Starting phenix.real_space_refine on Mon Sep 23 23:00:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/09_2024/7lqe_23483.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/09_2024/7lqe_23483.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/7lqe_23483/09_2024/7lqe_23483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/09_2024/7lqe_23483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/09_2024/7lqe_23483.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/09_2024/7lqe_23483.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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4320 2.51 5 N 792 2.21 5 O 936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6048 Number of models: 1 Model: "" Number of chains: 72 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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 Time building chain proxies: 4.15, per 1000 atoms: 0.69 Number of scatterers: 6048 At special positions: 0 Unit cell: (87.48, 77.76, 106.92, 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 936 8.00 N 792 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 346.0 milliseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 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 'B' and resid 6 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA7, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'h' and resid 2 through 6 removed outlier: 3.535A pdb=" N PHEEA 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE h 5 " --> pdb=" O PHEEA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 8 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE f 5 " --> pdb=" O PHE 8 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 2 105 " --> pdb=" O PHE d 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE d 5 " --> pdb=" O PHE 2 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE w 105 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE b 5 " --> pdb=" O PHE w 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE t 105 " --> pdb=" O PHE a 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE a 5 " --> pdb=" O PHE t 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE z 105 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE c 5 " --> pdb=" O PHE z 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE 5 105 " --> pdb=" O PHE e 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE e 5 " --> pdb=" O PHE 5 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEBA 105 " --> pdb=" O PHE g 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE g 5 " --> pdb=" O PHEBA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEHA 105 " --> pdb=" O PHE i 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE i 5 " --> pdb=" O PHEHA 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'FA' and resid 202 through 206 removed outlier: 3.521A pdb=" N LYSGA 302 " --> pdb=" O GMA 9 208 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS 9 206 " --> pdb=" O GLUGA 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAGA 308 " --> pdb=" O LYS 9 202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYSAA 302 " --> pdb=" O GMA 3 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 3 206 " --> pdb=" O GLUAA 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS 4 302 " --> pdb=" O GMA x 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS x 206 " --> pdb=" O GLU 4 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS y 302 " --> pdb=" O GMA u 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS u 206 " --> pdb=" O GLU y 304 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GMA y 308 " --> pdb=" O LYS u 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS v 302 " --> pdb=" O GMA 0 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS 0 206 " --> pdb=" O GLU v 304 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GMA v 308 " --> pdb=" O LYS 0 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS 1 302 " --> pdb=" O GMA 6 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS 6 206 " --> pdb=" O GLU 1 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 7 302 " --> pdb=" O GMACA 208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSCA 206 " --> pdb=" O GLU 7 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMA 7 308 " --> pdb=" O LYSCA 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSDA 302 " --> pdb=" O GMAIA 208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSIA 206 " --> pdb=" O GLUDA 304 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.64 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: 773 1.26 - 1.33: 667 1.33 - 1.41: 1800 1.41 - 1.48: 651 1.48 - 1.56: 2373 Bond restraints: 6264 Sorted by residual: 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 3.47e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+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 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.44e+01 ... (remaining 6259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 7119 1.98 - 3.96: 795 3.96 - 5.95: 159 5.95 - 7.93: 54 7.93 - 9.91: 9 Bond angle restraints: 8136 Sorted by residual: angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.82 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " pdb=" CAA 5CR h 1 " ideal model delta sigma weight residual 114.91 124.78 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 ... (remaining 8131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 2422 15.26 - 30.52: 395 30.52 - 45.78: 171 45.78 - 61.04: 99 61.04 - 76.30: 9 Dihedral angle restraints: 3096 sinusoidal: 1440 harmonic: 1656 Sorted by residual: dihedral pdb=" CA LYS q 106 " pdb=" CB LYS q 106 " pdb=" CG LYS q 106 " pdb=" CD LYS q 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS Y 106 " pdb=" CB LYS Y 106 " pdb=" CG LYS Y 106 " pdb=" CD LYS Y 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS M 106 " pdb=" CB LYS M 106 " pdb=" CG LYS M 106 " pdb=" CD LYS M 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.32 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 191 0.017 - 0.035: 166 0.035 - 0.052: 150 0.052 - 0.070: 53 0.070 - 0.087: 16 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA LYS W 202 " pdb=" N LYS W 202 " pdb=" C LYS W 202 " pdb=" CB LYS W 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.91e-01 chirality pdb=" CA LYS Q 202 " pdb=" N LYS Q 202 " pdb=" C LYS Q 202 " pdb=" CB LYS Q 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.90e-01 chirality pdb=" CA LYS N 202 " pdb=" N LYS N 202 " pdb=" C LYS N 202 " pdb=" CB LYS N 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.87e-01 ... (remaining 573 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE u 205 " -0.009 2.00e-02 2.50e+03 6.94e-03 8.42e-01 pdb=" CG PHE u 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE u 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 205 " -0.009 2.00e-02 2.50e+03 6.93e-03 8.39e-01 pdb=" CG PHE 6 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 6 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE x 205 " -0.009 2.00e-02 2.50e+03 6.90e-03 8.33e-01 pdb=" CG PHE x 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE x 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE x 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE x 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2593 2.92 - 3.41: 5352 3.41 - 3.91: 9925 3.91 - 4.40: 12294 4.40 - 4.90: 20848 Nonbonded interactions: 51012 Sorted by model distance: nonbonded pdb=" N GLU D 4 " pdb=" OE1 GLU D 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU E 4 " pdb=" OE1 GLU E 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU B 4 " pdb=" OE1 GLU B 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU F 4 " pdb=" OE1 GLU F 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU A 4 " pdb=" OE1 GLU A 4 " model vdw 2.423 3.120 ... (remaining 51007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain '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 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.360 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.420 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 6264 Z= 0.833 Angle : 1.417 9.910 8136 Z= 0.592 Chirality : 0.035 0.087 576 Planarity : 0.002 0.009 1080 Dihedral : 20.718 76.296 1944 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 23.27 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 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE u 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 143 time to evaluate : 0.674 Fit side-chains REVERT: A 2 LYS cc_start: 0.8975 (tttt) cc_final: 0.8577 (tptt) REVERT: J 102 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8362 (mtpt) REVERT: K 202 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8709 (ttmt) REVERT: K 206 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8037 (ttmm) REVERT: L 304 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6841 (mm-30) REVERT: L 306 LYS cc_start: 0.8718 (tttt) cc_final: 0.8208 (mmmm) REVERT: B 2 LYS cc_start: 0.8950 (tttt) cc_final: 0.8747 (tttp) REVERT: M 102 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8316 (ttmm) REVERT: N 202 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8696 (ttmm) REVERT: N 204 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7046 (mt-10) REVERT: O 306 LYS cc_start: 0.8895 (tttt) cc_final: 0.8380 (mmmm) REVERT: C 2 LYS cc_start: 0.8858 (tttt) cc_final: 0.8520 (ttmm) REVERT: P 102 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (ttmt) REVERT: P 104 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6835 (mm-30) REVERT: Q 204 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7270 (mt-10) REVERT: R 304 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6963 (mm-30) REVERT: R 306 LYS cc_start: 0.8731 (tttt) cc_final: 0.8294 (mmmm) REVERT: D 2 LYS cc_start: 0.8945 (tttt) cc_final: 0.8716 (ttmm) REVERT: S 102 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8641 (ttmt) REVERT: U 304 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6582 (mm-30) REVERT: U 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8235 (mmmm) REVERT: E 4 GLU cc_start: 0.7580 (mp0) cc_final: 0.5848 (mp0) REVERT: V 102 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8592 (ttmt) REVERT: V 104 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6989 (mm-30) REVERT: W 202 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8626 (ttmm) REVERT: W 204 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7274 (mt-10) REVERT: W 206 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8144 (ttmm) REVERT: X 304 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7245 (mm-30) REVERT: X 306 LYS cc_start: 0.8889 (tttt) cc_final: 0.8236 (mmmm) REVERT: F 2 LYS cc_start: 0.8964 (tttt) cc_final: 0.8518 (tttm) REVERT: F 4 GLU cc_start: 0.7595 (mp0) cc_final: 0.7012 (mp0) REVERT: Y 102 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8225 (ttpt) REVERT: Z 202 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8683 (ttmm) REVERT: Z 206 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8130 (ttmm) REVERT: j 304 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7285 (mm-30) REVERT: j 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8240 (mmmm) REVERT: G 2 LYS cc_start: 0.8756 (tttt) cc_final: 0.8452 (tttm) REVERT: G 4 GLU cc_start: 0.7496 (mp0) cc_final: 0.6174 (mp0) REVERT: G 6 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7922 (mtmt) REVERT: k 102 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8561 (mtpt) REVERT: l 202 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8598 (ttmt) REVERT: l 206 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7935 (ttmm) REVERT: m 302 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8498 (mtmt) REVERT: m 304 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7248 (mm-30) REVERT: m 306 LYS cc_start: 0.8693 (tttt) cc_final: 0.8127 (mmmm) REVERT: H 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8810 (ttmt) REVERT: n 102 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8275 (mtpt) REVERT: p 306 LYS cc_start: 0.8809 (tttt) cc_final: 0.8244 (mmmm) REVERT: r 202 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8843 (ttmt) REVERT: s 302 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8303 (mmtt) REVERT: s 306 LYS cc_start: 0.8710 (tttt) cc_final: 0.8340 (tppt) REVERT: a 6 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: w 104 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: z 105 PHE cc_start: 0.8273 (t80) cc_final: 0.7515 (t80) REVERT: 2 105 PHE cc_start: 0.8345 (t80) cc_final: 0.7759 (t80) REVERT: 4 303 PHE cc_start: 0.8424 (t80) cc_final: 0.8200 (t80) REVERT: 4 307 PHE cc_start: 0.7856 (t80) cc_final: 0.7604 (t80) REVERT: HA 104 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: HA 105 PHE cc_start: 0.8203 (t80) cc_final: 0.7558 (t80) REVERT: JA 303 PHE cc_start: 0.8181 (t80) cc_final: 0.7871 (t80) REVERT: JA 307 PHE cc_start: 0.7572 (t80) cc_final: 0.7215 (t80) outliers start: 63 outliers final: 25 residues processed: 178 average time/residue: 0.3893 time to fit residues: 79.3912 Evaluate side-chains 175 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain S residue 102 LYS Chi-restraints excluded: chain S residue 106 LYS Chi-restraints excluded: chain V residue 102 LYS Chi-restraints excluded: chain V residue 106 LYS Chi-restraints excluded: chain Y residue 102 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain k residue 102 LYS Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain m residue 302 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 104 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU 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: 0.8530 moved from start: 0.7734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.148 0.428 6264 Z= 8.143 Angle : 4.897 39.945 8136 Z= 2.276 Chirality : 0.383 1.034 576 Planarity : 0.025 0.081 1080 Dihedral : 23.687 142.877 861 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 123.95 Ramachandran Plot: Outliers : 3.82 % Allowed : 18.06 % Favored : 78.12 % Rotamer: Outliers : 22.45 % Allowed : 16.67 % Favored : 60.88 % Cbeta Deviations : 38.72 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.97 % 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: -6.55 (0.30), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.99 (0.23), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.174 0.027 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 140 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8287 (mp0) cc_final: 0.7499 (mp0) REVERT: J 104 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7370 (mm-30) REVERT: K 206 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8773 (ttmm) REVERT: L 304 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8386 (mm-30) REVERT: L 306 LYS cc_start: 0.9122 (tttt) cc_final: 0.8869 (mmmm) REVERT: M 106 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8770 (mmmm) REVERT: N 204 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7979 (mt-10) REVERT: O 306 LYS cc_start: 0.9081 (tttt) cc_final: 0.8871 (tttt) REVERT: O 307 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8491 (t80) REVERT: C 2 LYS cc_start: 0.9200 (tttt) cc_final: 0.8964 (tptm) REVERT: C 4 GLU cc_start: 0.7946 (mp0) cc_final: 0.6678 (mp0) REVERT: P 102 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8991 (ttpt) REVERT: P 104 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8179 (mm-30) REVERT: P 106 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8548 (mmmm) REVERT: D 2 LYS cc_start: 0.9418 (tttt) cc_final: 0.9168 (ttmm) REVERT: D 4 GLU cc_start: 0.8621 (mp0) cc_final: 0.7656 (mp0) REVERT: S 106 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8509 (mmmm) REVERT: U 306 LYS cc_start: 0.8981 (tttt) cc_final: 0.8534 (ttmm) REVERT: E 4 GLU cc_start: 0.8401 (mp0) cc_final: 0.7748 (mp0) REVERT: E 6 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8588 (mmmt) REVERT: V 104 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8743 (mp0) REVERT: W 205 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8648 (m-10) REVERT: X 307 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8540 (t80) REVERT: F 2 LYS cc_start: 0.9376 (tttt) cc_final: 0.8911 (tttp) REVERT: Y 104 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8206 (mm-30) REVERT: k 104 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8243 (mm-30) REVERT: k 106 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8521 (mmmm) REVERT: m 306 LYS cc_start: 0.9183 (tttt) cc_final: 0.8648 (ttmm) REVERT: H 2 LYS cc_start: 0.9409 (tttt) cc_final: 0.9124 (tttp) REVERT: n 106 LYS cc_start: 0.8872 (tptm) cc_final: 0.8529 (tptm) REVERT: p 306 LYS cc_start: 0.9098 (mttt) cc_final: 0.8768 (mmmm) REVERT: q 104 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8229 (mm-30) REVERT: s 302 LYS cc_start: 0.9336 (tttt) cc_final: 0.8639 (tptt) REVERT: s 306 LYS cc_start: 0.9167 (tttt) cc_final: 0.8806 (tptt) REVERT: a 4 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: y 303 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7938 (t80) REVERT: d 2 LYS cc_start: 0.8910 (ptpt) cc_final: 0.8571 (ptpt) REVERT: 3 204 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7654 (tm-30) REVERT: 4 302 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8646 (tptp) REVERT: 7 302 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8409 (tptp) REVERT: f 2 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8669 (ttpt) REVERT: f 4 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: 8 102 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8703 (tptm) REVERT: 8 104 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7967 (tm-30) REVERT: BA 107 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8650 (t80) REVERT: DA 306 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8214 (tptp) REVERT: FA 206 LYS cc_start: 0.8975 (tttt) cc_final: 0.8420 (pptt) REVERT: GA 302 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8484 (tptp) REVERT: HA 104 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8181 (pp20) outliers start: 97 outliers final: 56 residues processed: 214 average time/residue: 0.4033 time to fit residues: 97.9332 Evaluate side-chains 210 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 139 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain V residue 106 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain r residue 206 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain t residue 106 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 102 LYS Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 8 residue 105 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain HA residue 105 PHE Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.8265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.430 6264 Z= 8.186 Angle : 4.924 34.255 8136 Z= 2.294 Chirality : 0.384 1.042 576 Planarity : 0.024 0.088 1080 Dihedral : 23.351 89.664 767 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 129.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % Rotamer: Outliers : 23.15 % Allowed : 27.08 % Favored : 49.77 % Cbeta Deviations : 41.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.75 % 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: -6.98 (0.31), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.31 (0.24), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.188 0.025 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 138 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8702 (mtmt) REVERT: J 107 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8186 (t80) REVERT: K 204 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8547 (mm-30) REVERT: L 304 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8206 (mm-30) REVERT: L 306 LYS cc_start: 0.9164 (tttt) cc_final: 0.8890 (mmmm) REVERT: M 106 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8821 (mmmm) REVERT: N 204 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8030 (tt0) REVERT: O 306 LYS cc_start: 0.9052 (tttt) cc_final: 0.8819 (tttt) REVERT: O 307 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8519 (t80) REVERT: C 2 LYS cc_start: 0.9112 (tttt) cc_final: 0.8805 (tttm) REVERT: P 102 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8961 (ttpt) REVERT: P 104 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8043 (mp0) REVERT: P 106 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8444 (mmmm) REVERT: S 104 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8082 (mm-30) REVERT: S 106 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8492 (mmmm) REVERT: U 304 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7587 (mm-30) REVERT: U 306 LYS cc_start: 0.8959 (tttt) cc_final: 0.8477 (ttmm) REVERT: E 6 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8638 (mtmt) REVERT: W 205 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8701 (m-10) REVERT: X 307 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8735 (t80) REVERT: F 2 LYS cc_start: 0.9388 (tttt) cc_final: 0.8837 (tttp) REVERT: F 6 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8593 (mmmt) REVERT: Y 102 LYS cc_start: 0.9461 (mtpt) cc_final: 0.9141 (mtmt) REVERT: Y 104 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8246 (mm-30) REVERT: Z 206 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8813 (ttmm) REVERT: j 306 LYS cc_start: 0.9137 (mttt) cc_final: 0.8670 (mmmm) REVERT: j 307 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.7969 (t80) REVERT: G 4 GLU cc_start: 0.8393 (mp0) cc_final: 0.8017 (mp0) REVERT: k 104 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8190 (mm-30) REVERT: k 106 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8601 (mmmm) REVERT: m 306 LYS cc_start: 0.9205 (tttt) cc_final: 0.8773 (mmmm) REVERT: H 2 LYS cc_start: 0.9387 (tttt) cc_final: 0.9104 (tttp) REVERT: n 106 LYS cc_start: 0.8843 (tptm) cc_final: 0.8506 (tptm) REVERT: n 107 PHE cc_start: 0.9529 (OUTLIER) cc_final: 0.9325 (m-80) REVERT: o 207 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8468 (t80) REVERT: p 306 LYS cc_start: 0.9186 (mttt) cc_final: 0.8780 (mmmm) REVERT: I 6 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8589 (mtmt) REVERT: q 107 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: s 302 LYS cc_start: 0.9250 (tttt) cc_final: 0.8558 (tptt) REVERT: s 306 LYS cc_start: 0.9222 (tttt) cc_final: 0.8846 (tptt) REVERT: y 302 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8517 (tptp) REVERT: y 303 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8133 (t80) REVERT: 3 204 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7754 (tm-30) REVERT: f 4 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: AA 306 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8430 (tptp) REVERT: BA 103 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8674 (t80) REVERT: BA 107 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8656 (t80) REVERT: DA 306 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8225 (ptmm) REVERT: h 4 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: GA 302 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8533 (tptp) outliers start: 100 outliers final: 59 residues processed: 212 average time/residue: 0.3755 time to fit residues: 90.9749 Evaluate side-chains 217 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 137 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 102 LYS Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 305 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: 0.8555 moved from start: 0.8486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.451 6264 Z= 8.211 Angle : 4.952 37.711 8136 Z= 2.304 Chirality : 0.381 0.966 576 Planarity : 0.024 0.087 1080 Dihedral : 23.276 89.499 755 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 129.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.94 % Favored : 68.06 % Rotamer: Outliers : 24.31 % Allowed : 29.63 % Favored : 46.06 % Cbeta Deviations : 40.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.36 % 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: -7.30 (0.30), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.56 (0.23), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.184 0.024 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 142 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8125 (mp0) cc_final: 0.7481 (mp0) REVERT: A 6 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8674 (mtmt) REVERT: J 104 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7114 (mm-30) REVERT: K 204 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8629 (mm-30) REVERT: L 304 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8159 (mm-30) REVERT: L 306 LYS cc_start: 0.9191 (tttt) cc_final: 0.8906 (mmmm) REVERT: B 4 GLU cc_start: 0.8263 (mp0) cc_final: 0.8053 (mp0) REVERT: M 106 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8859 (mmmm) REVERT: N 204 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8090 (tt0) REVERT: O 306 LYS cc_start: 0.9061 (tttt) cc_final: 0.8794 (tttt) REVERT: O 307 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8514 (t80) REVERT: C 2 LYS cc_start: 0.9137 (tttt) cc_final: 0.8908 (tttm) REVERT: C 4 GLU cc_start: 0.8026 (mp0) cc_final: 0.6544 (mp0) REVERT: C 6 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8773 (ttmt) REVERT: P 102 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8975 (ttpt) REVERT: P 104 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: P 106 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8443 (mmmm) REVERT: R 304 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7519 (mm-30) REVERT: S 104 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8007 (mm-30) REVERT: S 106 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8458 (mmmm) REVERT: U 304 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7858 (mm-30) REVERT: U 306 LYS cc_start: 0.8929 (tttt) cc_final: 0.8449 (ttmm) REVERT: V 106 LYS cc_start: 0.8991 (tptm) cc_final: 0.8765 (tptm) REVERT: W 205 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8745 (m-10) REVERT: X 307 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8621 (t80) REVERT: F 2 LYS cc_start: 0.9348 (tttt) cc_final: 0.8876 (tttp) REVERT: F 6 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8627 (mmmt) REVERT: Y 104 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8260 (mm-30) REVERT: Z 202 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9003 (tttt) REVERT: Z 203 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8661 (m-10) REVERT: j 306 LYS cc_start: 0.9143 (mttt) cc_final: 0.8874 (mmmm) REVERT: j 307 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8024 (t80) REVERT: k 106 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8591 (mmmm) REVERT: m 306 LYS cc_start: 0.9203 (mttt) cc_final: 0.8806 (mmmm) REVERT: H 2 LYS cc_start: 0.9401 (tttt) cc_final: 0.9115 (tttp) REVERT: n 106 LYS cc_start: 0.8841 (tptm) cc_final: 0.8501 (tptm) REVERT: o 207 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8326 (t80) REVERT: q 104 GLU cc_start: 0.8409 (tp30) cc_final: 0.8183 (tp30) REVERT: q 107 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: s 302 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8524 (tptt) REVERT: s 306 LYS cc_start: 0.9286 (tttt) cc_final: 0.8878 (tppt) REVERT: a 4 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: b 7 PHE cc_start: 0.9473 (OUTLIER) cc_final: 0.9263 (t80) REVERT: y 302 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8381 (tptp) REVERT: y 303 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8285 (t80) REVERT: 3 204 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7727 (tm-30) REVERT: f 4 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: BA 107 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8590 (t80) REVERT: DA 306 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8293 (tptp) REVERT: GA 302 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8572 (tptp) outliers start: 105 outliers final: 70 residues processed: 219 average time/residue: 0.3711 time to fit residues: 92.8632 Evaluate side-chains 235 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 142 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain W residue 206 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.8586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.424 6264 Z= 8.218 Angle : 4.956 36.520 8136 Z= 2.307 Chirality : 0.382 0.960 576 Planarity : 0.024 0.084 1080 Dihedral : 23.388 89.140 752 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 130.83 Ramachandran Plot: Outliers : 0.35 % Allowed : 33.33 % Favored : 66.32 % Rotamer: Outliers : 28.01 % Allowed : 28.24 % Favored : 43.75 % Cbeta Deviations : 41.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.96 % 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: -7.41 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.65 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.024 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 142 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8128 (mp0) cc_final: 0.7511 (mp0) REVERT: A 6 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8691 (mtmt) REVERT: J 107 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8365 (t80) REVERT: K 204 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8671 (mm-30) REVERT: L 306 LYS cc_start: 0.9193 (tttt) cc_final: 0.8914 (mmmm) REVERT: B 4 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 6 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8579 (mtmt) REVERT: M 106 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8834 (mmmm) REVERT: N 204 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8163 (tt0) REVERT: N 205 PHE cc_start: 0.9440 (OUTLIER) cc_final: 0.9161 (m-10) REVERT: O 306 LYS cc_start: 0.9034 (tttt) cc_final: 0.8790 (tttt) REVERT: O 307 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8512 (t80) REVERT: C 2 LYS cc_start: 0.9116 (tttt) cc_final: 0.8746 (tttm) REVERT: C 4 GLU cc_start: 0.8007 (mp0) cc_final: 0.7318 (mp0) REVERT: C 6 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8784 (ttmt) REVERT: P 102 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8938 (ttpt) REVERT: P 106 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8436 (mmmm) REVERT: S 104 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8046 (mm-30) REVERT: S 106 LYS cc_start: 0.9027 (mmmm) cc_final: 0.8392 (mmmm) REVERT: U 302 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9085 (mttt) REVERT: U 304 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7896 (mm-30) REVERT: W 205 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8839 (m-80) REVERT: X 307 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8619 (t80) REVERT: F 2 LYS cc_start: 0.9345 (tttt) cc_final: 0.8846 (tttp) REVERT: F 6 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8620 (mmmt) REVERT: Y 104 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8259 (mm-30) REVERT: Y 106 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8613 (tptm) REVERT: Z 202 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8847 (tttt) REVERT: Z 203 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: Z 204 GLU cc_start: 0.8550 (tt0) cc_final: 0.8337 (tt0) REVERT: j 306 LYS cc_start: 0.9144 (mttt) cc_final: 0.8852 (mmmm) REVERT: j 307 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8019 (t80) REVERT: k 106 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8573 (mmmm) REVERT: m 306 LYS cc_start: 0.9181 (mttt) cc_final: 0.8779 (mmmm) REVERT: H 2 LYS cc_start: 0.9400 (tttt) cc_final: 0.9120 (tttp) REVERT: n 106 LYS cc_start: 0.8849 (tptm) cc_final: 0.8486 (tptm) REVERT: o 207 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8366 (t80) REVERT: p 303 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: I 4 GLU cc_start: 0.8394 (mp0) cc_final: 0.7865 (mp0) REVERT: q 107 PHE cc_start: 0.9375 (OUTLIER) cc_final: 0.8705 (m-80) REVERT: s 302 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8519 (tptt) REVERT: s 306 LYS cc_start: 0.9262 (tttt) cc_final: 0.8842 (tppt) REVERT: a 4 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7803 (tp30) REVERT: t 103 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8734 (t80) REVERT: y 302 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8396 (tptp) REVERT: y 303 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8247 (t80) REVERT: d 2 LYS cc_start: 0.9040 (ptpt) cc_final: 0.8746 (ptpt) REVERT: 3 204 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7729 (tm-30) REVERT: 4 303 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8188 (t80) REVERT: f 4 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7973 (tp30) REVERT: BA 102 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8877 (mtpt) REVERT: BA 107 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8636 (t80) REVERT: DA 306 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8302 (tptp) REVERT: GA 302 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8559 (tptp) outliers start: 121 outliers final: 73 residues processed: 223 average time/residue: 0.3695 time to fit residues: 94.5538 Evaluate side-chains 247 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 142 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 302 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 102 LYS Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.8644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.425 6264 Z= 8.211 Angle : 4.976 36.455 8136 Z= 2.315 Chirality : 0.383 0.960 576 Planarity : 0.024 0.083 1080 Dihedral : 23.449 89.190 752 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 129.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.64 % Favored : 67.36 % Rotamer: Outliers : 28.24 % Allowed : 28.94 % Favored : 42.82 % Cbeta Deviations : 41.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.56 % 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: -7.41 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.64 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.024 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 139 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8075 (mp0) cc_final: 0.7555 (mp0) REVERT: A 6 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8735 (mtmt) REVERT: J 107 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8286 (t80) REVERT: L 306 LYS cc_start: 0.9196 (mttt) cc_final: 0.8914 (mmmm) REVERT: B 4 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: B 6 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8571 (mtmt) REVERT: M 106 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8820 (mmmm) REVERT: N 204 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8198 (tt0) REVERT: N 205 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.9161 (m-10) REVERT: O 303 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8588 (m-10) REVERT: O 306 LYS cc_start: 0.9044 (tttt) cc_final: 0.8746 (tttt) REVERT: O 307 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8516 (t80) REVERT: C 2 LYS cc_start: 0.9133 (tttt) cc_final: 0.8768 (tttm) REVERT: C 4 GLU cc_start: 0.7987 (mp0) cc_final: 0.7371 (mp0) REVERT: C 6 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8787 (ttmt) REVERT: P 102 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8937 (ttpt) REVERT: P 106 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8427 (mmmm) REVERT: S 104 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8056 (mm-30) REVERT: S 106 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8377 (mmmm) REVERT: U 304 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7932 (mm-30) REVERT: W 205 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8840 (m-80) REVERT: X 307 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8668 (t80) REVERT: F 2 LYS cc_start: 0.9320 (tttt) cc_final: 0.8908 (tttp) REVERT: F 6 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8633 (mmmt) REVERT: Y 104 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8265 (mm-30) REVERT: Y 106 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8607 (tptm) REVERT: Z 202 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9000 (tttt) REVERT: Z 203 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8672 (m-10) REVERT: j 306 LYS cc_start: 0.9115 (mttt) cc_final: 0.8807 (mmmm) REVERT: j 307 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8025 (t80) REVERT: k 104 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8017 (mm-30) REVERT: k 106 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8728 (mmmm) REVERT: m 306 LYS cc_start: 0.9193 (mttt) cc_final: 0.8796 (mmmm) REVERT: H 2 LYS cc_start: 0.9397 (tttt) cc_final: 0.9104 (tttp) REVERT: H 4 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6093 (pm20) REVERT: n 106 LYS cc_start: 0.8831 (tptm) cc_final: 0.8483 (tptm) REVERT: n 107 PHE cc_start: 0.9514 (OUTLIER) cc_final: 0.9283 (m-80) REVERT: o 207 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8357 (t80) REVERT: p 303 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: q 107 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8704 (m-80) REVERT: s 302 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8515 (tptt) REVERT: s 306 LYS cc_start: 0.9298 (tttt) cc_final: 0.8956 (tptt) REVERT: a 4 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7804 (tp30) REVERT: y 302 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8362 (tptp) REVERT: y 303 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8268 (t80) REVERT: d 2 LYS cc_start: 0.9035 (ptpt) cc_final: 0.8703 (ptpt) REVERT: 3 204 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7771 (tm-30) REVERT: f 4 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7962 (tp30) REVERT: BA 107 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8638 (t80) REVERT: DA 306 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8301 (tptp) REVERT: GA 302 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8560 (tptp) outliers start: 122 outliers final: 74 residues processed: 224 average time/residue: 0.3520 time to fit residues: 90.6526 Evaluate side-chains 243 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 139 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 304 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.8708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.421 6264 Z= 8.220 Angle : 4.975 36.468 8136 Z= 2.314 Chirality : 0.383 0.959 576 Planarity : 0.024 0.084 1080 Dihedral : 23.491 89.041 752 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 130.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 26.62 % Allowed : 31.02 % Favored : 42.36 % Cbeta Deviations : 42.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.96 % 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: -7.36 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.61 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.180 0.024 PHE t 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 140 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8724 (mtmt) REVERT: J 107 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8355 (t80) REVERT: L 306 LYS cc_start: 0.9189 (mttt) cc_final: 0.8905 (mmmm) REVERT: B 4 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: B 6 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8596 (mtmt) REVERT: M 106 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8819 (mmmm) REVERT: N 204 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8234 (tt0) REVERT: N 205 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9154 (m-10) REVERT: O 303 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8575 (m-10) REVERT: O 306 LYS cc_start: 0.9048 (tttt) cc_final: 0.8747 (tttt) REVERT: O 307 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8520 (t80) REVERT: C 2 LYS cc_start: 0.9124 (tttt) cc_final: 0.8761 (tttm) REVERT: C 4 GLU cc_start: 0.8000 (mp0) cc_final: 0.7321 (mp0) REVERT: C 6 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8773 (ttmt) REVERT: P 102 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8935 (ttpt) REVERT: P 106 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8415 (mmmm) REVERT: S 104 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8051 (mm-30) REVERT: S 106 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8389 (mmmm) REVERT: U 304 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7971 (mm-30) REVERT: W 205 PHE cc_start: 0.9336 (OUTLIER) cc_final: 0.8817 (m-80) REVERT: W 206 LYS cc_start: 0.9006 (ptmm) cc_final: 0.8716 (ptmm) REVERT: X 307 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8677 (t80) REVERT: F 2 LYS cc_start: 0.9330 (tttt) cc_final: 0.8965 (tttp) REVERT: F 6 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8633 (mmmt) REVERT: Y 104 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8264 (mm-30) REVERT: Y 106 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8599 (tptm) REVERT: Z 202 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9007 (tttt) REVERT: Z 203 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8681 (m-10) REVERT: Z 204 GLU cc_start: 0.8477 (tt0) cc_final: 0.7403 (tm-30) REVERT: j 306 LYS cc_start: 0.9104 (mttt) cc_final: 0.8794 (mmmm) REVERT: j 307 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8012 (t80) REVERT: k 104 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8035 (mm-30) REVERT: k 106 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8744 (mmmm) REVERT: m 306 LYS cc_start: 0.9180 (mttt) cc_final: 0.8867 (mmmm) REVERT: H 4 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6111 (pm20) REVERT: H 6 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8269 (pptt) REVERT: n 106 LYS cc_start: 0.8825 (tptm) cc_final: 0.8470 (tptm) REVERT: n 107 PHE cc_start: 0.9525 (OUTLIER) cc_final: 0.9320 (m-80) REVERT: o 207 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8345 (t80) REVERT: p 303 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: q 107 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8698 (m-80) REVERT: s 302 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8514 (tptt) REVERT: s 306 LYS cc_start: 0.9296 (tttt) cc_final: 0.8917 (tptt) REVERT: a 4 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7804 (tp30) REVERT: y 303 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8501 (t80) REVERT: 0 204 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8059 (tm-30) REVERT: d 2 LYS cc_start: 0.9032 (ptpt) cc_final: 0.8691 (ptpt) REVERT: 3 204 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7826 (tm-30) REVERT: 4 303 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.7893 (t80) REVERT: e 7 PHE cc_start: 0.9507 (OUTLIER) cc_final: 0.9218 (t80) REVERT: f 4 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: BA 107 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8636 (t80) REVERT: DA 306 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8301 (tptp) REVERT: GA 302 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8553 (tptp) outliers start: 115 outliers final: 75 residues processed: 220 average time/residue: 0.3646 time to fit residues: 91.8579 Evaluate side-chains 246 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 140 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 0 residue 206 LYS Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.8744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.420 6264 Z= 8.221 Angle : 4.995 36.459 8136 Z= 2.323 Chirality : 0.383 0.961 576 Planarity : 0.024 0.086 1080 Dihedral : 23.438 89.231 746 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 129.36 Ramachandran Plot: Outliers : 0.35 % Allowed : 31.94 % Favored : 67.71 % Rotamer: Outliers : 27.78 % Allowed : 30.32 % Favored : 41.90 % Cbeta Deviations : 41.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.56 % 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: -7.33 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.58 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.185 0.024 PHE t 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 139 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8702 (mtmt) REVERT: J 107 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8350 (t80) REVERT: L 304 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8080 (mp0) REVERT: L 306 LYS cc_start: 0.9180 (mttt) cc_final: 0.8906 (mmmm) REVERT: B 4 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: B 6 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8565 (mtmt) REVERT: M 106 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8807 (mmmm) REVERT: N 204 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8253 (tt0) REVERT: N 205 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9148 (m-10) REVERT: O 303 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8574 (m-10) REVERT: O 306 LYS cc_start: 0.9049 (tttt) cc_final: 0.8751 (tttt) REVERT: O 307 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8516 (t80) REVERT: C 2 LYS cc_start: 0.9121 (tttt) cc_final: 0.8765 (tttm) REVERT: C 4 GLU cc_start: 0.8006 (mp0) cc_final: 0.7331 (mp0) REVERT: C 6 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8778 (ttmt) REVERT: P 102 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8936 (ttpt) REVERT: P 106 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8413 (mmmm) REVERT: Q 207 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8176 (t80) REVERT: S 104 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8061 (mm-30) REVERT: S 106 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8383 (mmmm) REVERT: U 302 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9076 (mttt) REVERT: U 304 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7951 (mm-30) REVERT: W 205 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: W 206 LYS cc_start: 0.8993 (ptmm) cc_final: 0.8650 (ptmm) REVERT: X 307 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8662 (t80) REVERT: F 2 LYS cc_start: 0.9336 (tttt) cc_final: 0.8917 (tttp) REVERT: F 6 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8657 (mmmt) REVERT: Y 104 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8266 (mm-30) REVERT: Y 106 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8597 (tptm) REVERT: Z 202 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9010 (tttt) REVERT: Z 203 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8679 (m-10) REVERT: Z 204 GLU cc_start: 0.8485 (tt0) cc_final: 0.7385 (tm-30) REVERT: j 306 LYS cc_start: 0.9116 (mttt) cc_final: 0.8817 (mmmm) REVERT: j 307 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8107 (t80) REVERT: k 104 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8031 (mm-30) REVERT: k 106 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8730 (mmmm) REVERT: m 306 LYS cc_start: 0.9190 (mttt) cc_final: 0.8875 (mmmm) REVERT: H 4 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6111 (pm20) REVERT: H 7 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8672 (t80) REVERT: n 106 LYS cc_start: 0.8839 (tptm) cc_final: 0.8508 (tptm) REVERT: o 207 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8356 (t80) REVERT: p 303 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: I 6 LYS cc_start: 0.9225 (mtmt) cc_final: 0.8895 (mtmt) REVERT: q 107 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: s 302 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8514 (tptt) REVERT: s 306 LYS cc_start: 0.9295 (tttt) cc_final: 0.8931 (tptt) REVERT: a 4 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7793 (tp30) REVERT: y 303 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8530 (t80) REVERT: 0 204 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8066 (tm-30) REVERT: d 2 LYS cc_start: 0.9037 (ptpt) cc_final: 0.8695 (ptpt) REVERT: 3 204 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7836 (tm-30) REVERT: 4 303 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7855 (t80) REVERT: f 4 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: BA 107 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8635 (t80) REVERT: DA 306 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8301 (tptp) REVERT: GA 302 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8551 (tptp) outliers start: 120 outliers final: 78 residues processed: 224 average time/residue: 0.3634 time to fit residues: 93.3088 Evaluate side-chains 249 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 139 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 302 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain Z residue 206 LYS Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 0 residue 206 LYS Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 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: 0.8558 moved from start: 0.8771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.418 6264 Z= 8.223 Angle : 4.986 36.280 8136 Z= 2.317 Chirality : 0.383 0.962 576 Planarity : 0.024 0.083 1080 Dihedral : 23.424 89.134 746 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 131.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.60 % Favored : 68.40 % Rotamer: Outliers : 27.55 % Allowed : 31.25 % Favored : 41.20 % Cbeta Deviations : 41.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.56 % 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: -7.34 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.59 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.178 0.024 PHE t 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 139 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8715 (mtmt) REVERT: J 107 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8349 (t80) REVERT: L 306 LYS cc_start: 0.9183 (mttt) cc_final: 0.8909 (mmmm) REVERT: B 4 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: B 6 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8574 (mtmt) REVERT: M 106 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8809 (mmmm) REVERT: N 204 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8246 (tt0) REVERT: N 205 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9148 (m-10) REVERT: O 303 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8566 (m-10) REVERT: O 306 LYS cc_start: 0.9049 (tttt) cc_final: 0.8748 (tttt) REVERT: O 307 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8517 (t80) REVERT: C 2 LYS cc_start: 0.9126 (tttt) cc_final: 0.8751 (tttm) REVERT: C 4 GLU cc_start: 0.8014 (mp0) cc_final: 0.7354 (mp0) REVERT: C 6 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8775 (ttmt) REVERT: P 102 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8936 (ttpt) REVERT: P 106 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8427 (mmmm) REVERT: Q 207 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8160 (t80) REVERT: R 304 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7337 (mm-30) REVERT: S 104 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8053 (mm-30) REVERT: S 106 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8399 (mmmm) REVERT: U 302 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9073 (mttt) REVERT: U 304 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7940 (mm-30) REVERT: W 204 GLU cc_start: 0.8504 (tt0) cc_final: 0.8008 (tt0) REVERT: W 205 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8689 (m-10) REVERT: W 206 LYS cc_start: 0.8997 (ptmm) cc_final: 0.8728 (ptmm) REVERT: X 307 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8658 (t80) REVERT: F 2 LYS cc_start: 0.9337 (tttt) cc_final: 0.8944 (tttp) REVERT: F 6 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8651 (mmmt) REVERT: Y 104 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8269 (mm-30) REVERT: Y 106 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8598 (tptm) REVERT: Z 202 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9009 (tttt) REVERT: Z 203 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8696 (m-10) REVERT: Z 204 GLU cc_start: 0.8497 (tt0) cc_final: 0.7267 (tm-30) REVERT: j 306 LYS cc_start: 0.9118 (mttt) cc_final: 0.8814 (mmmm) REVERT: j 307 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8107 (t80) REVERT: k 106 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8735 (mmmm) REVERT: m 306 LYS cc_start: 0.9187 (mttt) cc_final: 0.8869 (mmmm) REVERT: H 4 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6102 (pm20) REVERT: H 7 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8714 (t80) REVERT: n 106 LYS cc_start: 0.8817 (tptm) cc_final: 0.8467 (tptm) REVERT: n 107 PHE cc_start: 0.9492 (OUTLIER) cc_final: 0.9166 (m-80) REVERT: o 207 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8351 (t80) REVERT: p 303 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: q 107 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8693 (m-80) REVERT: s 302 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8515 (tptt) REVERT: s 306 LYS cc_start: 0.9316 (tttt) cc_final: 0.8911 (tptt) REVERT: a 4 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: y 303 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8543 (t80) REVERT: 0 204 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8097 (tm-30) REVERT: d 2 LYS cc_start: 0.9048 (ptpt) cc_final: 0.8698 (ptpt) REVERT: 3 204 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7839 (tm-30) REVERT: 4 303 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.7854 (t80) REVERT: f 4 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: BA 107 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8632 (t80) REVERT: CA 206 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8850 (ptmt) REVERT: DA 306 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8302 (tptp) REVERT: GA 302 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8555 (tptp) outliers start: 119 outliers final: 81 residues processed: 220 average time/residue: 0.3567 time to fit residues: 89.9555 Evaluate side-chains 254 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 139 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 302 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain Z residue 206 LYS Chi-restraints excluded: chain j residue 304 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 0 residue 206 LYS Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain CA residue 206 LYS Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.8787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.419 6264 Z= 8.226 Angle : 4.993 36.297 8136 Z= 2.321 Chirality : 0.383 0.962 576 Planarity : 0.024 0.083 1080 Dihedral : 23.437 89.217 746 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 131.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 30.90 % Favored : 68.75 % Rotamer: Outliers : 26.62 % Allowed : 32.64 % Favored : 40.74 % Cbeta Deviations : 41.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.76 % 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: -7.35 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.59 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.178 0.024 PHE t 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 139 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8725 (mtmt) REVERT: J 107 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8349 (t80) REVERT: L 306 LYS cc_start: 0.9180 (mttt) cc_final: 0.8892 (mmmm) REVERT: B 4 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: B 6 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8568 (mtmt) REVERT: M 106 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8808 (mmmm) REVERT: N 204 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8263 (tt0) REVERT: N 205 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.9151 (m-10) REVERT: O 303 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8565 (m-10) REVERT: O 306 LYS cc_start: 0.9052 (tttt) cc_final: 0.8745 (tttt) REVERT: O 307 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8519 (t80) REVERT: C 2 LYS cc_start: 0.9137 (tttt) cc_final: 0.8760 (tttm) REVERT: C 4 GLU cc_start: 0.8016 (mp0) cc_final: 0.7357 (mp0) REVERT: C 6 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8777 (ttmt) REVERT: P 102 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8939 (ttpt) REVERT: P 106 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8424 (mmmm) REVERT: Q 207 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8146 (t80) REVERT: R 304 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7392 (mm-30) REVERT: S 104 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8060 (mm-30) REVERT: S 106 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8393 (mmmm) REVERT: U 302 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9072 (mttt) REVERT: U 304 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7933 (mm-30) REVERT: V 106 LYS cc_start: 0.8896 (tptm) cc_final: 0.8576 (tptm) REVERT: W 205 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8737 (m-10) REVERT: W 206 LYS cc_start: 0.8996 (ptmm) cc_final: 0.8715 (ptmm) REVERT: X 307 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8656 (t80) REVERT: F 2 LYS cc_start: 0.9330 (tttt) cc_final: 0.8963 (tttp) REVERT: F 6 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8683 (mmmt) REVERT: Y 104 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8271 (mm-30) REVERT: Y 106 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8601 (tptm) REVERT: Z 202 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8843 (tttt) REVERT: Z 203 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: Z 204 GLU cc_start: 0.8488 (tt0) cc_final: 0.7249 (tm-30) REVERT: j 306 LYS cc_start: 0.9124 (mttt) cc_final: 0.8800 (mmmm) REVERT: j 307 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8108 (t80) REVERT: k 106 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8725 (mmmm) REVERT: m 306 LYS cc_start: 0.9185 (mttt) cc_final: 0.8868 (mmmm) REVERT: H 4 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6125 (pm20) REVERT: H 7 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8708 (t80) REVERT: n 106 LYS cc_start: 0.8825 (tptm) cc_final: 0.8503 (tptm) REVERT: o 207 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8349 (t80) REVERT: p 303 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: I 6 LYS cc_start: 0.9231 (mtmt) cc_final: 0.8918 (mtmt) REVERT: q 107 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: s 302 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8516 (tptt) REVERT: s 306 LYS cc_start: 0.9312 (tttt) cc_final: 0.8927 (tptt) REVERT: a 4 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7793 (tp30) REVERT: y 303 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8550 (t80) REVERT: 0 204 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8101 (tm-30) REVERT: d 2 LYS cc_start: 0.9050 (ptpt) cc_final: 0.8700 (ptpt) REVERT: 3 204 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7830 (tm-30) REVERT: 4 303 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.7855 (t80) REVERT: f 4 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: BA 107 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8634 (t80) REVERT: DA 306 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8303 (tptp) REVERT: GA 302 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8554 (tptp) outliers start: 115 outliers final: 82 residues processed: 216 average time/residue: 0.3687 time to fit residues: 91.7105 Evaluate side-chains 253 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 139 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 302 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain Z residue 206 LYS Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 0 residue 206 LYS Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain CA residue 206 LYS Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.050409 restraints weight = 19454.239| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.21 r_work: 0.2549 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.8795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.419 6264 Z= 8.220 Angle : 4.993 36.220 8136 Z= 2.320 Chirality : 0.384 0.962 576 Planarity : 0.024 0.083 1080 Dihedral : 23.436 89.150 746 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 131.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 30.56 % Favored : 69.10 % Rotamer: Outliers : 26.16 % Allowed : 33.10 % Favored : 40.74 % Cbeta Deviations : 41.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.56 % 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: -7.33 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.58 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.178 0.024 PHE t 103 =============================================================================== Job complete usr+sys time: 1540.27 seconds wall clock time: 28 minutes 32.65 seconds (1712.65 seconds total)