41.41 % Cbeta Deviations : 46.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.01 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -9.08 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.92 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.181 0.026 PHE 5 303 Details of bonding type rmsd covalent geometry : bond 0.15365 ( 5568) covalent geometry : angle 6.22368 ( 7232) hydrogen bonds : bond 0.31836 ( 52) hydrogen bonds : angle 15.83575 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 161 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8394 (m-10) REVERT: A 7 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8997 (m-10) REVERT: I 107 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8664 (m-10) REVERT: J 206 LYS cc_start: 0.9028 (tttm) cc_final: 0.8593 (ttpp) REVERT: K 306 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8322 (mmmm) REVERT: L 103 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8797 (m-80) REVERT: M 202 LYS cc_start: 0.9381 (ttmm) cc_final: 0.9100 (ttmm) REVERT: M 206 LYS cc_start: 0.8911 (tttm) cc_final: 0.8668 (tttm) REVERT: N 304 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8157 (tm-30) REVERT: N 306 LYS cc_start: 0.8753 (mmmm) cc_final: 0.8243 (mmmm) REVERT: N 307 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8420 (t80) REVERT: P 206 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8552 (tttm) REVERT: Q 302 LYS cc_start: 0.8974 (tppp) cc_final: 0.8736 (mmmm) REVERT: Q 303 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: Q 306 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7937 (mmmm) REVERT: Q 307 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8207 (t80) REVERT: S 202 LYS cc_start: 0.9466 (ttmm) cc_final: 0.8394 (ttpp) REVERT: S 206 LYS cc_start: 0.9009 (tttm) cc_final: 0.8713 (ttpp) REVERT: T 304 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7508 (tm-30) REVERT: T 306 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8268 (mmtp) REVERT: E 6 LYS cc_start: 0.9282 (mmmm) cc_final: 0.8922 (ttmm) REVERT: U 103 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: U 106 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8755 (tppt) REVERT: V 202 LYS cc_start: 0.9544 (ttmm) cc_final: 0.9292 (ttmm) REVERT: V 206 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8269 (ttpp) REVERT: W 302 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8704 (ttpp) REVERT: W 304 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7217 (tm-30) REVERT: Y 206 LYS cc_start: 0.8805 (tttm) cc_final: 0.8584 (tttm) REVERT: Z 302 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8362 (tppp) REVERT: Z 307 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: G 5 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: G 7 PHE cc_start: 0.9482 (OUTLIER) cc_final: 0.8737 (m-80) REVERT: i 102 LYS cc_start: 0.5833 (OUTLIER) cc_final: 0.5568 (mmmt) REVERT: l 102 LYS cc_start: 0.9490 (mmtt) cc_final: 0.9229 (mmtm) REVERT: l 103 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: m 204 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8771 (pt0) REVERT: m 206 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8335 (pttm) REVERT: n 304 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8059 (tm-30) REVERT: n 306 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8537 (mmmm) REVERT: n 307 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8822 (t80) REVERT: a 2 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8546 (mmtt) REVERT: o 107 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8337 (t80) REVERT: p 203 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8533 (t80) REVERT: q 303 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7678 (t80) REVERT: q 306 LYS cc_start: 0.9137 (tttt) cc_final: 0.8854 (tttp) REVERT: q 307 PHE cc_start: 0.8713 (t80) cc_final: 0.8182 (t80) REVERT: t 303 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7422 (t80) REVERT: v 204 GLU cc_start: 0.8727 (tm-30) cc_final: 0.7982 (tm-30) REVERT: v 207 PHE cc_start: 0.8889 (t80) cc_final: 0.7873 (t80) REVERT: y 202 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8774 (ttmm) REVERT: y 203 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8507 (t80) REVERT: z 302 LYS cc_start: 0.9142 (tmtt) cc_final: 0.8668 (tmtt) REVERT: 1 203 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8397 (t80) REVERT: 2 306 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8666 (tmtt) REVERT: f 2 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8605 (mmtt) REVERT: 3 102 LYS cc_start: 0.9136 (tptp) cc_final: 0.8912 (tptp) REVERT: 5 306 LYS cc_start: 0.8923 (tttp) cc_final: 0.8618 (tttt) REVERT: 5 307 PHE cc_start: 0.8968 (t80) cc_final: 0.8377 (t80) REVERT: g 2 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8675 (mmtt) REVERT: 6 102 LYS cc_start: 0.9058 (tptp) cc_final: 0.8852 (ttpt) REVERT: 8 307 PHE cc_start: 0.8598 (t80) cc_final: 0.8350 (t80) REVERT: 9 104 GLU cc_start: 0.8764 (tm-30) cc_final: 0.7925 (tm-30) REVERT: AA 206 LYS cc_start: 0.8731 (tptp) cc_final: 0.8428 (tptp) REVERT: BA 302 LYS cc_start: 0.9129 (tmtt) cc_final: 0.8878 (tmtt) REVERT: BA 307 PHE cc_start: 0.8808 (t80) cc_final: 0.8463 (t80) outliers start: 96 outliers final: 48 residues processed: 219 average time/residue: 0.1588 time to fit residues: 39.6004 Evaluate side-chains 238 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 161 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 205 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.055105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.047780 restraints weight = 20690.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.049582 restraints weight = 11216.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.050797 restraints weight = 7018.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.051660 restraints weight = 4765.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.052189 restraints weight = 3422.164| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.9993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.474 5568 Z= 6.742 Angle : 6.265 60.362 7232 Z= 2.771 Chirality : 0.415 1.055 512 Planarity : 0.028 0.091 960 Dihedral : 25.522 89.635 644 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 196.90 Ramachandran Plot: Outliers : 1.56 % Allowed : 57.03 % Favored : 41.41 % Rotamer: Outliers : 26.30 % Allowed : 31.77 % Favored : 41.93 % Cbeta Deviations : 48.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.90 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -9.13 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.95 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.026 PHE 5 303 Details of bonding type rmsd covalent geometry : bond 0.15400 ( 5568) covalent geometry : angle 6.26481 ( 7232) hydrogen bonds : bond 0.31847 ( 52) hydrogen bonds : angle 15.84795 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 162 time to evaluate : 0.209 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: A 5 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8425 (m-10) REVERT: A 7 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.9010 (m-10) REVERT: I 102 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8941 (mmtm) REVERT: I 107 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8669 (m-10) REVERT: J 206 LYS cc_start: 0.9108 (tttm) cc_final: 0.8725 (ttpp) REVERT: K 306 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8382 (mmmm) REVERT: L 103 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8927 (m-80) REVERT: M 206 LYS cc_start: 0.8901 (tttm) cc_final: 0.8653 (tttm) REVERT: N 304 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8187 (tm-30) REVERT: N 306 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8291 (mmmm) REVERT: N 307 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8426 (t80) REVERT: O 102 LYS cc_start: 0.9546 (mmtm) cc_final: 0.9334 (mmtm) REVERT: P 206 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8381 (ptmm) REVERT: Q 303 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: Q 306 LYS cc_start: 0.8304 (mmmm) cc_final: 0.7926 (mmmm) REVERT: Q 307 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8293 (t80) REVERT: S 202 LYS cc_start: 0.9472 (OUTLIER) cc_final: 0.8839 (ttpp) REVERT: S 206 LYS cc_start: 0.8953 (tttm) cc_final: 0.8247 (ttpp) REVERT: T 304 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7513 (tm-30) REVERT: T 306 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8267 (mmtp) REVERT: E 6 LYS cc_start: 0.9304 (mmmm) cc_final: 0.8965 (ttmm) REVERT: U 103 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: U 106 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8828 (tppt) REVERT: V 202 LYS cc_start: 0.9589 (OUTLIER) cc_final: 0.8836 (ttmm) REVERT: V 206 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8029 (ttpp) REVERT: W 302 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8555 (ttpp) REVERT: W 304 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7213 (tm-30) REVERT: X 103 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8771 (m-10) REVERT: X 106 LYS cc_start: 0.9084 (tppt) cc_final: 0.8565 (tppt) REVERT: Z 302 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8614 (tppp) REVERT: Z 304 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8298 (tm-30) REVERT: Z 306 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8142 (mmmm) REVERT: Z 307 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: G 5 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: G 7 PHE cc_start: 0.9510 (OUTLIER) cc_final: 0.8831 (m-80) REVERT: i 102 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.5721 (mmmt) REVERT: l 102 LYS cc_start: 0.9480 (mmtt) cc_final: 0.9262 (mmtm) REVERT: l 103 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: m 206 LYS cc_start: 0.8924 (tttm) cc_final: 0.8293 (pttm) REVERT: n 304 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8158 (tm-30) REVERT: n 306 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8657 (mmmm) REVERT: a 2 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8553 (mmtt) REVERT: o 107 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8424 (t80) REVERT: p 203 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8483 (t80) REVERT: q 302 LYS cc_start: 0.9309 (tmtt) cc_final: 0.8858 (tmtt) REVERT: q 303 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.7333 (t80) REVERT: q 305 PHE cc_start: 0.9079 (t80) cc_final: 0.8862 (t80) REVERT: q 306 LYS cc_start: 0.9125 (tttt) cc_final: 0.8768 (tttp) REVERT: q 307 PHE cc_start: 0.8727 (t80) cc_final: 0.8083 (t80) REVERT: r 102 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8341 (ttpp) REVERT: s 202 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8892 (tppp) REVERT: t 303 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7635 (t80) REVERT: c 3 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8114 (t80) REVERT: v 204 GLU cc_start: 0.8733 (tm-30) cc_final: 0.7978 (tm-30) REVERT: v 207 PHE cc_start: 0.8897 (t80) cc_final: 0.7875 (t80) REVERT: y 203 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8502 (t80) REVERT: z 302 LYS cc_start: 0.9144 (tmtt) cc_final: 0.8671 (tmtt) REVERT: 1 203 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8511 (t80) REVERT: 2 306 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8668 (tmtt) REVERT: f 2 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8548 (mmtt) REVERT: 3 102 LYS cc_start: 0.9167 (tptp) cc_final: 0.8921 (tptp) REVERT: 4 202 LYS cc_start: 0.9216 (tptp) cc_final: 0.8852 (tppp) REVERT: 5 306 LYS cc_start: 0.9010 (tttp) cc_final: 0.8615 (tttp) REVERT: 5 307 PHE cc_start: 0.8950 (t80) cc_final: 0.8599 (t80) REVERT: g 2 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8697 (mmtt) REVERT: 7 202 LYS cc_start: 0.9202 (tptp) cc_final: 0.8807 (tptp) REVERT: 7 203 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8395 (t80) REVERT: 8 307 PHE cc_start: 0.8538 (t80) cc_final: 0.8313 (t80) REVERT: 9 104 GLU cc_start: 0.8835 (tm-30) cc_final: 0.7936 (tm-30) REVERT: AA 206 LYS cc_start: 0.8736 (tptp) cc_final: 0.8468 (tptp) REVERT: BA 307 PHE cc_start: 0.8792 (t80) cc_final: 0.8395 (t80) outliers start: 101 outliers final: 54 residues processed: 223 average time/residue: 0.1525 time to fit residues: 38.9496 Evaluate side-chains 248 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 161 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 305 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 205 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.2835 r_free = 0.2835 target = 0.055003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.047695 restraints weight = 20511.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.049491 restraints weight = 11071.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.050705 restraints weight = 6931.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.051570 restraints weight = 4702.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.052196 restraints weight = 3369.862| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 1.0033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.473 5568 Z= 6.736 Angle : 6.242 61.814 7232 Z= 2.760 Chirality : 0.415 1.083 512 Planarity : 0.028 0.092 960 Dihedral : 25.424 89.561 644 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 196.03 Ramachandran Plot: Outliers : 1.56 % Allowed : 55.47 % Favored : 42.97 % Rotamer: Outliers : 28.12 % Allowed : 32.03 % Favored : 39.84 % Cbeta Deviations : 48.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -9.10 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.93 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.025 PHE 5 303 Details of bonding type rmsd covalent geometry : bond 0.15381 ( 5568) covalent geometry : angle 6.24169 ( 7232) hydrogen bonds : bond 0.31769 ( 52) hydrogen bonds : angle 15.88570 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 163 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8447 (m-10) REVERT: A 7 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.9012 (m-10) REVERT: I 102 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8946 (mmtm) REVERT: I 107 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8669 (m-10) REVERT: J 206 LYS cc_start: 0.9042 (tttm) cc_final: 0.8699 (ttpp) REVERT: K 306 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8389 (mmmm) REVERT: L 103 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8920 (m-80) REVERT: M 206 LYS cc_start: 0.8913 (tttm) cc_final: 0.8663 (tttm) REVERT: N 304 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8168 (tm-30) REVERT: N 306 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8266 (mmmm) REVERT: N 307 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8423 (t80) REVERT: O 105 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8428 (m-10) REVERT: P 206 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8353 (ptmm) REVERT: Q 303 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: S 202 LYS cc_start: 0.9475 (OUTLIER) cc_final: 0.8909 (ttpp) REVERT: S 206 LYS cc_start: 0.8938 (tttm) cc_final: 0.8259 (ttpp) REVERT: T 304 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7575 (tm-30) REVERT: T 306 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8273 (mmtp) REVERT: E 6 LYS cc_start: 0.9299 (mmmm) cc_final: 0.8951 (ttmm) REVERT: U 103 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: V 202 LYS cc_start: 0.9603 (OUTLIER) cc_final: 0.8854 (ttmm) REVERT: W 302 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8560 (ttpp) REVERT: W 304 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7678 (tm-30) REVERT: F 5 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8573 (m-80) REVERT: X 103 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8779 (m-10) REVERT: X 106 LYS cc_start: 0.9075 (tppt) cc_final: 0.8559 (tppt) REVERT: Z 302 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8684 (tppp) REVERT: Z 306 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8112 (mmmm) REVERT: Z 307 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: G 5 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8688 (m-80) REVERT: l 102 LYS cc_start: 0.9475 (mmtt) cc_final: 0.9242 (mmtm) REVERT: l 103 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: m 206 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8308 (pttm) REVERT: n 304 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8145 (tm-30) REVERT: a 2 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8785 (mtmm) REVERT: o 107 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8332 (t80) REVERT: p 203 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8453 (t80) REVERT: q 302 LYS cc_start: 0.9301 (tmtt) cc_final: 0.8874 (tmtt) REVERT: q 303 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.7315 (t80) REVERT: q 305 PHE cc_start: 0.9078 (t80) cc_final: 0.8844 (t80) REVERT: q 306 LYS cc_start: 0.9121 (tttt) cc_final: 0.8755 (tttp) REVERT: q 307 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8096 (t80) REVERT: s 202 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8882 (tppp) REVERT: t 303 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.7540 (t80) REVERT: c 3 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8108 (t80) REVERT: v 204 GLU cc_start: 0.8732 (tm-30) cc_final: 0.7977 (tm-30) REVERT: v 207 PHE cc_start: 0.8909 (t80) cc_final: 0.7910 (t80) REVERT: x 104 GLU cc_start: 0.9138 (pp20) cc_final: 0.8838 (pp20) REVERT: y 203 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8481 (t80) REVERT: z 302 LYS cc_start: 0.9139 (tmtt) cc_final: 0.8677 (tmtt) REVERT: 1 203 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8508 (t80) REVERT: 2 306 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8659 (tmtt) REVERT: f 2 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8487 (mmtt) REVERT: 3 102 LYS cc_start: 0.9157 (tptp) cc_final: 0.8922 (tptp) REVERT: 4 202 LYS cc_start: 0.9233 (tptp) cc_final: 0.8850 (tppp) REVERT: 5 306 LYS cc_start: 0.9034 (tttp) cc_final: 0.8652 (tttp) REVERT: 5 307 PHE cc_start: 0.8914 (t80) cc_final: 0.8606 (t80) REVERT: g 2 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8689 (mmtt) REVERT: 7 202 LYS cc_start: 0.9225 (tptp) cc_final: 0.8885 (tptp) REVERT: 7 203 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8568 (t80) REVERT: 8 307 PHE cc_start: 0.8507 (t80) cc_final: 0.8250 (t80) REVERT: h 2 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8675 (mmtt) REVERT: 9 104 GLU cc_start: 0.8750 (tm-30) cc_final: 0.7860 (tm-30) REVERT: AA 206 LYS cc_start: 0.8724 (tptp) cc_final: 0.8465 (tptp) REVERT: BA 307 PHE cc_start: 0.8771 (t80) cc_final: 0.8373 (t80) outliers start: 108 outliers final: 56 residues processed: 225 average time/residue: 0.1602 time to fit residues: 41.1238 Evaluate side-chains 249 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 161 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 205 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain z residue 306 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS 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 = 0.2830 r_free = 0.2830 target = 0.054610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.047380 restraints weight = 20763.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.049164 restraints weight = 11166.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.050369 restraints weight = 6979.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.051225 restraints weight = 4713.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.051857 restraints weight = 3374.287| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 1.0091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.477 5568 Z= 6.739 Angle : 6.259 58.581 7232 Z= 2.764 Chirality : 0.415 1.078 512 Planarity : 0.028 0.090 960 Dihedral : 25.429 89.842 644 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 198.86 Ramachandran Plot: Outliers : 1.17 % Allowed : 57.03 % Favored : 41.80 % Rotamer: Outliers : 26.82 % Allowed : 34.38 % Favored : 38.80 % Cbeta Deviations : 46.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -9.07 (0.24), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.91 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE 5 303 Details of bonding type rmsd covalent geometry : bond 0.15393 ( 5568) covalent geometry : angle 6.25937 ( 7232) hydrogen bonds : bond 0.32060 ( 52) hydrogen bonds : angle 15.75580 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 165 time to evaluate : 0.324 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: A 5 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8467 (m-10) REVERT: A 7 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.9019 (m-10) REVERT: I 102 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8898 (mmtm) REVERT: I 107 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8676 (m-10) REVERT: J 206 LYS cc_start: 0.9063 (tttm) cc_final: 0.8785 (ttpp) REVERT: K 306 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8400 (mmmm) REVERT: B 6 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8803 (mmmm) REVERT: L 103 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8925 (m-80) REVERT: M 206 LYS cc_start: 0.8921 (tttm) cc_final: 0.8660 (tttm) REVERT: N 304 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8191 (tm-30) REVERT: N 306 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8278 (mmmm) REVERT: N 307 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8414 (t80) REVERT: O 102 LYS cc_start: 0.9446 (mmtm) cc_final: 0.9203 (mmtm) REVERT: O 105 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8443 (m-10) REVERT: P 206 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8387 (ptmm) REVERT: Q 303 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: Q 307 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8413 (t80) REVERT: S 202 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.8903 (ttpp) REVERT: S 206 LYS cc_start: 0.8835 (tttm) cc_final: 0.8350 (ttpp) REVERT: T 304 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7577 (tm-30) REVERT: T 306 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8271 (mmtp) REVERT: E 6 LYS cc_start: 0.9289 (mmmm) cc_final: 0.8957 (ttmm) REVERT: U 103 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: U 106 LYS cc_start: 0.9147 (tppt) cc_final: 0.8900 (tppt) REVERT: V 202 LYS cc_start: 0.9599 (OUTLIER) cc_final: 0.8856 (ttmm) REVERT: V 206 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8406 (ttpp) REVERT: W 302 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8573 (ttpp) REVERT: W 304 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7194 (tm-30) REVERT: F 5 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: X 106 LYS cc_start: 0.9077 (tppt) cc_final: 0.8574 (tppt) REVERT: Y 202 LYS cc_start: 0.9390 (ttmm) cc_final: 0.9154 (ttmm) REVERT: Z 302 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8687 (tppp) REVERT: Z 304 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8177 (tm-30) REVERT: Z 306 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8254 (mmmm) REVERT: Z 307 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: G 5 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8605 (m-80) REVERT: k 303 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: l 102 LYS cc_start: 0.9472 (mmtm) cc_final: 0.9233 (mmtm) REVERT: l 103 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: m 206 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8311 (pttm) REVERT: n 304 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8165 (tm-30) REVERT: a 2 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8810 (mtmm) REVERT: o 107 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8322 (t80) REVERT: p 203 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8468 (t80) REVERT: q 302 LYS cc_start: 0.9303 (tmtt) cc_final: 0.8874 (tmtt) REVERT: q 303 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.7310 (t80) REVERT: q 305 PHE cc_start: 0.9083 (t80) cc_final: 0.8877 (t80) REVERT: q 306 LYS cc_start: 0.9125 (tttt) cc_final: 0.8772 (tttp) REVERT: q 307 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8112 (t80) REVERT: s 202 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8910 (tppp) REVERT: s 206 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8344 (tptp) REVERT: t 303 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7555 (t80) REVERT: c 3 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8097 (t80) REVERT: v 204 GLU cc_start: 0.8719 (tm-30) cc_final: 0.7956 (tm-30) REVERT: v 207 PHE cc_start: 0.8899 (t80) cc_final: 0.7894 (t80) REVERT: x 104 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8960 (pp20) REVERT: y 203 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8477 (t80) REVERT: z 302 LYS cc_start: 0.9143 (tmtt) cc_final: 0.8683 (tmtt) REVERT: 1 203 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8563 (t80) REVERT: 2 306 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8664 (tmtt) REVERT: f 2 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8442 (mmtt) REVERT: 3 102 LYS cc_start: 0.9129 (tptp) cc_final: 0.8921 (tptp) REVERT: 4 202 LYS cc_start: 0.9225 (tptp) cc_final: 0.8848 (tppp) REVERT: 5 306 LYS cc_start: 0.8987 (tttp) cc_final: 0.8620 (tttp) REVERT: 5 307 PHE cc_start: 0.8916 (t80) cc_final: 0.8637 (t80) REVERT: g 2 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8717 (mmtt) REVERT: 9 104 GLU cc_start: 0.8774 (tm-30) cc_final: 0.7879 (tm-30) REVERT: AA 206 LYS cc_start: 0.8730 (tptp) cc_final: 0.8488 (tptp) REVERT: BA 307 PHE cc_start: 0.8763 (t80) cc_final: 0.8400 (t80) outliers start: 103 outliers final: 55 residues processed: 225 average time/residue: 0.1670 time to fit residues: 42.8313 Evaluate side-chains 253 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 163 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 303 PHE Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain s residue 206 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain z residue 306 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.2838 r_free = 0.2838 target = 0.055075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.047865 restraints weight = 20306.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049639 restraints weight = 10970.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.050840 restraints weight = 6884.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.051694 restraints weight = 4670.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.052318 restraints weight = 3352.667| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 1.0138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.474 5568 Z= 6.735 Angle : 6.237 58.978 7232 Z= 2.760 Chirality : 0.415 1.085 512 Planarity : 0.028 0.089 960 Dihedral : 25.500 89.622 644 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 201.26 Ramachandran Plot: Outliers : 1.17 % Allowed : 55.86 % Favored : 42.97 % Rotamer: Outliers : 25.78 % Allowed : 36.20 % Favored : 38.02 % Cbeta Deviations : 48.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -9.08 (0.24), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.92 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.176 0.025 PHE P 205 Details of bonding type rmsd covalent geometry : bond 0.15386 ( 5568) covalent geometry : angle 6.23662 ( 7232) hydrogen bonds : bond 0.31713 ( 52) hydrogen bonds : angle 15.72940 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 164 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8463 (m-10) REVERT: A 7 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.9019 (m-10) REVERT: I 102 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8927 (mmtm) REVERT: I 107 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8679 (m-10) REVERT: J 206 LYS cc_start: 0.9053 (tttm) cc_final: 0.8797 (ttpp) REVERT: K 306 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8404 (mmmm) REVERT: L 103 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8921 (m-80) REVERT: M 206 LYS cc_start: 0.8933 (tttm) cc_final: 0.8676 (tttm) REVERT: N 304 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8201 (tm-30) REVERT: N 306 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8282 (mmmm) REVERT: N 307 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8416 (t80) REVERT: O 105 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8440 (m-10) REVERT: P 206 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8383 (ptmm) REVERT: Q 303 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: S 202 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.8909 (ttpp) REVERT: S 206 LYS cc_start: 0.8789 (tttm) cc_final: 0.8304 (ttpp) REVERT: T 304 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7598 (tm-30) REVERT: T 306 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8263 (mmtp) REVERT: E 6 LYS cc_start: 0.9280 (mmmm) cc_final: 0.8937 (ttmm) REVERT: U 103 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: U 106 LYS cc_start: 0.9043 (tppt) cc_final: 0.8812 (tppt) REVERT: V 202 LYS cc_start: 0.9603 (OUTLIER) cc_final: 0.8865 (ttmm) REVERT: W 302 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8563 (ttpp) REVERT: W 304 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7682 (tm-30) REVERT: F 5 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: X 103 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8767 (m-10) REVERT: X 106 LYS cc_start: 0.9113 (tppt) cc_final: 0.8614 (tppt) REVERT: Y 202 LYS cc_start: 0.9360 (ttmm) cc_final: 0.9133 (ttmm) REVERT: Z 302 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8649 (tppp) REVERT: Z 306 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8207 (mmmm) REVERT: Z 307 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: G 5 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: k 303 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7462 (m-10) REVERT: l 102 LYS cc_start: 0.9471 (mmtm) cc_final: 0.9238 (mmtm) REVERT: l 103 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: m 206 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8353 (pttm) REVERT: n 304 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8160 (tm-30) REVERT: a 2 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8803 (mtmm) REVERT: o 107 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8314 (t80) REVERT: p 203 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8479 (t80) REVERT: q 302 LYS cc_start: 0.9303 (tmtt) cc_final: 0.8875 (tmtt) REVERT: q 303 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7322 (t80) REVERT: q 305 PHE cc_start: 0.9084 (t80) cc_final: 0.8876 (t80) REVERT: q 306 LYS cc_start: 0.9122 (tttt) cc_final: 0.8763 (tttp) REVERT: q 307 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8102 (t80) REVERT: s 202 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8910 (tppp) REVERT: s 206 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8278 (tptp) REVERT: t 303 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7609 (t80) REVERT: c 3 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8117 (t80) REVERT: v 204 GLU cc_start: 0.8733 (tm-30) cc_final: 0.7969 (tm-30) REVERT: v 207 PHE cc_start: 0.8867 (t80) cc_final: 0.7861 (t80) REVERT: x 104 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8962 (pp20) REVERT: y 203 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8519 (t80) REVERT: z 302 LYS cc_start: 0.9141 (tmtt) cc_final: 0.8676 (tmtt) REVERT: 1 203 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8511 (t80) REVERT: 2 306 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8668 (tmtt) REVERT: f 2 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8439 (mmtt) REVERT: 3 102 LYS cc_start: 0.9112 (tptp) cc_final: 0.8912 (tptp) REVERT: 4 202 LYS cc_start: 0.9213 (tptp) cc_final: 0.8840 (tppp) REVERT: 5 306 LYS cc_start: 0.8999 (tttp) cc_final: 0.8633 (tttp) REVERT: 5 307 PHE cc_start: 0.8905 (t80) cc_final: 0.8639 (t80) REVERT: g 2 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8793 (mtmm) REVERT: 7 202 LYS cc_start: 0.9209 (tptp) cc_final: 0.8885 (tptp) REVERT: 9 104 GLU cc_start: 0.8715 (tm-30) cc_final: 0.7783 (tm-30) REVERT: AA 206 LYS cc_start: 0.8729 (tptp) cc_final: 0.8491 (tptp) REVERT: BA 307 PHE cc_start: 0.8765 (t80) cc_final: 0.8450 (t80) outliers start: 99 outliers final: 59 residues processed: 222 average time/residue: 0.1707 time to fit residues: 43.1045 Evaluate side-chains 256 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 164 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 303 PHE Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain s residue 206 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain z residue 306 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.2836 r_free = 0.2836 target = 0.054955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.047789 restraints weight = 20693.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049577 restraints weight = 11135.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.050776 restraints weight = 6936.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.051626 restraints weight = 4693.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.052253 restraints weight = 3359.208| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 1.0174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.475 5568 Z= 6.742 Angle : 6.252 58.583 7232 Z= 2.765 Chirality : 0.416 1.081 512 Planarity : 0.027 0.088 960 Dihedral : 25.444 89.194 644 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 201.74 Ramachandran Plot: Outliers : 1.17 % Allowed : 56.64 % Favored : 42.19 % Rotamer: Outliers : 26.56 % Allowed : 37.76 % Favored : 35.68 % Cbeta Deviations : 49.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -9.07 (0.24), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.91 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE P 205 Details of bonding type rmsd covalent geometry : bond 0.15405 ( 5568) covalent geometry : angle 6.25199 ( 7232) hydrogen bonds : bond 0.32087 ( 52) hydrogen bonds : angle 15.71629 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 166 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8471 (m-10) REVERT: A 7 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.9024 (m-10) REVERT: I 102 LYS cc_start: 0.9167 (mmtm) cc_final: 0.8919 (mmtm) REVERT: I 107 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8687 (m-10) REVERT: J 206 LYS cc_start: 0.9078 (tttm) cc_final: 0.8817 (ttpp) REVERT: K 306 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8492 (mmmm) REVERT: B 6 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8802 (mmmm) REVERT: L 103 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: M 206 LYS cc_start: 0.8938 (tttm) cc_final: 0.8619 (tttm) REVERT: N 304 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8226 (tm-30) REVERT: N 306 LYS cc_start: 0.8787 (mmmm) cc_final: 0.8269 (mmmm) REVERT: N 307 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8410 (t80) REVERT: O 102 LYS cc_start: 0.9461 (mmtm) cc_final: 0.9260 (mmtm) REVERT: O 105 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8448 (m-10) REVERT: P 206 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8490 (ptmm) REVERT: Q 303 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: Q 304 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8344 (tm-30) REVERT: Q 306 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7945 (mmmm) REVERT: S 202 LYS cc_start: 0.9497 (OUTLIER) cc_final: 0.8920 (ttpp) REVERT: S 206 LYS cc_start: 0.8810 (tttm) cc_final: 0.8181 (ttpp) REVERT: T 304 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7600 (tm-30) REVERT: T 306 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8238 (mmtp) REVERT: E 6 LYS cc_start: 0.9285 (mmmm) cc_final: 0.8948 (ttmm) REVERT: U 103 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: U 106 LYS cc_start: 0.9047 (tppt) cc_final: 0.8809 (tppt) REVERT: V 202 LYS cc_start: 0.9604 (OUTLIER) cc_final: 0.8873 (ttmm) REVERT: W 302 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8572 (ttpp) REVERT: W 304 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7168 (tm-30) REVERT: F 5 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: X 106 LYS cc_start: 0.9106 (tppt) cc_final: 0.8618 (tppt) REVERT: Z 302 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8680 (tppp) REVERT: Z 306 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8123 (mmmm) REVERT: Z 307 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: G 5 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: k 303 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: l 102 LYS cc_start: 0.9471 (mmtm) cc_final: 0.9238 (mmtm) REVERT: l 103 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: m 206 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8348 (pttm) REVERT: n 304 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8172 (tm-30) REVERT: a 2 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8822 (mtmm) REVERT: o 107 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8319 (t80) REVERT: p 203 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8484 (t80) REVERT: q 302 LYS cc_start: 0.9313 (tmtt) cc_final: 0.8890 (tmtt) REVERT: q 303 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.7328 (t80) REVERT: q 306 LYS cc_start: 0.9119 (tttt) cc_final: 0.8774 (tttp) REVERT: q 307 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8108 (t80) REVERT: r 104 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8620 (pp20) REVERT: s 202 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8914 (tppp) REVERT: s 206 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8293 (tptp) REVERT: t 303 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.7603 (t80) REVERT: c 3 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8114 (t80) REVERT: v 204 GLU cc_start: 0.8745 (tm-30) cc_final: 0.7975 (tm-30) REVERT: v 207 PHE cc_start: 0.8867 (t80) cc_final: 0.7862 (t80) REVERT: x 104 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8995 (pp20) REVERT: y 203 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8521 (t80) REVERT: z 302 LYS cc_start: 0.9143 (tmtt) cc_final: 0.8685 (tmtt) REVERT: 1 203 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8546 (t80) REVERT: 2 306 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8679 (tmtt) REVERT: f 2 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8437 (mmtt) REVERT: f 5 PHE cc_start: 0.8678 (t80) cc_final: 0.8446 (t80) REVERT: 4 202 LYS cc_start: 0.9216 (tptp) cc_final: 0.8850 (tppp) REVERT: g 2 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8808 (mtmm) REVERT: 7 202 LYS cc_start: 0.9235 (tptp) cc_final: 0.8854 (tptp) REVERT: h 3 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7642 (t80) REVERT: 9 104 GLU cc_start: 0.8719 (tm-30) cc_final: 0.7856 (tm-30) REVERT: AA 206 LYS cc_start: 0.8728 (tptp) cc_final: 0.8496 (tptp) REVERT: BA 307 PHE cc_start: 0.8776 (t80) cc_final: 0.8468 (t80) outliers start: 102 outliers final: 58 residues processed: 226 average time/residue: 0.1665 time to fit residues: 42.8273 Evaluate side-chains 259 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 166 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 303 PHE Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain s residue 206 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS 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 = 0.2835 r_free = 0.2835 target = 0.054952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.047776 restraints weight = 20721.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.049577 restraints weight = 11150.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.050771 restraints weight = 6940.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.051627 restraints weight = 4694.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.052248 restraints weight = 3356.029| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 1.0199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.473 5568 Z= 6.742 Angle : 6.256 58.690 7232 Z= 2.767 Chirality : 0.415 1.085 512 Planarity : 0.027 0.088 960 Dihedral : 25.375 89.267 644 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 201.12 Ramachandran Plot: Outliers : 1.17 % Allowed : 56.25 % Favored : 42.58 % Rotamer: Outliers : 26.82 % Allowed : 37.24 % Favored : 35.94 % Cbeta Deviations : 47.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -9.09 (0.25), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.92 (0.19), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.178 0.025 PHE P 205 Details of bonding type rmsd covalent geometry : bond 0.15408 ( 5568) covalent geometry : angle 6.25649 ( 7232) hydrogen bonds : bond 0.31949 ( 52) hydrogen bonds : angle 15.69635 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 166 time to evaluate : 0.210 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: A 5 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8445 (m-10) REVERT: A 7 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.9028 (m-10) REVERT: I 102 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8920 (mmtm) REVERT: I 107 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8689 (m-10) REVERT: J 206 LYS cc_start: 0.9048 (tttm) cc_final: 0.8801 (ttpp) REVERT: K 306 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8392 (mmmm) REVERT: B 6 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8799 (mmmm) REVERT: L 103 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8920 (m-80) REVERT: M 206 LYS cc_start: 0.8927 (tttm) cc_final: 0.8614 (tttm) REVERT: N 304 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8247 (tm-30) REVERT: N 306 LYS cc_start: 0.8780 (mmmm) cc_final: 0.8276 (mmmm) REVERT: N 307 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8397 (t80) REVERT: O 105 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8445 (m-10) REVERT: P 206 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8452 (ptmm) REVERT: Q 303 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: S 202 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.8913 (ttpp) REVERT: T 304 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7600 (tm-30) REVERT: T 306 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8244 (mmtp) REVERT: E 6 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8944 (ttmm) REVERT: U 103 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: U 106 LYS cc_start: 0.9023 (tppt) cc_final: 0.8785 (tppt) REVERT: V 202 LYS cc_start: 0.9603 (OUTLIER) cc_final: 0.8859 (ttmm) REVERT: W 302 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8567 (ttpp) REVERT: W 304 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7188 (tm-30) REVERT: F 5 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: X 103 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8772 (m-10) REVERT: X 106 LYS cc_start: 0.9105 (tppt) cc_final: 0.8619 (tppt) REVERT: Z 302 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8640 (tppp) REVERT: Z 306 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8313 (mmmm) REVERT: Z 307 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: G 5 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: l 102 LYS cc_start: 0.9471 (OUTLIER) cc_final: 0.9241 (mmtm) REVERT: l 103 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: m 206 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8296 (pttm) REVERT: n 304 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8171 (tm-30) REVERT: n 307 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8693 (t80) REVERT: a 2 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8817 (mtmm) REVERT: o 107 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8315 (t80) REVERT: p 203 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8476 (t80) REVERT: q 302 LYS cc_start: 0.9307 (tmtt) cc_final: 0.8884 (tmtt) REVERT: q 303 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.7308 (t80) REVERT: q 306 LYS cc_start: 0.9085 (tttt) cc_final: 0.8775 (tttp) REVERT: q 307 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8103 (t80) REVERT: r 104 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8585 (pp20) REVERT: s 202 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8909 (tppp) REVERT: s 206 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8274 (tptp) REVERT: t 303 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.7617 (t80) REVERT: c 3 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8119 (t80) REVERT: v 204 GLU cc_start: 0.8711 (tm-30) cc_final: 0.7952 (tm-30) REVERT: v 207 PHE cc_start: 0.8864 (t80) cc_final: 0.7860 (t80) REVERT: x 104 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8978 (pp20) REVERT: y 203 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8527 (t80) REVERT: z 302 LYS cc_start: 0.9140 (tmtt) cc_final: 0.8678 (tmtt) REVERT: 1 203 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8560 (t80) REVERT: 2 306 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8666 (tmtt) REVERT: f 2 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8444 (mmtt) REVERT: f 5 PHE cc_start: 0.8677 (t80) cc_final: 0.8474 (t80) REVERT: 4 202 LYS cc_start: 0.9225 (tptp) cc_final: 0.8841 (tppp) REVERT: 5 306 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8600 (tttp) REVERT: 5 307 PHE cc_start: 0.8902 (t80) cc_final: 0.8555 (t80) REVERT: g 2 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8803 (mtmm) REVERT: 7 202 LYS cc_start: 0.9225 (tptp) cc_final: 0.8876 (tptp) REVERT: h 3 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7675 (t80) REVERT: 9 104 GLU cc_start: 0.8699 (tm-30) cc_final: 0.7796 (tm-30) REVERT: AA 206 LYS cc_start: 0.8729 (tptp) cc_final: 0.8499 (tptp) REVERT: BA 307 PHE cc_start: 0.8804 (t80) cc_final: 0.8543 (t80) outliers start: 103 outliers final: 58 residues processed: 225 average time/residue: 0.1676 time to fit residues: 43.0200 Evaluate side-chains 262 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 166 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 102 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain s residue 206 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 5 residue 306 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS 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 = 0.2837 r_free = 0.2837 target = 0.054958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.047795 restraints weight = 20669.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.049584 restraints weight = 11152.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.050783 restraints weight = 6948.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051643 restraints weight = 4707.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.052258 restraints weight = 3363.104| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 1.0217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.475 5568 Z= 6.747 Angle : 6.255 58.767 7232 Z= 2.765 Chirality : 0.416 1.082 512 Planarity : 0.027 0.088 960 Dihedral : 25.368 89.793 644 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 201.78 Ramachandran Plot: Outliers : 1.17 % Allowed : 56.64 % Favored : 42.19 % Rotamer: Outliers : 26.30 % Allowed : 38.28 % Favored : 35.42 % Cbeta Deviations : 48.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.90 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -9.10 (0.24), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.93 (0.19), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE P 205 Details of bonding type rmsd covalent geometry : bond 0.15418 ( 5568) covalent geometry : angle 6.25500 ( 7232) hydrogen bonds : bond 0.31977 ( 52) hydrogen bonds : angle 15.74200 ( 126) =============================================================================== Job complete usr+sys time: 903.31 seconds wall clock time: 16 minutes 44.57 seconds (1004.57 seconds total)