Starting phenix.real_space_refine on Thu Sep 26 04:24:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/09_2024/7lqh_23486.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/09_2024/7lqh_23486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/09_2024/7lqh_23486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/09_2024/7lqh_23486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/09_2024/7lqh_23486.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/09_2024/7lqh_23486.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 8640 2.51 5 N 1584 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 324 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 144 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "UA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "VA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "WA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "XA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "aA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "cA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "dA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "eA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "fA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "gA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "hA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "iA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "jA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "kA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "lA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "mA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "nA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "oA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "pA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "qA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "rA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "sA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "tA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "uA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "vA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "wA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "xA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "yA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "zA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.67, per 1000 atoms: 0.63 Number of scatterers: 12096 At special positions: 0 Unit cell: (89.64, 89.64, 111.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1872 8.00 N 1584 7.00 C 8640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=35, symmetry=0 Number of additional bonds: simple=35, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 662.8 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'M' and resid 1006 through 1007 Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'T' and resid 1006 through 1007 Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'j' and resid 1006 through 1007 Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'q' and resid 1006 through 1007 Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'x' and resid 1006 through 1007 Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AB3, first strand: chain '4' and resid 1006 through 1007 Processing sheet with id=AB4, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'BA' and resid 1006 through 1007 Processing sheet with id=AB6, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'IA' and resid 1006 through 1007 Processing sheet with id=AB8, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AB9, first strand: chain 'PA' and resid 1006 through 1007 Processing sheet with id=AC1, first strand: chain 'h' and resid 2 through 6 removed outlier: 3.535A pdb=" N PHEGB 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE h 5 " --> pdb=" O PHEGB 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE2A 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE f 5 " --> pdb=" O PHE2A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEoA 105 " --> pdb=" O PHE d 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE d 5 " --> pdb=" O PHEoA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEaA 105 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE b 5 " --> pdb=" O PHEaA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHETA 105 " --> pdb=" O PHE a 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE a 5 " --> pdb=" O PHETA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHEhA 105 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE c 5 " --> pdb=" O PHEhA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEvA 105 " --> pdb=" O PHE e 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE e 5 " --> pdb=" O PHEvA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE9A 105 " --> pdb=" O PHE g 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE g 5 " --> pdb=" O PHE9A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHENB 105 " --> pdb=" O PHE i 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE i 5 " --> pdb=" O PHENB 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HB' and resid 202 through 206 removed outlier: 3.521A pdb=" N LYSIB 302 " --> pdb=" O GMA3A 208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS3A 206 " --> pdb=" O GLUIB 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAIB 308 " --> pdb=" O LYS3A 202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS4A 302 " --> pdb=" O GMApA 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSpA 206 " --> pdb=" O GLU4A 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSqA 302 " --> pdb=" O GMAbA 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSbA 206 " --> pdb=" O GLUqA 304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYScA 302 " --> pdb=" O GMAUA 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSUA 206 " --> pdb=" O GLUcA 304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAcA 308 " --> pdb=" O LYSUA 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSVA 302 " --> pdb=" O GMAiA 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSiA 206 " --> pdb=" O GLUVA 304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAVA 308 " --> pdb=" O LYSiA 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSjA 302 " --> pdb=" O GMAwA 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYSwA 206 " --> pdb=" O GLUjA 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSxA 302 " --> pdb=" O GMAAB 208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSAB 206 " --> pdb=" O GLUxA 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMAxA 308 " --> pdb=" O LYSAB 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSBB 302 " --> pdb=" O GMAOB 208 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYSOB 206 " --> pdb=" O GLUBB 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'JB' and resid 1002 through 1006 removed outlier: 3.536A pdb=" N PHEKB1105 " --> pdb=" O PHEJB1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEJB1005 " --> pdb=" O PHEKB1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE6A1105 " --> pdb=" O PHE5A1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE5A1005 " --> pdb=" O PHE6A1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEsA1105 " --> pdb=" O PHErA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHErA1005 " --> pdb=" O PHEsA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEeA1105 " --> pdb=" O PHEdA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEdA1005 " --> pdb=" O PHEeA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEXA1105 " --> pdb=" O PHEWA1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEWA1005 " --> pdb=" O PHEXA1103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHElA1105 " --> pdb=" O PHEkA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEkA1005 " --> pdb=" O PHElA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEzA1105 " --> pdb=" O PHEyA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEyA1005 " --> pdb=" O PHEzA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEDB1105 " --> pdb=" O PHECB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHECB1005 " --> pdb=" O PHEDB1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHERB1105 " --> pdb=" O PHEQB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEQB1005 " --> pdb=" O PHERB1103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LB' and resid 1202 through 1206 removed outlier: 3.521A pdb=" N LYSMB1302 " --> pdb=" O GMA7A1208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS7A1206 " --> pdb=" O GLUMB1304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAMB1308 " --> pdb=" O LYS7A1202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS8A1302 " --> pdb=" O GMAtA1208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYStA1206 " --> pdb=" O GLU8A1304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSuA1302 " --> pdb=" O GMAfA1208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSfA1206 " --> pdb=" O GLUuA1304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSgA1302 " --> pdb=" O GMAYA1208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSYA1206 " --> pdb=" O GLUgA1304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAgA1308 " --> pdb=" O LYSYA1202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSZA1302 " --> pdb=" O GMAmA1208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSmA1206 " --> pdb=" O GLUZA1304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAZA1308 " --> pdb=" O LYSmA1202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSnA1302 " --> pdb=" O GMA0A1208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS0A1206 " --> pdb=" O GLUnA1304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS1A1302 " --> pdb=" O GMAEB1208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSEB1206 " --> pdb=" O GLU1A1304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMA1A1308 " --> pdb=" O LYSEB1202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSFB1302 " --> pdb=" O GMASB1208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSSB1206 " --> pdb=" O GLUFB1304 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 1489 1.26 - 1.33: 1391 1.33 - 1.41: 3600 1.41 - 1.48: 1308 1.48 - 1.56: 4740 Bond restraints: 12528 Sorted by residual: bond pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRrA1001 " pdb=" CAL 5CRrA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRyA1001 " pdb=" CAL 5CRyA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 12523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 14239 1.98 - 3.96: 1589 3.96 - 5.94: 318 5.94 - 7.92: 108 7.92 - 9.90: 18 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.81 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.80 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR5A1001 " pdb=" CAL 5CR5A1001 " pdb=" CAA 5CR5A1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " pdb=" CAA 5CR a 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CRWA1001 " pdb=" CAL 5CRWA1001 " pdb=" CAA 5CRWA1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 4844 15.26 - 30.52: 790 30.52 - 45.79: 342 45.79 - 61.05: 198 61.05 - 76.31: 18 Dihedral angle restraints: 6192 sinusoidal: 2880 harmonic: 3312 Sorted by residual: dihedral pdb=" CA LYSMA 106 " pdb=" CB LYSMA 106 " pdb=" CG LYSMA 106 " pdb=" CD LYSMA 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.26 58.74 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYSQA1106 " pdb=" CB LYSQA1106 " pdb=" CG LYSQA1106 " pdb=" CD LYSQA1106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS 1 106 " pdb=" CB LYS 1 106 " pdb=" CG LYS 1 106 " pdb=" CD LYS 1 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.018: 407 0.018 - 0.036: 334 0.036 - 0.054: 299 0.054 - 0.073: 89 0.073 - 0.091: 23 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.06e-01 chirality pdb=" CA LYS V1202 " pdb=" N LYS V1202 " pdb=" C LYS V1202 " pdb=" CB LYS V1202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.02e-01 chirality pdb=" CA LYS Y 202 " pdb=" N LYS Y 202 " pdb=" C LYS Y 202 " pdb=" CB LYS Y 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.86e-01 ... (remaining 1149 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEUA 205 " -0.008 2.00e-02 2.50e+03 7.00e-03 8.57e-01 pdb=" CG PHEUA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEUA 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEUA 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEUA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEYA1205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-01 pdb=" CG PHEYA1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEYA1205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEYA1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEYA1205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEAB 205 " -0.009 2.00e-02 2.50e+03 6.97e-03 8.51e-01 pdb=" CG PHEAB 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEAB 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 281 2.66 - 3.22: 10092 3.22 - 3.78: 19029 3.78 - 4.34: 28093 4.34 - 4.90: 46315 Nonbonded interactions: 103810 Sorted by model distance: nonbonded pdb=" CD LYS N1102 " pdb=" OE2 GMA 9 208 " model vdw 2.098 2.752 nonbonded pdb=" OE2 GMA Y 208 " pdb=" CD LYS r1102 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS U1102 " pdb=" OE2 GMA v 208 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS k1102 " pdb=" OE2 GMANA 208 " model vdw 2.117 2.752 nonbonded pdb=" CD LYS Q 102 " pdb=" OE2 GMADA1208 " model vdw 2.118 2.752 ... (remaining 103805 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '0A' selection = chain '1' selection = chain '1A' selection = chain '2' selection = chain '2A' selection = chain '3' selection = chain '3A' selection = chain '4' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '6A' selection = chain '7' selection = chain '7A' selection = chain '8' selection = chain '8A' selection = chain '9' selection = chain '9A' selection = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'RA' selection = chain 'RB' selection = chain 'S' selection = chain 'SA' selection = chain 'SB' selection = chain 'T' selection = chain 'TA' selection = chain 'TB' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' selection = chain 'a' selection = chain 'aA' selection = chain 'b' selection = chain 'bA' selection = chain 'c' selection = chain 'cA' selection = chain 'd' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'v' selection = chain 'vA' selection = chain 'w' selection = chain 'wA' selection = chain 'x' selection = chain 'xA' selection = chain 'y' selection = chain 'yA' selection = chain 'z' selection = chain 'zA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.180 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.118 12528 Z= 0.917 Angle : 1.417 9.902 16272 Z= 0.592 Chirality : 0.035 0.091 1152 Planarity : 0.002 0.009 2160 Dihedral : 20.718 76.311 3888 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 31.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEUA 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 472 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7369 (mp0) cc_final: 0.6755 (pm20) REVERT: B 4 GLU cc_start: 0.7493 (mp0) cc_final: 0.6748 (pm20) REVERT: S 306 LYS cc_start: 0.8629 (tttt) cc_final: 0.8357 (mttt) REVERT: Y 206 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8180 (ttmm) REVERT: Z 306 LYS cc_start: 0.8563 (tttt) cc_final: 0.8262 (tttt) REVERT: j 1006 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8034 (mtmt) REVERT: m 1306 LYS cc_start: 0.8633 (tttt) cc_final: 0.8339 (mttt) REVERT: o 204 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7064 (mt-10) REVERT: s 1206 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8228 (ttmm) REVERT: t 1306 LYS cc_start: 0.8695 (tttt) cc_final: 0.8441 (mttt) REVERT: v 206 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8231 (ttmm) REVERT: w 304 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7091 (mm-30) REVERT: w 306 LYS cc_start: 0.8689 (tttt) cc_final: 0.8339 (mttt) REVERT: x 1004 GLU cc_start: 0.7152 (mp0) cc_final: 0.6745 (mp0) REVERT: 0 1304 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7144 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8594 (tttt) cc_final: 0.8264 (tttt) REVERT: F 4 GLU cc_start: 0.7397 (mp0) cc_final: 0.6657 (pm20) REVERT: 3 304 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7148 (mm-30) REVERT: 6 1204 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6808 (mt-10) REVERT: 6 1206 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8366 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8772 (tttt) cc_final: 0.8420 (mttt) REVERT: G 4 GLU cc_start: 0.7313 (mp0) cc_final: 0.6485 (pm20) REVERT: 9 204 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6532 (mt-10) REVERT: AA 306 LYS cc_start: 0.8673 (tttt) cc_final: 0.8387 (mttt) REVERT: DA 1204 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7037 (mt-10) REVERT: EA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8431 (mttt) REVERT: HA 306 LYS cc_start: 0.8699 (tttt) cc_final: 0.8363 (mttt) REVERT: LA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8323 (mttt) REVERT: OA 306 LYS cc_start: 0.8570 (tttt) cc_final: 0.8318 (mttt) REVERT: SA 1306 LYS cc_start: 0.8648 (tttt) cc_final: 0.8295 (tttt) REVERT: a 2 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8344 (ttpt) REVERT: TA 104 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: TA 105 PHE cc_start: 0.9072 (t80) cc_final: 0.8761 (t80) REVERT: UA 202 LYS cc_start: 0.8784 (tttm) cc_final: 0.8340 (ttmm) REVERT: VA 305 PHE cc_start: 0.8549 (t80) cc_final: 0.8266 (t80) REVERT: WA 1003 PHE cc_start: 0.9115 (t80) cc_final: 0.8755 (t80) REVERT: WA 1005 PHE cc_start: 0.8951 (t80) cc_final: 0.8609 (t80) REVERT: WA 1007 PHE cc_start: 0.9301 (t80) cc_final: 0.8997 (t80) REVERT: XA 1103 PHE cc_start: 0.8930 (t80) cc_final: 0.8678 (t80) REVERT: XA 1107 PHE cc_start: 0.8921 (t80) cc_final: 0.8714 (t80) REVERT: YA 1202 LYS cc_start: 0.8788 (tttm) cc_final: 0.8391 (tttm) REVERT: ZA 1304 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8190 (tm-30) REVERT: aA 103 PHE cc_start: 0.9101 (t80) cc_final: 0.8425 (t80) REVERT: aA 106 LYS cc_start: 0.8822 (tttp) cc_final: 0.8564 (tttp) REVERT: bA 202 LYS cc_start: 0.8841 (tttm) cc_final: 0.8397 (ttmm) REVERT: cA 303 PHE cc_start: 0.9015 (t80) cc_final: 0.8654 (t80) REVERT: cA 304 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8429 (tm-30) REVERT: fA 1202 LYS cc_start: 0.8656 (tttm) cc_final: 0.8373 (tttm) REVERT: c 5 PHE cc_start: 0.8932 (t80) cc_final: 0.8452 (t80) REVERT: c 7 PHE cc_start: 0.9209 (t80) cc_final: 0.8995 (t80) REVERT: hA 106 LYS cc_start: 0.8870 (tttp) cc_final: 0.8657 (tttp) REVERT: iA 202 LYS cc_start: 0.8878 (tttm) cc_final: 0.8562 (ttmm) REVERT: jA 306 LYS cc_start: 0.8334 (tptp) cc_final: 0.8046 (tptp) REVERT: kA 1005 PHE cc_start: 0.9077 (t80) cc_final: 0.8703 (t80) REVERT: lA 1103 PHE cc_start: 0.8901 (t80) cc_final: 0.8521 (t80) REVERT: mA 1206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8582 (tttt) REVERT: nA 1305 PHE cc_start: 0.8662 (t80) cc_final: 0.8453 (t80) REVERT: d 3 PHE cc_start: 0.9295 (t80) cc_final: 0.8996 (t80) REVERT: d 5 PHE cc_start: 0.9090 (t80) cc_final: 0.8869 (t80) REVERT: d 7 PHE cc_start: 0.9253 (t80) cc_final: 0.8845 (t80) REVERT: oA 107 PHE cc_start: 0.8813 (t80) cc_final: 0.8347 (t80) REVERT: pA 202 LYS cc_start: 0.8916 (tttm) cc_final: 0.8524 (mmmm) REVERT: pA 206 LYS cc_start: 0.8826 (tttt) cc_final: 0.8593 (tttt) REVERT: qA 305 PHE cc_start: 0.8722 (t80) cc_final: 0.8402 (t80) REVERT: rA 1005 PHE cc_start: 0.8915 (t80) cc_final: 0.8588 (t80) REVERT: sA 1103 PHE cc_start: 0.9020 (t80) cc_final: 0.8784 (t80) REVERT: tA 1206 LYS cc_start: 0.8812 (tttt) cc_final: 0.8431 (tttt) REVERT: vA 106 LYS cc_start: 0.8825 (tttp) cc_final: 0.8561 (tttp) REVERT: wA 202 LYS cc_start: 0.8733 (tttm) cc_final: 0.8401 (mmmm) REVERT: wA 206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8503 (tttt) REVERT: xA 303 PHE cc_start: 0.8927 (t80) cc_final: 0.8677 (t80) REVERT: zA 1106 LYS cc_start: 0.8767 (tttp) cc_final: 0.8557 (tttp) REVERT: 1A 1303 PHE cc_start: 0.8829 (t80) cc_final: 0.8602 (t80) REVERT: 1A 1305 PHE cc_start: 0.8465 (t80) cc_final: 0.8239 (t80) REVERT: 3A 202 LYS cc_start: 0.8922 (tttm) cc_final: 0.8551 (mmmm) REVERT: 3A 206 LYS cc_start: 0.8739 (tttt) cc_final: 0.8527 (tttt) REVERT: 4A 306 LYS cc_start: 0.8459 (tptp) cc_final: 0.8229 (tptp) REVERT: 4A 307 PHE cc_start: 0.8508 (t80) cc_final: 0.8127 (t80) REVERT: 5A 1003 PHE cc_start: 0.9169 (t80) cc_final: 0.8731 (t80) REVERT: 5A 1005 PHE cc_start: 0.9041 (t80) cc_final: 0.8732 (t80) REVERT: 5A 1007 PHE cc_start: 0.9152 (t80) cc_final: 0.8671 (t80) REVERT: 6A 1106 LYS cc_start: 0.8863 (tttp) cc_final: 0.8585 (tttp) REVERT: 7A 1205 PHE cc_start: 0.8502 (t80) cc_final: 0.8271 (t80) REVERT: 7A 1206 LYS cc_start: 0.8695 (tttt) cc_final: 0.8343 (tttm) REVERT: 9A 104 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: 9A 106 LYS cc_start: 0.8906 (tttp) cc_final: 0.8655 (tttm) REVERT: BB 305 PHE cc_start: 0.8766 (t80) cc_final: 0.8355 (t80) REVERT: BB 307 PHE cc_start: 0.8514 (t80) cc_final: 0.8208 (t80) REVERT: CB 1003 PHE cc_start: 0.9123 (t80) cc_final: 0.8740 (t80) REVERT: CB 1005 PHE cc_start: 0.9008 (t80) cc_final: 0.8652 (t80) REVERT: CB 1007 PHE cc_start: 0.9161 (t80) cc_final: 0.8929 (t80) REVERT: DB 1106 LYS cc_start: 0.8792 (tttp) cc_final: 0.8527 (tttp) REVERT: EB 1202 LYS cc_start: 0.8867 (tttm) cc_final: 0.8491 (tttm) REVERT: EB 1206 LYS cc_start: 0.8740 (tttt) cc_final: 0.8538 (tttm) REVERT: FB 1304 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8667 (tm-30) REVERT: GB 103 PHE cc_start: 0.9078 (t80) cc_final: 0.8876 (t80) REVERT: GB 106 LYS cc_start: 0.8643 (tttp) cc_final: 0.8431 (tttm) REVERT: HB 206 LYS cc_start: 0.8809 (tttt) cc_final: 0.8555 (tttm) REVERT: IB 303 PHE cc_start: 0.8906 (t80) cc_final: 0.8678 (t80) REVERT: IB 304 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8429 (tm-30) REVERT: KB 1105 PHE cc_start: 0.8731 (t80) cc_final: 0.8308 (t80) REVERT: KB 1106 LYS cc_start: 0.8655 (tttp) cc_final: 0.8378 (tttp) REVERT: MB 1303 PHE cc_start: 0.8794 (t80) cc_final: 0.8553 (t80) REVERT: i 6 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8467 (ttpt) REVERT: NB 104 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: OB 206 LYS cc_start: 0.8866 (tttt) cc_final: 0.8654 (tttt) REVERT: PB 304 GLU cc_start: 0.8840 (tm-30) cc_final: 0.6113 (pm20) REVERT: PB 305 PHE cc_start: 0.8434 (t80) cc_final: 0.7272 (t80) REVERT: TB 1305 PHE cc_start: 0.8317 (t80) cc_final: 0.8019 (t80) REVERT: TB 1307 PHE cc_start: 0.8067 (t80) cc_final: 0.7620 (t80) outliers start: 126 outliers final: 85 residues processed: 495 average time/residue: 0.4431 time to fit residues: 267.3942 Evaluate side-chains 550 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 460 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain U residue 1106 LYS Chi-restraints excluded: chain W residue 1302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain k residue 1102 LYS Chi-restraints excluded: chain k residue 1106 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain p residue 302 LYS Chi-restraints excluded: chain r residue 1102 LYS Chi-restraints excluded: chain r residue 1106 LYS Chi-restraints excluded: chain t residue 1302 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain y residue 1102 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 302 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1102 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain FA residue 102 LYS Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain JA residue 1102 LYS Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain QA residue 1102 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain yA residue 1006 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain CB residue 1006 LYS Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain JB residue 1006 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.341 12528 Z= 6.053 Angle : 3.929 32.936 16272 Z= 1.769 Chirality : 0.301 1.035 1152 Planarity : 0.017 0.058 2160 Dihedral : 21.336 111.528 1779 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 100.64 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.76 % Favored : 84.90 % Rotamer: Outliers : 15.16 % Allowed : 18.06 % Favored : 66.78 % Cbeta Deviations : 13.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.31 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.80 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.118 0.018 PHE4A 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 453 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8616 (mtmt) REVERT: J 106 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8674 (mmmm) REVERT: M 1004 GLU cc_start: 0.7853 (mp0) cc_final: 0.7100 (mp0) REVERT: M 1006 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8824 (mtmt) REVERT: N 1104 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7860 (mm-30) REVERT: N 1106 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8487 (mmmm) REVERT: B 4 GLU cc_start: 0.7981 (mp0) cc_final: 0.7412 (mp0) REVERT: Q 106 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8684 (mmmm) REVERT: T 1006 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8510 (mtmt) REVERT: U 1104 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7769 (mm-30) REVERT: U 1106 LYS cc_start: 0.8724 (tptm) cc_final: 0.8448 (tptm) REVERT: W 1302 LYS cc_start: 0.9203 (ttpt) cc_final: 0.8794 (mtpp) REVERT: C 6 LYS cc_start: 0.9001 (mtmt) cc_final: 0.8768 (mtmt) REVERT: X 106 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8532 (mmmm) REVERT: Y 206 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8821 (mtpp) REVERT: j 1004 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: j 1006 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8643 (mtmt) REVERT: k 1102 LYS cc_start: 0.8000 (ttpt) cc_final: 0.7326 (ttpt) REVERT: k 1106 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8660 (mmmm) REVERT: l 1206 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8697 (ttmm) REVERT: D 4 GLU cc_start: 0.7930 (mp0) cc_final: 0.7448 (mp0) REVERT: n 106 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8454 (mmmm) REVERT: o 204 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7548 (mt-10) REVERT: q 1004 GLU cc_start: 0.8320 (mp0) cc_final: 0.8036 (mp0) REVERT: r 1106 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8720 (mmmm) REVERT: s 1204 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7456 (mt-10) REVERT: t 1304 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7467 (mm-30) REVERT: u 102 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8609 (ttpt) REVERT: u 104 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7602 (mm-30) REVERT: u 106 LYS cc_start: 0.8771 (mmmm) cc_final: 0.8356 (mmmm) REVERT: v 202 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8863 (mmmm) REVERT: y 1102 LYS cc_start: 0.9081 (ttpt) cc_final: 0.8707 (ttpt) REVERT: y 1106 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8592 (mmmm) REVERT: F 4 GLU cc_start: 0.7934 (mp0) cc_final: 0.6955 (mp0) REVERT: 1 106 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8656 (mmmm) REVERT: 3 304 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7719 (mm-30) REVERT: 4 1004 GLU cc_start: 0.7786 (mp0) cc_final: 0.7561 (mp0) REVERT: 4 1006 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8701 (ttmt) REVERT: 5 1104 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7781 (mm-30) REVERT: 6 1202 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8715 (mmmm) REVERT: 6 1204 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7294 (mt-10) REVERT: 7 1304 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7381 (mm-30) REVERT: G 4 GLU cc_start: 0.7906 (mp0) cc_final: 0.7074 (mp0) REVERT: G 6 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8719 (mtmt) REVERT: 8 102 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8758 (ttpt) REVERT: 8 104 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7277 (mm-30) REVERT: BA 1006 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8398 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8545 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8778 (ttmm) REVERT: EA 1304 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7780 (mm-30) REVERT: EA 1306 LYS cc_start: 0.9030 (tttt) cc_final: 0.8765 (mttt) REVERT: FA 106 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8347 (mmmm) REVERT: JA 1106 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8412 (mmmm) REVERT: LA 1304 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7128 (mm-30) REVERT: I 4 GLU cc_start: 0.7986 (mp0) cc_final: 0.6687 (mp0) REVERT: MA 106 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8648 (mmmt) REVERT: PA 1004 GLU cc_start: 0.7771 (mp0) cc_final: 0.6733 (mp0) REVERT: QA 1102 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8652 (mmmt) REVERT: RA 1202 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8769 (mtpp) REVERT: RA 1204 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7760 (mt-10) REVERT: SA 1304 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8146 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9007 (tttt) cc_final: 0.8778 (tttt) REVERT: a 2 LYS cc_start: 0.9116 (tppt) cc_final: 0.8656 (tppt) REVERT: a 4 GLU cc_start: 0.8641 (tp30) cc_final: 0.8320 (tp30) REVERT: TA 106 LYS cc_start: 0.9048 (tttp) cc_final: 0.8664 (ptmm) REVERT: UA 202 LYS cc_start: 0.9342 (tttm) cc_final: 0.8921 (ttmm) REVERT: UA 204 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7627 (tm-30) REVERT: VA 306 LYS cc_start: 0.9058 (tptp) cc_final: 0.8843 (tptp) REVERT: WA 1004 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: YA 1202 LYS cc_start: 0.9188 (tttm) cc_final: 0.8873 (tttm) REVERT: ZA 1304 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8420 (tm-30) REVERT: aA 106 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8618 (ptmm) REVERT: bA 202 LYS cc_start: 0.9273 (tttm) cc_final: 0.8793 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8911 (ttmt) REVERT: dA 1004 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: iA 202 LYS cc_start: 0.9329 (tttm) cc_final: 0.8997 (tppp) REVERT: lA 1103 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.9079 (t80) REVERT: d 2 LYS cc_start: 0.9078 (tppt) cc_final: 0.8576 (tppt) REVERT: d 4 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8186 (tp30) REVERT: pA 202 LYS cc_start: 0.9272 (tttm) cc_final: 0.8995 (tttm) REVERT: pA 204 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7383 (tm-30) REVERT: qA 306 LYS cc_start: 0.9014 (tptp) cc_final: 0.8771 (tptp) REVERT: rA 1002 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8971 (ttpt) REVERT: sA 1103 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8946 (t80) REVERT: tA 1204 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7817 (tm-30) REVERT: e 4 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: vA 104 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8379 (tm-30) REVERT: wA 202 LYS cc_start: 0.9302 (tttm) cc_final: 0.8860 (tppp) REVERT: wA 204 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7885 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8933 (tppt) REVERT: yA 1004 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: 1A 1304 GLU cc_start: 0.9314 (tm-30) cc_final: 0.7884 (tm-30) REVERT: f 2 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8777 (ttmt) REVERT: f 4 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: 3A 202 LYS cc_start: 0.9270 (tttm) cc_final: 0.8862 (ttmm) REVERT: 3A 204 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7440 (tm-30) REVERT: 4A 302 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8655 (tptp) REVERT: 4A 304 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8192 (tm-30) REVERT: 4A 306 LYS cc_start: 0.8983 (tptp) cc_final: 0.8773 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9159 (ptpt) cc_final: 0.8938 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7549 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8669 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8178 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.8764 (tptp) cc_final: 0.8473 (tptp) REVERT: g 2 LYS cc_start: 0.9048 (tppt) cc_final: 0.8572 (tppt) REVERT: g 4 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8388 (tp30) REVERT: 9A 105 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9053 (t80) REVERT: AB 202 LYS cc_start: 0.9291 (tttm) cc_final: 0.8893 (ttmm) REVERT: BB 302 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8828 (tptp) REVERT: CB 1004 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8448 (tp30) REVERT: DB 1102 LYS cc_start: 0.9162 (tptm) cc_final: 0.8943 (tptm) REVERT: EB 1204 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7195 (tm-30) REVERT: FB 1303 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8346 (t80) REVERT: HB 202 LYS cc_start: 0.9386 (tttm) cc_final: 0.8950 (pttm) REVERT: IB 306 LYS cc_start: 0.8885 (tptp) cc_final: 0.8643 (tptp) REVERT: IB 307 PHE cc_start: 0.9330 (t80) cc_final: 0.9078 (t80) REVERT: JB 1004 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: KB 1106 LYS cc_start: 0.9098 (tttp) cc_final: 0.8866 (tttm) REVERT: LB 1202 LYS cc_start: 0.9189 (tttm) cc_final: 0.8943 (pptt) REVERT: i 4 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: NB 102 LYS cc_start: 0.9227 (tptm) cc_final: 0.9021 (pttt) REVERT: NB 103 PHE cc_start: 0.9064 (t80) cc_final: 0.8655 (t80) REVERT: NB 104 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: OB 202 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8984 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8139 (tp30) REVERT: QB 1006 LYS cc_start: 0.9206 (ttpt) cc_final: 0.8868 (ttpt) REVERT: SB 1204 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8071 (tm-30) outliers start: 131 outliers final: 67 residues processed: 497 average time/residue: 0.4598 time to fit residues: 277.3164 Evaluate side-chains 547 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 453 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.339 12528 Z= 6.067 Angle : 4.021 36.728 16272 Z= 1.813 Chirality : 0.298 1.008 1152 Planarity : 0.017 0.055 2160 Dihedral : 20.741 89.207 1519 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 106.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.53 % Favored : 82.29 % Rotamer: Outliers : 20.95 % Allowed : 21.64 % Favored : 57.41 % Cbeta Deviations : 14.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.71 (0.25), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.19), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.124 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 437 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8714 (mtmt) REVERT: K 206 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8792 (ttmm) REVERT: M 1004 GLU cc_start: 0.7884 (mp0) cc_final: 0.7127 (mp0) REVERT: M 1006 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8830 (mtmt) REVERT: N 1104 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8035 (mm-30) REVERT: N 1106 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8475 (mmmm) REVERT: B 4 GLU cc_start: 0.8031 (mp0) cc_final: 0.7612 (mp0) REVERT: Q 106 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8657 (mmmm) REVERT: R 206 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8709 (ttmm) REVERT: S 307 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.9068 (m-80) REVERT: T 1004 GLU cc_start: 0.8194 (mp0) cc_final: 0.7542 (mp0) REVERT: T 1006 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8744 (mtmt) REVERT: U 1104 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7728 (mm-30) REVERT: U 1106 LYS cc_start: 0.8848 (tptm) cc_final: 0.8495 (tptm) REVERT: C 4 GLU cc_start: 0.7930 (mp0) cc_final: 0.7516 (mp0) REVERT: X 106 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8563 (mmmm) REVERT: Z 304 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8356 (mm-30) REVERT: j 1004 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: j 1006 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8636 (mtmt) REVERT: k 1106 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8570 (mmmm) REVERT: l 1202 LYS cc_start: 0.9193 (mtpt) cc_final: 0.8875 (mtpp) REVERT: l 1204 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8068 (mm-30) REVERT: D 4 GLU cc_start: 0.7999 (mp0) cc_final: 0.7506 (mp0) REVERT: n 106 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8489 (mmmm) REVERT: o 202 LYS cc_start: 0.9194 (ttpt) cc_final: 0.8926 (ttpt) REVERT: o 204 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7746 (mt-10) REVERT: q 1004 GLU cc_start: 0.8327 (mp0) cc_final: 0.8001 (mp0) REVERT: r 1104 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7577 (mm-30) REVERT: r 1106 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8648 (mmmm) REVERT: s 1204 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7825 (mt-10) REVERT: t 1304 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7809 (mm-30) REVERT: E 6 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8660 (mtmt) REVERT: u 106 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8327 (mmmm) REVERT: v 206 LYS cc_start: 0.9235 (ttmm) cc_final: 0.9021 (ttmm) REVERT: w 307 PHE cc_start: 0.9485 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: x 1003 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: y 1102 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8644 (ttpt) REVERT: y 1106 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8701 (mmmm) REVERT: 1 106 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8401 (mmmm) REVERT: 3 304 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8086 (mm-30) REVERT: 4 1004 GLU cc_start: 0.7799 (mp0) cc_final: 0.7555 (mp0) REVERT: 4 1006 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8710 (ttmt) REVERT: 6 1202 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8803 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7830 (mm-30) REVERT: G 4 GLU cc_start: 0.7981 (mp0) cc_final: 0.7477 (mp0) REVERT: G 6 LYS cc_start: 0.9010 (mtmt) cc_final: 0.8764 (mtmt) REVERT: 8 106 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8339 (mmmm) REVERT: AA 306 LYS cc_start: 0.9066 (mttt) cc_final: 0.8822 (mttt) REVERT: BA 1004 GLU cc_start: 0.7932 (mp0) cc_final: 0.7677 (mp0) REVERT: DA 1206 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8788 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9067 (mttt) cc_final: 0.8666 (mttt) REVERT: FA 104 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7496 (mm-30) REVERT: FA 106 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8447 (mmmm) REVERT: HA 302 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8668 (mmmm) REVERT: JA 1106 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8374 (mmmm) REVERT: KA 1207 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8868 (t80) REVERT: LA 1306 LYS cc_start: 0.9032 (tttt) cc_final: 0.8810 (ttpt) REVERT: I 4 GLU cc_start: 0.7747 (mp0) cc_final: 0.7434 (mp0) REVERT: I 6 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8704 (ttmt) REVERT: QA 1106 LYS cc_start: 0.5388 (tptt) cc_final: 0.4855 (tptp) REVERT: RA 1202 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8816 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8203 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: a 2 LYS cc_start: 0.9148 (tppt) cc_final: 0.8776 (tppt) REVERT: a 4 GLU cc_start: 0.8714 (tp30) cc_final: 0.8416 (tp30) REVERT: TA 106 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8664 (ptmm) REVERT: UA 204 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7708 (tm-30) REVERT: VA 302 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.9032 (tptp) REVERT: WA 1002 LYS cc_start: 0.9211 (tppt) cc_final: 0.8842 (tppt) REVERT: WA 1004 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: XA 1105 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8774 (p90) REVERT: YA 1202 LYS cc_start: 0.9263 (tttm) cc_final: 0.9001 (tttm) REVERT: ZA 1302 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8869 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8567 (tm-30) REVERT: bA 202 LYS cc_start: 0.9271 (tttm) cc_final: 0.8883 (ttmm) REVERT: bA 204 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7708 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8916 (ttmt) REVERT: gA 1304 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8172 (tm-30) REVERT: iA 202 LYS cc_start: 0.9376 (tttm) cc_final: 0.8992 (tppp) REVERT: iA 204 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7768 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.9067 (t80) REVERT: nA 1306 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8774 (tptp) REVERT: d 4 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: oA 102 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8919 (tptm) REVERT: pA 204 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7414 (tm-30) REVERT: qA 306 LYS cc_start: 0.9008 (tptp) cc_final: 0.8744 (tptp) REVERT: rA 1006 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8863 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7709 (tm-30) REVERT: e 4 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: e 6 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8768 (ttpt) REVERT: wA 202 LYS cc_start: 0.9297 (tttm) cc_final: 0.8833 (tppp) REVERT: wA 204 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7855 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8804 (tppt) REVERT: yA 1004 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: zA 1102 LYS cc_start: 0.9223 (tptm) cc_final: 0.8989 (tptm) REVERT: 1A 1305 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.9048 (t80) REVERT: f 2 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8765 (ttmt) REVERT: f 4 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8347 (tp30) REVERT: 3A 202 LYS cc_start: 0.9265 (tttm) cc_final: 0.8884 (ttmm) REVERT: 4A 304 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8234 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.9129 (ptpt) cc_final: 0.8916 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7618 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8723 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8110 (tm-30) REVERT: g 2 LYS cc_start: 0.9030 (tppt) cc_final: 0.8550 (tppt) REVERT: g 4 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: 9A 105 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9117 (t80) REVERT: AB 202 LYS cc_start: 0.9328 (tttm) cc_final: 0.8921 (ttmm) REVERT: AB 204 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7870 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8480 (tp30) REVERT: EB 1204 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7770 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8914 (tptp) cc_final: 0.8697 (tptp) REVERT: h 4 GLU cc_start: 0.8617 (tp30) cc_final: 0.7850 (pm20) REVERT: HB 202 LYS cc_start: 0.9300 (tttm) cc_final: 0.8863 (pttm) REVERT: JB 1004 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: i 4 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8316 (tp30) REVERT: NB 102 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.9021 (pttt) REVERT: NB 104 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: NB 106 LYS cc_start: 0.9109 (tttp) cc_final: 0.8656 (pptt) REVERT: OB 202 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9017 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8084 (tp30) REVERT: RB 1103 PHE cc_start: 0.8990 (t80) cc_final: 0.8497 (t80) REVERT: SB 1204 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8091 (tm-30) outliers start: 181 outliers final: 111 residues processed: 507 average time/residue: 0.4460 time to fit residues: 275.5833 Evaluate side-chains 583 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 436 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain T residue 1002 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.7468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.398 12528 Z= 6.076 Angle : 4.063 33.133 16272 Z= 1.836 Chirality : 0.298 0.972 1152 Planarity : 0.017 0.057 2160 Dihedral : 20.771 80.364 1507 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 107.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 18.40 % Favored : 81.42 % Rotamer: Outliers : 24.19 % Allowed : 21.18 % Favored : 54.63 % Cbeta Deviations : 15.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.88 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 426 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7518 (mp0) cc_final: 0.6715 (mp0) REVERT: K 206 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8799 (ttmm) REVERT: M 1004 GLU cc_start: 0.8045 (mp0) cc_final: 0.7264 (mp0) REVERT: M 1006 LYS cc_start: 0.9065 (mtmt) cc_final: 0.8829 (mtmt) REVERT: N 1104 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8079 (mm-30) REVERT: N 1106 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8358 (mmmm) REVERT: B 4 GLU cc_start: 0.8010 (mp0) cc_final: 0.7617 (mp0) REVERT: S 307 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8978 (m-80) REVERT: T 1004 GLU cc_start: 0.8241 (mp0) cc_final: 0.7529 (mp0) REVERT: T 1006 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8762 (mtmt) REVERT: U 1104 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7756 (mm-30) REVERT: U 1106 LYS cc_start: 0.8833 (tptm) cc_final: 0.8478 (tptm) REVERT: W 1302 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8790 (mtpp) REVERT: C 4 GLU cc_start: 0.7962 (mp0) cc_final: 0.7650 (mp0) REVERT: X 106 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8648 (mmmm) REVERT: Z 304 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8321 (mm-30) REVERT: j 1004 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: j 1006 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8599 (mtmt) REVERT: k 1106 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8602 (mmmm) REVERT: l 1202 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8805 (mtpp) REVERT: l 1206 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8818 (ttmm) REVERT: D 4 GLU cc_start: 0.7955 (mp0) cc_final: 0.7315 (mp0) REVERT: D 6 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8414 (mtmt) REVERT: D 7 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8601 (t80) REVERT: n 106 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8413 (mmmm) REVERT: o 202 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8955 (ttpt) REVERT: q 1004 GLU cc_start: 0.8247 (mp0) cc_final: 0.7899 (mp0) REVERT: r 1104 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7583 (mm-30) REVERT: r 1106 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8563 (mmmm) REVERT: s 1204 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7810 (mt-10) REVERT: t 1302 LYS cc_start: 0.9261 (tttt) cc_final: 0.9055 (tttt) REVERT: E 6 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8606 (mtmt) REVERT: u 106 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8180 (mmmm) REVERT: v 206 LYS cc_start: 0.9255 (ttmm) cc_final: 0.9011 (ttmm) REVERT: x 1003 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: x 1006 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8317 (mtmt) REVERT: y 1102 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8629 (ttpt) REVERT: y 1106 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8678 (mmmm) REVERT: 1 104 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7466 (mm-30) REVERT: 1 106 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8389 (mmmm) REVERT: 3 304 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8119 (mm-30) REVERT: 4 1004 GLU cc_start: 0.8205 (mp0) cc_final: 0.8000 (mp0) REVERT: 4 1006 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8695 (ttmt) REVERT: 5 1104 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7935 (mm-30) REVERT: 5 1106 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8540 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9266 (mtpt) cc_final: 0.8766 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7792 (mm-30) REVERT: G 3 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: G 4 GLU cc_start: 0.8022 (mp0) cc_final: 0.7717 (mp0) REVERT: G 6 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8785 (mtmt) REVERT: 8 104 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7313 (mm-30) REVERT: 8 106 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8141 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8178 (mp0) cc_final: 0.7760 (mp0) REVERT: CA 1104 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7439 (mm-30) REVERT: DA 1206 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8915 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9109 (mttt) cc_final: 0.8721 (mttt) REVERT: FA 104 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7666 (mm-30) REVERT: FA 106 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8524 (mmmm) REVERT: GA 207 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8759 (t80) REVERT: HA 302 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8709 (mtpp) REVERT: HA 304 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8147 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8392 (mmmm) REVERT: I 4 GLU cc_start: 0.7740 (mp0) cc_final: 0.6728 (mp0) REVERT: I 6 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8644 (mtmt) REVERT: MA 106 LYS cc_start: 0.3033 (OUTLIER) cc_final: 0.2823 (tptp) REVERT: NA 202 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8681 (mptt) REVERT: QA 1106 LYS cc_start: 0.3305 (OUTLIER) cc_final: 0.1481 (mmmt) REVERT: RA 1202 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8801 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: a 2 LYS cc_start: 0.9145 (tppt) cc_final: 0.8848 (tppt) REVERT: a 4 GLU cc_start: 0.8708 (tp30) cc_final: 0.8390 (tp30) REVERT: TA 106 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8681 (ptmm) REVERT: WA 1002 LYS cc_start: 0.9219 (tppt) cc_final: 0.8846 (tppt) REVERT: WA 1004 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: XA 1105 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8823 (p90) REVERT: ZA 1302 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8952 (tptp) REVERT: ZA 1303 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8688 (t80) REVERT: ZA 1304 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8619 (tm-30) REVERT: bA 202 LYS cc_start: 0.9259 (tttm) cc_final: 0.8889 (ttmm) REVERT: bA 204 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7755 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9139 (ttmt) cc_final: 0.8918 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8201 (tm-30) REVERT: c 4 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: iA 202 LYS cc_start: 0.9397 (tttm) cc_final: 0.8998 (tppp) REVERT: iA 204 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7741 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.9097 (t80) REVERT: d 4 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: oA 102 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8917 (tptm) REVERT: pA 204 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7339 (tm-30) REVERT: qA 306 LYS cc_start: 0.9006 (tptp) cc_final: 0.8723 (tptp) REVERT: rA 1006 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8882 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7777 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9104 (tttt) cc_final: 0.8903 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9444 (OUTLIER) cc_final: 0.9055 (t80) REVERT: e 4 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: e 6 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8809 (ttpt) REVERT: vA 104 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8360 (tm-30) REVERT: wA 202 LYS cc_start: 0.9287 (tttm) cc_final: 0.8890 (ttmm) REVERT: wA 204 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7906 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: zA 1102 LYS cc_start: 0.9221 (tptm) cc_final: 0.8994 (tptm) REVERT: 1A 1304 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8380 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.9033 (t80) REVERT: f 2 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8755 (ttmt) REVERT: f 4 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8355 (tp30) REVERT: 3A 202 LYS cc_start: 0.9247 (tttm) cc_final: 0.8926 (mmmm) REVERT: 3A 204 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7588 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8713 (tptp) REVERT: 4A 304 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8263 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.9124 (ptpt) cc_final: 0.8884 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7662 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8766 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8199 (tm-30) REVERT: g 2 LYS cc_start: 0.9047 (tppt) cc_final: 0.8534 (tppt) REVERT: g 4 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: 9A 105 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.9139 (t80) REVERT: AB 202 LYS cc_start: 0.9344 (tttm) cc_final: 0.8962 (ttmm) REVERT: AB 204 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7903 (tm-30) REVERT: BB 305 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.9189 (t80) REVERT: CB 1004 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8453 (tp30) REVERT: DB 1102 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8995 (tptm) REVERT: FB 1306 LYS cc_start: 0.8931 (tptp) cc_final: 0.8675 (tptp) REVERT: h 4 GLU cc_start: 0.8663 (tp30) cc_final: 0.8089 (pm20) REVERT: GB 103 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.9112 (t80) REVERT: HB 202 LYS cc_start: 0.9396 (tttm) cc_final: 0.8983 (pttt) REVERT: IB 306 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8730 (tptp) REVERT: JB 1004 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: MB 1306 LYS cc_start: 0.8912 (tptp) cc_final: 0.8664 (tptp) REVERT: i 4 GLU cc_start: 0.8782 (tp30) cc_final: 0.8277 (tp30) REVERT: NB 102 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.9034 (pttt) REVERT: NB 104 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8068 (pm20) REVERT: NB 106 LYS cc_start: 0.9157 (tttp) cc_final: 0.8731 (pptt) REVERT: OB 202 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9017 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: QB 1005 PHE cc_start: 0.9252 (t80) cc_final: 0.8607 (t80) outliers start: 209 outliers final: 130 residues processed: 511 average time/residue: 0.4771 time to fit residues: 298.5396 Evaluate side-chains 597 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 425 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain T residue 1002 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 4 residue 1002 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain QA residue 1104 GLU Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.7586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.351 12528 Z= 6.074 Angle : 4.072 30.119 16272 Z= 1.841 Chirality : 0.298 0.970 1152 Planarity : 0.017 0.057 2160 Dihedral : 20.607 82.090 1493 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 107.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.10 % Favored : 80.73 % Rotamer: Outliers : 24.77 % Allowed : 24.19 % Favored : 51.04 % Cbeta Deviations : 15.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.91 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 425 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7863 (mp0) cc_final: 0.6926 (mp0) REVERT: A 6 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8766 (mtmt) REVERT: J 104 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7625 (mm-30) REVERT: M 1004 GLU cc_start: 0.8174 (mp0) cc_final: 0.7426 (mp0) REVERT: N 1104 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8205 (mm-30) REVERT: N 1106 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8348 (mmmm) REVERT: O 1206 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8642 (ttmm) REVERT: B 4 GLU cc_start: 0.8043 (mp0) cc_final: 0.7679 (mp0) REVERT: B 5 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.9059 (m-80) REVERT: Q 106 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8615 (mmmm) REVERT: S 307 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8993 (m-80) REVERT: T 1004 GLU cc_start: 0.8262 (mp0) cc_final: 0.7517 (mp0) REVERT: T 1006 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8710 (mtmt) REVERT: U 1104 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7676 (mm-30) REVERT: U 1106 LYS cc_start: 0.8802 (tptm) cc_final: 0.8463 (tptm) REVERT: W 1302 LYS cc_start: 0.9224 (mtpt) cc_final: 0.8888 (mtpt) REVERT: C 4 GLU cc_start: 0.7988 (mp0) cc_final: 0.7011 (mp0) REVERT: X 106 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8640 (mmmm) REVERT: j 1004 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: j 1006 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8537 (mtmt) REVERT: k 1106 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8611 (mmmm) REVERT: l 1202 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8812 (mtpp) REVERT: l 1204 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8029 (mm-30) REVERT: D 4 GLU cc_start: 0.7977 (mp0) cc_final: 0.7191 (mp0) REVERT: D 6 LYS cc_start: 0.8984 (mtmt) cc_final: 0.8456 (mtmt) REVERT: D 7 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8705 (t80) REVERT: n 106 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8421 (mmmm) REVERT: o 202 LYS cc_start: 0.9230 (ttpt) cc_final: 0.9008 (ttpt) REVERT: q 1004 GLU cc_start: 0.8227 (mp0) cc_final: 0.7964 (mp0) REVERT: r 1104 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7640 (mm-30) REVERT: r 1106 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8504 (mmmm) REVERT: E 6 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8614 (mtmt) REVERT: u 106 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8120 (mmmm) REVERT: v 206 LYS cc_start: 0.9276 (ttmm) cc_final: 0.9020 (ttmm) REVERT: w 307 PHE cc_start: 0.9553 (OUTLIER) cc_final: 0.8809 (m-80) REVERT: x 1003 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: x 1006 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8405 (mtmt) REVERT: y 1106 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8775 (mmmm) REVERT: F 6 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8609 (mtmt) REVERT: 1 104 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7599 (mm-30) REVERT: 1 106 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8386 (mmmm) REVERT: 4 1006 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8705 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8399 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9225 (mtpt) cc_final: 0.8749 (mtpp) REVERT: G 3 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: G 4 GLU cc_start: 0.8008 (mp0) cc_final: 0.7646 (mp0) REVERT: G 6 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8785 (mtmt) REVERT: 8 104 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7330 (mm-30) REVERT: 8 106 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8232 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8078 (mp0) cc_final: 0.7419 (mp0) REVERT: CA 1104 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7095 (mm-30) REVERT: DA 1206 LYS cc_start: 0.9253 (ttmm) cc_final: 0.9012 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9095 (mttt) cc_final: 0.8708 (mttt) REVERT: H 4 GLU cc_start: 0.2921 (OUTLIER) cc_final: 0.2077 (pm20) REVERT: FA 106 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8587 (mmmm) REVERT: HA 302 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8695 (mmmm) REVERT: HA 304 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8166 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8409 (mmmm) REVERT: I 4 GLU cc_start: 0.7760 (mp0) cc_final: 0.6793 (mp0) REVERT: PA 1004 GLU cc_start: 0.7485 (mp0) cc_final: 0.6134 (mp0) REVERT: PA 1006 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8710 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8805 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: a 2 LYS cc_start: 0.9156 (tppt) cc_final: 0.8871 (tppt) REVERT: a 4 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8255 (tp30) REVERT: TA 106 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8701 (ptmm) REVERT: WA 1002 LYS cc_start: 0.9236 (tppt) cc_final: 0.8846 (tppt) REVERT: WA 1004 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8461 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8882 (tptp) REVERT: ZA 1303 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8672 (t80) REVERT: ZA 1304 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8638 (tm-30) REVERT: aA 104 GLU cc_start: 0.8703 (tm-30) cc_final: 0.7824 (tm-30) REVERT: bA 202 LYS cc_start: 0.9237 (tttm) cc_final: 0.8830 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8919 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8168 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9306 (t80) cc_final: 0.8948 (t80) REVERT: c 4 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: iA 204 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7809 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.9091 (t80) REVERT: d 4 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: oA 102 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8923 (tptm) REVERT: pA 204 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7380 (tm-30) REVERT: qA 306 LYS cc_start: 0.9003 (tptp) cc_final: 0.8726 (tptp) REVERT: tA 1204 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7781 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9117 (tttt) cc_final: 0.8905 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.9122 (t80) REVERT: e 4 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8216 (tp30) REVERT: e 6 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8784 (ttpt) REVERT: vA 104 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8359 (tm-30) REVERT: wA 202 LYS cc_start: 0.9280 (tttm) cc_final: 0.8877 (ttmm) REVERT: wA 204 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7902 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: zA 1102 LYS cc_start: 0.9216 (tptm) cc_final: 0.8999 (tptm) REVERT: 1A 1304 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8337 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8996 (t80) REVERT: f 2 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8759 (ttmt) REVERT: f 4 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8352 (tp30) REVERT: 3A 202 LYS cc_start: 0.9237 (tttm) cc_final: 0.8929 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7664 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8737 (tptp) REVERT: 4A 304 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8275 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.9115 (ptpt) cc_final: 0.8871 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7642 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8777 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8162 (tm-30) REVERT: g 2 LYS cc_start: 0.9044 (tppt) cc_final: 0.8535 (tppt) REVERT: g 4 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: AB 202 LYS cc_start: 0.9354 (tttm) cc_final: 0.8955 (ttmm) REVERT: AB 204 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7807 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: DB 1102 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8976 (tptm) REVERT: EB 1204 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7357 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8900 (tptp) cc_final: 0.8577 (tptp) REVERT: h 4 GLU cc_start: 0.8682 (tp30) cc_final: 0.7990 (pm20) REVERT: GB 103 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.9146 (t80) REVERT: HB 202 LYS cc_start: 0.9374 (tttm) cc_final: 0.8965 (pttt) REVERT: IB 306 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8783 (tptp) REVERT: JB 1004 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: i 4 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: NB 102 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9021 (pttt) REVERT: NB 104 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8119 (pm20) REVERT: NB 106 LYS cc_start: 0.9094 (tttp) cc_final: 0.8678 (pptt) REVERT: OB 202 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9014 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: QB 1005 PHE cc_start: 0.9266 (t80) cc_final: 0.8641 (t80) outliers start: 214 outliers final: 154 residues processed: 520 average time/residue: 0.4387 time to fit residues: 279.3901 Evaluate side-chains 620 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 426 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.352 12528 Z= 6.073 Angle : 4.064 30.015 16272 Z= 1.837 Chirality : 0.299 0.970 1152 Planarity : 0.017 0.061 2160 Dihedral : 20.547 83.061 1493 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 108.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.27 % Favored : 80.56 % Rotamer: Outliers : 25.93 % Allowed : 24.65 % Favored : 49.42 % Cbeta Deviations : 15.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.92 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 425 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8719 (mtmt) REVERT: J 104 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7662 (mm-30) REVERT: M 1004 GLU cc_start: 0.8109 (mp0) cc_final: 0.7274 (mp0) REVERT: N 1104 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8138 (mm-30) REVERT: N 1106 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8315 (mmmm) REVERT: O 1206 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8667 (ttmm) REVERT: B 4 GLU cc_start: 0.8025 (mp0) cc_final: 0.7722 (mp0) REVERT: Q 104 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7821 (mm-30) REVERT: Q 106 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8633 (mmmm) REVERT: T 1004 GLU cc_start: 0.8247 (mp0) cc_final: 0.7507 (mp0) REVERT: T 1006 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8694 (mtmt) REVERT: U 1104 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7709 (mm-30) REVERT: U 1106 LYS cc_start: 0.8786 (tptm) cc_final: 0.8373 (tptm) REVERT: W 1302 LYS cc_start: 0.9208 (mtpt) cc_final: 0.8935 (mtpt) REVERT: C 4 GLU cc_start: 0.8004 (mp0) cc_final: 0.7070 (mp0) REVERT: X 106 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8647 (mmmm) REVERT: Y 202 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8817 (ttpt) REVERT: j 1004 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: j 1006 LYS cc_start: 0.9021 (mtmt) cc_final: 0.8532 (mtmt) REVERT: k 1106 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8590 (mmmm) REVERT: l 1202 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8821 (mtpp) REVERT: l 1204 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8018 (mm-30) REVERT: D 4 GLU cc_start: 0.7982 (mp0) cc_final: 0.7266 (mp0) REVERT: D 6 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8429 (mtmt) REVERT: D 7 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8605 (t80) REVERT: n 106 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8416 (mmmm) REVERT: o 202 LYS cc_start: 0.9239 (ttpt) cc_final: 0.9015 (ttpt) REVERT: q 1004 GLU cc_start: 0.8272 (mp0) cc_final: 0.7986 (mp0) REVERT: r 1104 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: r 1106 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8484 (mmmm) REVERT: t 1302 LYS cc_start: 0.9242 (tttt) cc_final: 0.9026 (tttp) REVERT: E 6 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8630 (mtmt) REVERT: u 106 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8189 (mmmm) REVERT: v 206 LYS cc_start: 0.9281 (ttmm) cc_final: 0.9020 (ttmm) REVERT: w 307 PHE cc_start: 0.9559 (OUTLIER) cc_final: 0.8858 (m-80) REVERT: x 1006 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8397 (mtmt) REVERT: y 1106 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8787 (mmmm) REVERT: F 6 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8665 (mtmt) REVERT: 1 104 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7679 (mm-30) REVERT: 1 106 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8376 (mmmm) REVERT: 4 1006 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8716 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8362 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9217 (mtpt) cc_final: 0.8731 (mtpp) REVERT: G 3 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: G 4 GLU cc_start: 0.8051 (mp0) cc_final: 0.7715 (mp0) REVERT: G 6 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8666 (mtmt) REVERT: 8 104 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7354 (mm-30) REVERT: 8 106 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8268 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8148 (mp0) cc_final: 0.7761 (mp0) REVERT: CA 1104 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7198 (mm-30) REVERT: DA 1206 LYS cc_start: 0.9261 (ttmm) cc_final: 0.9016 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9093 (mttt) cc_final: 0.8746 (mttt) REVERT: H 4 GLU cc_start: 0.2924 (OUTLIER) cc_final: 0.2187 (pm20) REVERT: FA 106 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8617 (mmmm) REVERT: HA 302 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8697 (mmmm) REVERT: HA 304 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8183 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8041 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8423 (mmmm) REVERT: I 4 GLU cc_start: 0.7764 (mp0) cc_final: 0.6794 (mp0) REVERT: PA 1004 GLU cc_start: 0.7512 (mp0) cc_final: 0.6220 (mp0) REVERT: RA 1202 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8799 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: a 2 LYS cc_start: 0.9127 (tppt) cc_final: 0.8850 (tppt) REVERT: a 4 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8281 (tp30) REVERT: TA 106 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8700 (ptmm) REVERT: UA 202 LYS cc_start: 0.9384 (tttm) cc_final: 0.8954 (ttmm) REVERT: WA 1002 LYS cc_start: 0.9228 (tppt) cc_final: 0.8840 (tppt) REVERT: WA 1004 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8458 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8856 (tptp) REVERT: ZA 1303 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8732 (t80) REVERT: ZA 1304 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8661 (tm-30) REVERT: b 6 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8901 (ttpt) REVERT: aA 104 GLU cc_start: 0.8708 (tm-30) cc_final: 0.7808 (tm-30) REVERT: bA 202 LYS cc_start: 0.9243 (tttm) cc_final: 0.8867 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8918 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8180 (tm-30) REVERT: iA 204 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7811 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.9084 (t80) REVERT: d 4 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7986 (tp30) REVERT: oA 102 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8910 (tptm) REVERT: pA 204 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7378 (tm-30) REVERT: qA 306 LYS cc_start: 0.9005 (tptp) cc_final: 0.8722 (tptp) REVERT: tA 1204 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7772 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9134 (tttt) cc_final: 0.8910 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.9150 (t80) REVERT: e 4 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: e 6 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8808 (ttpt) REVERT: vA 104 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8351 (tm-30) REVERT: wA 202 LYS cc_start: 0.9284 (tttm) cc_final: 0.8888 (ttmm) REVERT: wA 204 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7909 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8202 (tp30) REVERT: zA 1102 LYS cc_start: 0.9219 (tptm) cc_final: 0.9014 (tptm) REVERT: 0A 1204 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7893 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8522 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.9058 (t80) REVERT: f 2 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8754 (ttmt) REVERT: f 4 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8348 (tp30) REVERT: 3A 202 LYS cc_start: 0.9235 (tttm) cc_final: 0.8930 (mmmm) REVERT: 3A 204 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7611 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8747 (tptp) REVERT: 4A 304 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8267 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.9123 (ptpt) cc_final: 0.8884 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7647 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8780 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8152 (tm-30) REVERT: g 2 LYS cc_start: 0.9024 (tppt) cc_final: 0.8524 (tppt) REVERT: g 4 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: 9A 105 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9200 (t80) REVERT: AB 202 LYS cc_start: 0.9354 (tttm) cc_final: 0.8980 (ttmm) REVERT: AB 204 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7813 (tm-30) REVERT: BB 305 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9130 (t80) REVERT: CB 1004 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: DB 1102 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9004 (tptm) REVERT: h 4 GLU cc_start: 0.8680 (tp30) cc_final: 0.8157 (pm20) REVERT: GB 103 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.9136 (t80) REVERT: HB 202 LYS cc_start: 0.9390 (tttm) cc_final: 0.8967 (pttt) REVERT: IB 306 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8789 (tptp) REVERT: JB 1004 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: i 4 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8314 (tp30) REVERT: NB 102 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9023 (pttt) REVERT: NB 104 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8110 (pm20) REVERT: NB 106 LYS cc_start: 0.9123 (tttp) cc_final: 0.8682 (pptt) REVERT: OB 202 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9010 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7887 (tp30) REVERT: QB 1005 PHE cc_start: 0.9270 (t80) cc_final: 0.8630 (t80) outliers start: 224 outliers final: 171 residues processed: 522 average time/residue: 0.4424 time to fit residues: 282.0175 Evaluate side-chains 636 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 425 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 4 residue 1006 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.7672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.349 12528 Z= 6.076 Angle : 4.078 30.176 16272 Z= 1.845 Chirality : 0.299 0.967 1152 Planarity : 0.017 0.061 2160 Dihedral : 20.544 83.199 1493 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 108.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.62 % Favored : 80.21 % Rotamer: Outliers : 27.08 % Allowed : 23.26 % Favored : 49.65 % Cbeta Deviations : 15.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.91 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 426 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7713 (mp0) cc_final: 0.6797 (mp0) REVERT: A 6 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8645 (mtmt) REVERT: J 104 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7654 (mm-30) REVERT: J 106 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8560 (tmmm) REVERT: M 1004 GLU cc_start: 0.8015 (mp0) cc_final: 0.7233 (mp0) REVERT: N 1104 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8121 (mm-30) REVERT: N 1106 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8353 (mmmm) REVERT: O 1206 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8654 (ttmm) REVERT: B 4 GLU cc_start: 0.8047 (mp0) cc_final: 0.7703 (mp0) REVERT: Q 104 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7495 (mm-30) REVERT: Q 106 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8637 (mmmm) REVERT: T 1004 GLU cc_start: 0.8248 (mp0) cc_final: 0.7516 (mp0) REVERT: T 1006 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8670 (mtmt) REVERT: U 1104 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7704 (mm-30) REVERT: U 1106 LYS cc_start: 0.8787 (tptm) cc_final: 0.8379 (tptm) REVERT: W 1302 LYS cc_start: 0.9209 (mtpt) cc_final: 0.8944 (mtpt) REVERT: C 4 GLU cc_start: 0.8025 (mp0) cc_final: 0.7082 (mp0) REVERT: X 106 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8664 (mmmm) REVERT: Y 202 LYS cc_start: 0.9099 (ttpt) cc_final: 0.8872 (ttpt) REVERT: j 1004 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: j 1006 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8597 (mtmt) REVERT: k 1106 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8597 (mmmm) REVERT: l 1202 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8795 (mtpp) REVERT: D 4 GLU cc_start: 0.7987 (mp0) cc_final: 0.7293 (mp0) REVERT: D 6 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8427 (mtmt) REVERT: D 7 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8618 (t80) REVERT: n 106 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8426 (mmmm) REVERT: o 202 LYS cc_start: 0.9244 (ttpt) cc_final: 0.9027 (ttpt) REVERT: q 1004 GLU cc_start: 0.8264 (mp0) cc_final: 0.8012 (mp0) REVERT: r 1104 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: r 1106 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8476 (mmmm) REVERT: t 1302 LYS cc_start: 0.9236 (tttt) cc_final: 0.8992 (tttp) REVERT: E 6 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8635 (mtmt) REVERT: u 106 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8183 (mmmm) REVERT: v 206 LYS cc_start: 0.9283 (ttmm) cc_final: 0.9012 (ttmm) REVERT: w 302 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8759 (mmmm) REVERT: x 1003 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: x 1006 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8439 (mtmt) REVERT: y 1106 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8760 (mmmm) REVERT: F 6 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8691 (mtmt) REVERT: 1 104 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7704 (mm-30) REVERT: 1 106 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8382 (mmmm) REVERT: 4 1006 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8688 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8436 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8718 (mtpp) REVERT: G 3 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: G 4 GLU cc_start: 0.8047 (mp0) cc_final: 0.7719 (mp0) REVERT: G 6 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8682 (mtmt) REVERT: 8 104 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7376 (mm-30) REVERT: 8 106 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8270 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8044 (mp0) cc_final: 0.7718 (mp0) REVERT: CA 1104 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7346 (mm-30) REVERT: DA 1206 LYS cc_start: 0.9290 (ttmm) cc_final: 0.9047 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9093 (mttt) cc_final: 0.8742 (mttt) REVERT: H 4 GLU cc_start: 0.2926 (OUTLIER) cc_final: 0.2100 (pm20) REVERT: FA 106 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8632 (mmmm) REVERT: HA 302 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8704 (mmmm) REVERT: HA 304 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8180 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7885 (tm-30) REVERT: JA 1106 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8392 (mmmm) REVERT: I 4 GLU cc_start: 0.7771 (mp0) cc_final: 0.6842 (mp0) REVERT: MA 106 LYS cc_start: 0.3110 (OUTLIER) cc_final: 0.2679 (tptt) REVERT: PA 1004 GLU cc_start: 0.7529 (mp0) cc_final: 0.6323 (mp0) REVERT: PA 1006 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8715 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: RA 1202 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8809 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: a 2 LYS cc_start: 0.9135 (tppt) cc_final: 0.8861 (tppt) REVERT: a 4 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: TA 106 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8702 (ptmm) REVERT: UA 202 LYS cc_start: 0.9381 (tttm) cc_final: 0.8954 (ttmm) REVERT: WA 1002 LYS cc_start: 0.9215 (tppt) cc_final: 0.8844 (tppt) REVERT: WA 1004 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8463 (tp30) REVERT: YA 1204 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7338 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8717 (t80) REVERT: ZA 1304 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8655 (tm-30) REVERT: aA 104 GLU cc_start: 0.8710 (tm-30) cc_final: 0.7803 (tm-30) REVERT: bA 202 LYS cc_start: 0.9245 (tttm) cc_final: 0.8866 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8914 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9088 (tm-30) cc_final: 0.7701 (tm-30) REVERT: c 4 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: iA 202 LYS cc_start: 0.9391 (tttm) cc_final: 0.9074 (mmmm) REVERT: lA 1103 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.9096 (t80) REVERT: d 2 LYS cc_start: 0.9098 (tppt) cc_final: 0.8820 (tppt) REVERT: d 4 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: oA 102 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8920 (tptm) REVERT: pA 204 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7397 (tm-30) REVERT: qA 306 LYS cc_start: 0.9000 (tptp) cc_final: 0.8723 (tptp) REVERT: tA 1204 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7756 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8909 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9164 (t80) REVERT: e 4 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: e 6 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8812 (ttpt) REVERT: vA 104 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8352 (tm-30) REVERT: wA 202 LYS cc_start: 0.9285 (tttm) cc_final: 0.8883 (ttmm) REVERT: wA 204 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7945 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7874 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8236 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.9044 (t80) REVERT: f 2 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8751 (ttmt) REVERT: f 4 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8343 (tp30) REVERT: 3A 202 LYS cc_start: 0.9231 (tttm) cc_final: 0.8940 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7631 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8748 (tptp) REVERT: 4A 304 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8270 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.9121 (ptpt) cc_final: 0.8877 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7651 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8784 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8142 (tm-30) REVERT: g 2 LYS cc_start: 0.9026 (tppt) cc_final: 0.8522 (tppt) REVERT: g 4 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: 9A 105 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9126 (t80) REVERT: AB 202 LYS cc_start: 0.9355 (tttm) cc_final: 0.8982 (ttmm) REVERT: AB 204 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7799 (tm-30) REVERT: BB 305 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9142 (t80) REVERT: CB 1004 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8378 (tp30) REVERT: DB 1102 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9005 (tptm) REVERT: EB 1204 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7292 (tm-30) REVERT: h 4 GLU cc_start: 0.8649 (tp30) cc_final: 0.8109 (pm20) REVERT: GB 103 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.9137 (t80) REVERT: HB 202 LYS cc_start: 0.9388 (tttm) cc_final: 0.8968 (pttt) REVERT: IB 306 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8763 (tptp) REVERT: JB 1004 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: i 4 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: NB 102 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9021 (pttt) REVERT: NB 104 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8105 (pm20) REVERT: NB 106 LYS cc_start: 0.9119 (tttp) cc_final: 0.8663 (pptt) REVERT: OB 202 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9004 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: QB 1005 PHE cc_start: 0.9274 (t80) cc_final: 0.8637 (t80) REVERT: QB 1006 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8907 (ttpt) REVERT: TB 1304 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8630 (tm-30) outliers start: 234 outliers final: 167 residues processed: 529 average time/residue: 0.4519 time to fit residues: 292.5707 Evaluate side-chains 639 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 426 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 4 residue 1006 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.348 12528 Z= 6.074 Angle : 4.108 38.299 16272 Z= 1.854 Chirality : 0.299 0.966 1152 Planarity : 0.017 0.063 2160 Dihedral : 20.533 83.422 1493 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 109.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.44 % Favored : 80.38 % Rotamer: Outliers : 26.97 % Allowed : 23.96 % Favored : 49.07 % Cbeta Deviations : 15.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.89 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.49 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 428 time to evaluate : 1.254 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 4 GLU cc_start: 0.7775 (mp0) cc_final: 0.6635 (mp0) REVERT: A 6 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8644 (mtmt) REVERT: J 104 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7718 (mm-30) REVERT: J 106 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8537 (tmmm) REVERT: M 1004 GLU cc_start: 0.8102 (mp0) cc_final: 0.7208 (mp0) REVERT: N 1104 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8123 (mm-30) REVERT: N 1106 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8307 (mmmm) REVERT: O 1206 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8655 (ttmm) REVERT: P 1304 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8244 (mm-30) REVERT: B 4 GLU cc_start: 0.8040 (mp0) cc_final: 0.7732 (mp0) REVERT: B 5 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.9095 (m-80) REVERT: Q 104 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7192 (mm-30) REVERT: Q 106 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8654 (mmmm) REVERT: T 1004 GLU cc_start: 0.8242 (mp0) cc_final: 0.7510 (mp0) REVERT: T 1006 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8610 (mtmt) REVERT: U 1104 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7688 (mm-30) REVERT: U 1106 LYS cc_start: 0.8789 (tptm) cc_final: 0.8376 (tptm) REVERT: W 1302 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8949 (mtpt) REVERT: C 4 GLU cc_start: 0.8016 (mp0) cc_final: 0.7066 (mp0) REVERT: X 106 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8674 (mmmm) REVERT: Y 202 LYS cc_start: 0.9072 (ttpt) cc_final: 0.8843 (ttpt) REVERT: j 1004 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: j 1006 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8489 (mtmt) REVERT: k 1106 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8602 (mmmm) REVERT: l 1202 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8829 (mtpp) REVERT: l 1204 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7991 (mm-30) REVERT: D 4 GLU cc_start: 0.7987 (mp0) cc_final: 0.7317 (mp0) REVERT: D 6 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8415 (mtmt) REVERT: D 7 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8615 (t80) REVERT: n 106 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8411 (mmmm) REVERT: o 202 LYS cc_start: 0.9248 (ttpt) cc_final: 0.9021 (ttpt) REVERT: q 1004 GLU cc_start: 0.8293 (mp0) cc_final: 0.8020 (mp0) REVERT: r 1104 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: r 1106 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8447 (mmmm) REVERT: t 1302 LYS cc_start: 0.9237 (tttt) cc_final: 0.8939 (tttp) REVERT: E 6 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8646 (mtmt) REVERT: u 106 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8186 (mmmm) REVERT: v 206 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8988 (ttmm) REVERT: w 307 PHE cc_start: 0.9533 (OUTLIER) cc_final: 0.8939 (m-80) REVERT: x 1003 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8715 (m-80) REVERT: x 1006 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8475 (mtmt) REVERT: y 1106 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8776 (mmmm) REVERT: F 6 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8703 (mtmt) REVERT: 1 104 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7710 (mm-30) REVERT: 1 106 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8415 (mmmm) REVERT: 4 1006 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8705 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8428 (mmmm) REVERT: G 3 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: G 4 GLU cc_start: 0.8059 (mp0) cc_final: 0.7724 (mp0) REVERT: G 6 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8688 (mtmt) REVERT: 8 104 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7372 (mm-30) REVERT: 8 106 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8291 (mmmm) REVERT: CA 1104 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7413 (mm-30) REVERT: EA 1306 LYS cc_start: 0.9113 (mttt) cc_final: 0.8892 (mttt) REVERT: H 4 GLU cc_start: 0.2925 (OUTLIER) cc_final: 0.2122 (pm20) REVERT: FA 106 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8651 (mmmm) REVERT: HA 302 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8705 (mmmm) REVERT: HA 304 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8188 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7852 (tm-30) REVERT: JA 1106 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8401 (mmmm) REVERT: I 4 GLU cc_start: 0.7767 (mp0) cc_final: 0.6867 (mp0) REVERT: MA 106 LYS cc_start: 0.3105 (OUTLIER) cc_final: 0.2564 (tptt) REVERT: OA 304 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: PA 1004 GLU cc_start: 0.7535 (mp0) cc_final: 0.6410 (mp0) REVERT: PA 1006 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8711 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8856 (m-80) REVERT: RA 1202 LYS cc_start: 0.9162 (mtpt) cc_final: 0.8798 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: a 2 LYS cc_start: 0.9140 (tppt) cc_final: 0.8873 (tppt) REVERT: a 4 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: TA 106 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8697 (ptmm) REVERT: UA 202 LYS cc_start: 0.9378 (tttm) cc_final: 0.8952 (ttmm) REVERT: WA 1002 LYS cc_start: 0.9214 (tppt) cc_final: 0.8841 (tppt) REVERT: WA 1004 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: ZA 1304 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8520 (tm-30) REVERT: aA 104 GLU cc_start: 0.8712 (tm-30) cc_final: 0.7797 (tm-30) REVERT: bA 202 LYS cc_start: 0.9244 (tttm) cc_final: 0.8825 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8914 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8210 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9236 (t80) cc_final: 0.8902 (t80) REVERT: c 4 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8136 (tp30) REVERT: iA 202 LYS cc_start: 0.9385 (tttm) cc_final: 0.9065 (mmmm) REVERT: lA 1103 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.9100 (t80) REVERT: d 2 LYS cc_start: 0.9093 (tppt) cc_final: 0.8821 (tppt) REVERT: d 4 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: oA 102 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8923 (tptm) REVERT: pA 204 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7356 (tm-30) REVERT: qA 306 LYS cc_start: 0.9008 (tptp) cc_final: 0.8736 (tptp) REVERT: rA 1006 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8962 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8015 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8925 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9153 (t80) REVERT: e 4 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8212 (tp30) REVERT: e 6 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8813 (ttpt) REVERT: vA 104 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8356 (tm-30) REVERT: wA 202 LYS cc_start: 0.9286 (tttm) cc_final: 0.8877 (ttmm) REVERT: wA 204 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7943 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7873 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8237 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.9047 (t80) REVERT: f 2 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8751 (ttmt) REVERT: f 4 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8348 (tp30) REVERT: 3A 202 LYS cc_start: 0.9234 (tttm) cc_final: 0.8877 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7623 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8746 (tptp) REVERT: 4A 304 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8266 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.9122 (ptpt) cc_final: 0.8880 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7672 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8788 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8809 (tptp) cc_final: 0.8569 (tptp) REVERT: g 2 LYS cc_start: 0.9023 (tppt) cc_final: 0.8521 (tppt) REVERT: g 4 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: 9A 105 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.9119 (t80) REVERT: AB 202 LYS cc_start: 0.9354 (tttm) cc_final: 0.8981 (ttmm) REVERT: AB 204 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7805 (tm-30) REVERT: BB 305 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9143 (t80) REVERT: CB 1004 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8380 (tp30) REVERT: DB 1102 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9001 (tptm) REVERT: EB 1204 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7297 (tm-30) REVERT: h 4 GLU cc_start: 0.8648 (tp30) cc_final: 0.8107 (pm20) REVERT: GB 103 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.9138 (t80) REVERT: HB 202 LYS cc_start: 0.9389 (tttm) cc_final: 0.8968 (pttt) REVERT: IB 306 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8759 (tptp) REVERT: JB 1004 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: i 4 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: NB 102 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9023 (pttt) REVERT: NB 104 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8106 (pm20) REVERT: NB 106 LYS cc_start: 0.9121 (tttp) cc_final: 0.8664 (pptt) REVERT: OB 202 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9009 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: QB 1005 PHE cc_start: 0.9274 (t80) cc_final: 0.8630 (t80) REVERT: QB 1006 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8936 (ttpt) REVERT: TB 1304 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8655 (tm-30) outliers start: 233 outliers final: 170 residues processed: 531 average time/residue: 0.4338 time to fit residues: 282.2423 Evaluate side-chains 646 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 428 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1302 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.7725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.343 12528 Z= 6.079 Angle : 4.127 49.320 16272 Z= 1.859 Chirality : 0.300 0.964 1152 Planarity : 0.017 0.063 2160 Dihedral : 20.511 83.353 1493 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 109.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.14 % Favored : 79.86 % Rotamer: Outliers : 26.74 % Allowed : 24.88 % Favored : 48.38 % Cbeta Deviations : 15.54 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.87 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 427 time to evaluate : 1.637 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 4 GLU cc_start: 0.7842 (mp0) cc_final: 0.6658 (mp0) REVERT: A 6 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8608 (mtmt) REVERT: J 104 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7716 (mm-30) REVERT: J 106 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8493 (tmmm) REVERT: M 1004 GLU cc_start: 0.8174 (mp0) cc_final: 0.7341 (mp0) REVERT: N 1104 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8128 (mm-30) REVERT: N 1106 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8309 (mmmm) REVERT: O 1206 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8659 (ttmm) REVERT: P 1304 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8271 (mm-30) REVERT: B 4 GLU cc_start: 0.8021 (mp0) cc_final: 0.7762 (mp0) REVERT: Q 104 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7129 (mm-30) REVERT: Q 106 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8655 (mmmm) REVERT: T 1004 GLU cc_start: 0.8228 (mp0) cc_final: 0.7492 (mp0) REVERT: T 1006 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8556 (mtmt) REVERT: U 1104 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7707 (mm-30) REVERT: U 1106 LYS cc_start: 0.8797 (tptm) cc_final: 0.8373 (tptm) REVERT: W 1302 LYS cc_start: 0.9199 (mtpt) cc_final: 0.8946 (mtpt) REVERT: C 4 GLU cc_start: 0.8021 (mp0) cc_final: 0.7079 (mp0) REVERT: X 106 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8674 (mmmm) REVERT: Y 202 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8865 (ttpt) REVERT: j 1004 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: j 1006 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8518 (mtmt) REVERT: k 1106 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8600 (mmmm) REVERT: l 1202 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8729 (mtpp) REVERT: l 1204 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7994 (mm-30) REVERT: D 4 GLU cc_start: 0.7986 (mp0) cc_final: 0.7339 (mp0) REVERT: D 6 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8436 (mtmt) REVERT: D 7 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.8618 (t80) REVERT: n 106 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8388 (mmmm) REVERT: o 202 LYS cc_start: 0.9250 (ttpt) cc_final: 0.9020 (ttpt) REVERT: q 1004 GLU cc_start: 0.8307 (mp0) cc_final: 0.8104 (mp0) REVERT: r 1104 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: r 1106 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8417 (mmmm) REVERT: t 1302 LYS cc_start: 0.9235 (tttt) cc_final: 0.8965 (tttp) REVERT: E 6 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8659 (mtmt) REVERT: u 106 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8184 (mmmm) REVERT: v 206 LYS cc_start: 0.9282 (ttmm) cc_final: 0.8993 (ttmm) REVERT: w 302 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8748 (mmmm) REVERT: w 307 PHE cc_start: 0.9538 (OUTLIER) cc_final: 0.8933 (m-80) REVERT: x 1003 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: x 1006 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8460 (mtmt) REVERT: y 1106 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8785 (mmmm) REVERT: F 6 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8741 (mtmt) REVERT: 1 104 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7730 (mm-30) REVERT: 1 106 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8457 (mmmm) REVERT: 4 1006 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8677 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8433 (mmmm) REVERT: G 3 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: G 4 GLU cc_start: 0.8061 (mp0) cc_final: 0.7723 (mp0) REVERT: G 6 LYS cc_start: 0.9099 (mtmt) cc_final: 0.8702 (mtmt) REVERT: 8 104 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7398 (mm-30) REVERT: 8 106 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8293 (mmmm) REVERT: CA 1104 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7385 (mm-30) REVERT: EA 1306 LYS cc_start: 0.9110 (mttt) cc_final: 0.8770 (mttt) REVERT: H 4 GLU cc_start: 0.2919 (OUTLIER) cc_final: 0.2056 (pm20) REVERT: FA 106 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8652 (mmmm) REVERT: HA 302 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8706 (mmmm) REVERT: HA 304 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8183 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7893 (tm-30) REVERT: JA 1106 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8403 (mmmm) REVERT: I 4 GLU cc_start: 0.7776 (mp0) cc_final: 0.6894 (mp0) REVERT: MA 106 LYS cc_start: 0.3174 (OUTLIER) cc_final: 0.2655 (tptt) REVERT: PA 1004 GLU cc_start: 0.7532 (mp0) cc_final: 0.6360 (mp0) REVERT: PA 1006 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8714 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8856 (m-80) REVERT: RA 1202 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8806 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.8645 (m-80) REVERT: a 2 LYS cc_start: 0.9135 (tppt) cc_final: 0.8881 (tppt) REVERT: a 4 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8287 (tp30) REVERT: TA 106 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8703 (ptmm) REVERT: UA 202 LYS cc_start: 0.9382 (tttm) cc_final: 0.8960 (ttmm) REVERT: WA 1002 LYS cc_start: 0.9213 (tppt) cc_final: 0.8823 (tppt) REVERT: WA 1004 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: ZA 1303 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8777 (t80) REVERT: ZA 1304 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8548 (tm-30) REVERT: aA 104 GLU cc_start: 0.8690 (tm-30) cc_final: 0.7780 (tm-30) REVERT: bA 202 LYS cc_start: 0.9246 (tttm) cc_final: 0.8826 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8915 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8183 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9248 (t80) cc_final: 0.8945 (t80) REVERT: iA 202 LYS cc_start: 0.9380 (tttm) cc_final: 0.9072 (mmmm) REVERT: lA 1103 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.9104 (t80) REVERT: d 2 LYS cc_start: 0.9096 (tppt) cc_final: 0.8825 (tppt) REVERT: d 4 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: oA 102 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8925 (tptm) REVERT: pA 204 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7358 (tm-30) REVERT: qA 306 LYS cc_start: 0.9009 (tptp) cc_final: 0.8734 (tptp) REVERT: tA 1204 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8005 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8948 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.9164 (t80) REVERT: e 4 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: e 6 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8815 (ttpt) REVERT: vA 104 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8354 (tm-30) REVERT: wA 202 LYS cc_start: 0.9289 (tttm) cc_final: 0.8879 (ttmm) REVERT: wA 204 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7958 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7875 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8248 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.9049 (t80) REVERT: f 2 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8752 (ttmt) REVERT: f 4 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8348 (tp30) REVERT: 3A 202 LYS cc_start: 0.9234 (tttm) cc_final: 0.8904 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7606 (tm-30) REVERT: 4A 302 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8681 (tptp) REVERT: 4A 304 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8284 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.9121 (ptpt) cc_final: 0.8879 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7658 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8781 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8807 (tptp) cc_final: 0.8570 (tptp) REVERT: g 2 LYS cc_start: 0.9027 (tppt) cc_final: 0.8523 (tppt) REVERT: g 4 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8267 (tp30) REVERT: 9A 105 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.9120 (t80) REVERT: AB 202 LYS cc_start: 0.9354 (tttm) cc_final: 0.8982 (ttmm) REVERT: AB 204 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7779 (tm-30) REVERT: BB 305 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9141 (t80) REVERT: CB 1004 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: DB 1102 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.9011 (tptm) REVERT: EB 1204 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7279 (tm-30) REVERT: h 4 GLU cc_start: 0.8651 (tp30) cc_final: 0.8107 (pm20) REVERT: GB 103 PHE cc_start: 0.9444 (OUTLIER) cc_final: 0.9140 (t80) REVERT: HB 202 LYS cc_start: 0.9389 (tttm) cc_final: 0.8967 (pttt) REVERT: IB 306 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8729 (tptp) REVERT: JB 1004 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8090 (tp30) REVERT: i 4 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8341 (tp30) REVERT: NB 102 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9022 (pttt) REVERT: NB 104 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8113 (pm20) REVERT: NB 106 LYS cc_start: 0.9117 (tttp) cc_final: 0.8672 (pptt) REVERT: OB 202 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9007 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7851 (tp30) REVERT: QB 1005 PHE cc_start: 0.9276 (t80) cc_final: 0.8632 (t80) REVERT: QB 1006 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8895 (ttpt) REVERT: TB 1304 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8675 (tm-30) outliers start: 231 outliers final: 175 residues processed: 531 average time/residue: 0.4439 time to fit residues: 288.4384 Evaluate side-chains 647 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 427 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.7742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.338 12528 Z= 6.080 Angle : 4.117 31.360 16272 Z= 1.856 Chirality : 0.300 0.963 1152 Planarity : 0.017 0.063 2160 Dihedral : 20.473 83.363 1493 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 109.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.14 % Favored : 79.86 % Rotamer: Outliers : 26.85 % Allowed : 24.65 % Favored : 48.50 % Cbeta Deviations : 15.54 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.84 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.19), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 426 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7972 (mp0) cc_final: 0.6913 (mp0) REVERT: A 6 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8648 (mtmt) REVERT: J 104 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7712 (mm-30) REVERT: J 106 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8495 (tmmm) REVERT: L 303 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: M 1004 GLU cc_start: 0.8016 (mp0) cc_final: 0.7228 (mp0) REVERT: N 1104 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8124 (mm-30) REVERT: N 1106 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8341 (mmmm) REVERT: O 1206 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8660 (ttmm) REVERT: B 4 GLU cc_start: 0.8027 (mp0) cc_final: 0.7777 (mp0) REVERT: Q 104 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7232 (mm-30) REVERT: Q 106 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8660 (mmmm) REVERT: T 1004 GLU cc_start: 0.8228 (mp0) cc_final: 0.7491 (mp0) REVERT: T 1006 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8506 (mtmt) REVERT: U 1104 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7707 (mm-30) REVERT: U 1106 LYS cc_start: 0.8802 (tptm) cc_final: 0.8373 (tptm) REVERT: W 1302 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8955 (mtpt) REVERT: C 4 GLU cc_start: 0.8025 (mp0) cc_final: 0.7071 (mp0) REVERT: X 106 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8681 (mmmm) REVERT: Y 202 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8857 (ttpt) REVERT: j 1004 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: j 1006 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8582 (mtmt) REVERT: k 1106 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8597 (mmmm) REVERT: l 1202 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8730 (mtpp) REVERT: l 1204 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7989 (mm-30) REVERT: D 4 GLU cc_start: 0.7986 (mp0) cc_final: 0.7342 (mp0) REVERT: D 6 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8439 (mtmt) REVERT: D 7 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.8618 (t80) REVERT: n 106 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8363 (mmmm) REVERT: o 202 LYS cc_start: 0.9250 (ttpt) cc_final: 0.9025 (ttpt) REVERT: q 1004 GLU cc_start: 0.8307 (mp0) cc_final: 0.8090 (mp0) REVERT: r 1104 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: r 1106 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8407 (mmmm) REVERT: t 1302 LYS cc_start: 0.9235 (tttt) cc_final: 0.8973 (tttp) REVERT: E 6 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8665 (mtmt) REVERT: u 106 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8192 (mmmm) REVERT: v 206 LYS cc_start: 0.9286 (ttmm) cc_final: 0.8988 (ttmm) REVERT: w 302 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8747 (mmmm) REVERT: w 307 PHE cc_start: 0.9540 (OUTLIER) cc_final: 0.8942 (m-80) REVERT: x 1003 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8776 (m-80) REVERT: x 1006 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8461 (mtmt) REVERT: y 1106 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8783 (mmmm) REVERT: F 6 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8690 (mtmt) REVERT: 1 104 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7745 (mm-30) REVERT: 1 106 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8483 (mmmm) REVERT: 4 1006 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8675 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8377 (mmmm) REVERT: G 3 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: G 4 GLU cc_start: 0.8063 (mp0) cc_final: 0.7723 (mp0) REVERT: G 6 LYS cc_start: 0.9098 (mtmt) cc_final: 0.8722 (mtmt) REVERT: 8 104 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7396 (mm-30) REVERT: 8 106 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8292 (mmmm) REVERT: CA 1104 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7394 (mm-30) REVERT: EA 1306 LYS cc_start: 0.9080 (mttt) cc_final: 0.8872 (mttt) REVERT: H 4 GLU cc_start: 0.2910 (OUTLIER) cc_final: 0.2150 (pm20) REVERT: FA 106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8649 (mmmm) REVERT: HA 302 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8707 (mmmm) REVERT: HA 304 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8180 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7922 (tm-30) REVERT: JA 1106 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8412 (mmmm) REVERT: I 4 GLU cc_start: 0.7774 (mp0) cc_final: 0.6894 (mp0) REVERT: MA 106 LYS cc_start: 0.2969 (OUTLIER) cc_final: 0.2383 (tptt) REVERT: PA 1004 GLU cc_start: 0.7521 (mp0) cc_final: 0.6350 (mp0) REVERT: PA 1006 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8723 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9471 (OUTLIER) cc_final: 0.8880 (m-80) REVERT: RA 1202 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8800 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: a 2 LYS cc_start: 0.9126 (tppt) cc_final: 0.8885 (tppt) REVERT: a 4 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: TA 106 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8703 (ptmm) REVERT: UA 202 LYS cc_start: 0.9383 (tttm) cc_final: 0.8945 (ttmm) REVERT: WA 1002 LYS cc_start: 0.9216 (tppt) cc_final: 0.8826 (tppt) REVERT: WA 1004 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: ZA 1303 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8838 (t80) REVERT: ZA 1304 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8518 (tm-30) REVERT: aA 104 GLU cc_start: 0.8665 (tm-30) cc_final: 0.7781 (tm-30) REVERT: bA 202 LYS cc_start: 0.9248 (tttm) cc_final: 0.8826 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8914 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8188 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9250 (t80) cc_final: 0.8950 (t80) REVERT: iA 202 LYS cc_start: 0.9382 (tttm) cc_final: 0.9073 (mmmm) REVERT: lA 1103 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.9102 (t80) REVERT: d 2 LYS cc_start: 0.9097 (tppt) cc_final: 0.8815 (tppt) REVERT: d 4 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7997 (tp30) REVERT: oA 102 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8927 (tptm) REVERT: pA 204 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7366 (tm-30) REVERT: qA 306 LYS cc_start: 0.9008 (tptp) cc_final: 0.8718 (tptp) REVERT: tA 1204 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8007 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8948 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.9140 (t80) REVERT: e 4 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: e 6 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8813 (ttpt) REVERT: vA 104 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8354 (tm-30) REVERT: wA 202 LYS cc_start: 0.9289 (tttm) cc_final: 0.8882 (ttmm) REVERT: wA 204 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7957 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7877 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8253 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.9050 (t80) REVERT: f 2 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8753 (ttmt) REVERT: f 4 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8348 (tp30) REVERT: 3A 202 LYS cc_start: 0.9235 (tttm) cc_final: 0.8904 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7609 (tm-30) REVERT: 4A 302 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8698 (tptp) REVERT: 4A 304 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8285 (tm-30) REVERT: 5A 1002 LYS cc_start: 0.9120 (ptpt) cc_final: 0.8879 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7666 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8784 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8808 (tptp) cc_final: 0.8566 (tptp) REVERT: g 2 LYS cc_start: 0.9026 (tppt) cc_final: 0.8523 (tppt) REVERT: g 4 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: 9A 105 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.9119 (t80) REVERT: AB 202 LYS cc_start: 0.9354 (tttm) cc_final: 0.8982 (ttmm) REVERT: AB 204 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7767 (tm-30) REVERT: BB 305 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.9142 (t80) REVERT: CB 1004 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8381 (tp30) REVERT: DB 1102 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9014 (tptm) REVERT: EB 1204 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7391 (tm-30) REVERT: h 4 GLU cc_start: 0.8650 (tp30) cc_final: 0.8105 (pm20) REVERT: GB 103 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.9140 (t80) REVERT: HB 202 LYS cc_start: 0.9389 (tttm) cc_final: 0.8966 (pttt) REVERT: IB 306 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8688 (tptp) REVERT: JB 1004 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8089 (tp30) REVERT: i 4 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: NB 102 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9019 (pttt) REVERT: NB 104 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8113 (pm20) REVERT: NB 106 LYS cc_start: 0.9118 (tttp) cc_final: 0.8673 (pptt) REVERT: OB 202 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9009 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7780 (tp30) REVERT: QB 1005 PHE cc_start: 0.9273 (t80) cc_final: 0.8624 (t80) REVERT: QB 1006 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8903 (ttpt) REVERT: TB 1304 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8677 (tm-30) outliers start: 232 outliers final: 173 residues processed: 531 average time/residue: 0.4520 time to fit residues: 293.7443 Evaluate side-chains 645 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 426 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 303 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1205 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.072031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061620 restraints weight = 34368.769| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.16 r_work: 0.2685 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.7758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.339 12528 Z= 6.077 Angle : 4.105 30.676 16272 Z= 1.851 Chirality : 0.300 0.964 1152 Planarity : 0.017 0.063 2160 Dihedral : 20.521 83.414 1493 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 109.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.31 % Favored : 79.69 % Rotamer: Outliers : 26.74 % Allowed : 25.23 % Favored : 48.03 % Cbeta Deviations : 15.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.87 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.128 0.017 PHE 2 205 =============================================================================== Job complete usr+sys time: 3944.59 seconds wall clock time: 70 minutes 29.53 seconds (4229.53 seconds total)