Starting phenix.real_space_refine on Sun Mar 10 21:49:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/03_2024/7lqf_23484_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/03_2024/7lqf_23484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/03_2024/7lqf_23484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/03_2024/7lqf_23484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/03_2024/7lqf_23484_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/03_2024/7lqf_23484_updated.pdb" } resolution = 3.8 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 3840 2.51 5 N 704 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 104": "OE1" <-> "OE2" Residue "o PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 304": "OE1" <-> "OE2" Residue "b PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 104": "OE1" <-> "OE2" Residue "r PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 304": "OE1" <-> "OE2" Residue "c PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 304": "OE1" <-> "OE2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 104": "OE1" <-> "OE2" Residue "x PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 304": "OE1" <-> "OE2" Residue "e PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 104": "OE1" <-> "OE2" Residue "0 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 304": "OE1" <-> "OE2" Residue "f PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 104": "OE1" <-> "OE2" Residue "3 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 304": "OE1" <-> "OE2" Residue "g PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 104": "OE1" <-> "OE2" Residue "6 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 304": "OE1" <-> "OE2" Residue "h PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 104": "OE1" <-> "OE2" Residue "9 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA GLU 304": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5376 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.72, per 1000 atoms: 0.51 Number of scatterers: 5376 At special positions: 0 Unit cell: (70.2, 87.48, 101.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 832 8.00 N 704 7.00 C 3840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.78 Conformation dependent library (CDL) restraints added in 485.9 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 649 1.25 - 1.33: 411 1.33 - 1.40: 1820 1.40 - 1.47: 576 1.47 - 1.54: 2112 Bond restraints: 5568 Sorted by residual: bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.32e+01 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 105.49 - 109.76: 526 109.76 - 114.03: 1763 114.03 - 118.30: 915 118.30 - 122.57: 3299 122.57 - 126.84: 729 Bond angle restraints: 7232 Sorted by residual: angle pdb=" C 5CR q 301 " pdb=" CA 5CR q 301 " pdb=" CB 5CR q 301 " ideal model delta sigma weight residual 110.10 116.12 -6.02 1.90e+00 2.77e-01 1.00e+01 angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.41 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C 5CR t 301 " pdb=" CA 5CR t 301 " pdb=" CB 5CR t 301 " ideal model delta sigma weight residual 110.10 116.11 -6.01 1.90e+00 2.77e-01 1.00e+01 angle pdb=" C 5CR 5 301 " pdb=" CA 5CR 5 301 " pdb=" CB 5CR 5 301 " ideal model delta sigma weight residual 110.10 116.10 -6.00 1.90e+00 2.77e-01 9.99e+00 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.39 -9.48 3.00e+00 1.11e-01 9.99e+00 ... (remaining 7227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.80: 1977 10.80 - 21.61: 416 21.61 - 32.41: 159 32.41 - 43.21: 144 43.21 - 54.01: 56 Dihedral angle restraints: 2752 sinusoidal: 1280 harmonic: 1472 Sorted by residual: dihedral pdb=" CA LYS r 106 " pdb=" CB LYS r 106 " pdb=" CG LYS r 106 " pdb=" CD LYS r 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS 9 106 " pdb=" CB LYS 9 106 " pdb=" CG LYS 9 106 " pdb=" CD LYS 9 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS u 106 " pdb=" CB LYS u 106 " pdb=" CG LYS u 106 " pdb=" CD LYS u 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.00 54.00 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.017: 172 0.017 - 0.034: 140 0.034 - 0.051: 124 0.051 - 0.067: 60 0.067 - 0.084: 16 Chirality restraints: 512 Sorted by residual: chirality pdb=" CA PHE j 203 " pdb=" N PHE j 203 " pdb=" C PHE j 203 " pdb=" CB PHE j 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.76e-01 chirality pdb=" CA PHE Y 203 " pdb=" N PHE Y 203 " pdb=" C PHE Y 203 " pdb=" CB PHE Y 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.73e-01 chirality pdb=" CA PHE m 203 " pdb=" N PHE m 203 " pdb=" C PHE m 203 " pdb=" CB PHE m 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.71e-01 ... (remaining 509 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE p 203 " 0.009 2.00e-02 2.50e+03 6.10e-03 6.51e-01 pdb=" CG PHE p 203 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE p 203 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE p 203 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE p 203 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE p 203 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE p 203 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEBA 303 " 0.005 2.00e-02 2.50e+03 5.92e-03 6.14e-01 pdb=" CG PHEBA 303 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHEBA 303 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEBA 303 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEBA 303 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHEBA 303 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHEBA 303 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 4 203 " -0.009 2.00e-02 2.50e+03 5.91e-03 6.11e-01 pdb=" CG PHE 4 203 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE 4 203 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE 4 203 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE 4 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 4 203 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE 4 203 " -0.004 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1737 2.79 - 3.31: 4568 3.31 - 3.84: 8800 3.84 - 4.37: 11221 4.37 - 4.90: 19454 Nonbonded interactions: 45780 Sorted by model distance: nonbonded pdb=" O GMA I 108 " pdb=" N 5CR J 201 " model vdw 2.258 2.520 nonbonded pdb=" O GMA i 108 " pdb=" N 5CR j 201 " model vdw 2.258 2.520 nonbonded pdb=" O GMA X 108 " pdb=" N 5CR Y 201 " model vdw 2.258 2.520 nonbonded pdb=" O GMA l 108 " pdb=" N 5CR m 201 " model vdw 2.258 2.520 nonbonded pdb=" O GMA R 108 " pdb=" N 5CR S 201 " model vdw 2.258 2.520 ... (remaining 45775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.690 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 16.570 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.116 5568 Z= 0.776 Angle : 1.461 9.501 7232 Z= 0.602 Chirality : 0.035 0.084 512 Planarity : 0.002 0.007 960 Dihedral : 18.365 54.014 1728 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.77 (0.32), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.24), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9136 (tttt) cc_final: 0.8811 (tptm) REVERT: A 7 PHE cc_start: 0.8216 (m-10) cc_final: 0.7886 (m-10) REVERT: J 202 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7898 (ttmm) REVERT: K 306 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7586 (mmmm) REVERT: B 2 LYS cc_start: 0.9157 (tttt) cc_final: 0.8892 (tptm) REVERT: B 6 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7432 (mmmm) REVERT: L 102 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8600 (mmtt) REVERT: M 204 GLU cc_start: 0.8113 (pt0) cc_final: 0.7204 (pm20) REVERT: N 306 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7691 (mmmm) REVERT: Q 306 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7608 (mmmm) REVERT: D 2 LYS cc_start: 0.9124 (tttt) cc_final: 0.8722 (tptm) REVERT: D 3 PHE cc_start: 0.8401 (m-80) cc_final: 0.8172 (m-80) REVERT: D 6 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7546 (mmmm) REVERT: R 104 GLU cc_start: 0.7921 (tm-30) cc_final: 0.6923 (tm-30) REVERT: S 204 GLU cc_start: 0.8108 (pt0) cc_final: 0.7535 (pm20) REVERT: T 305 PHE cc_start: 0.8456 (m-80) cc_final: 0.8254 (m-10) REVERT: T 306 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7671 (mmmm) REVERT: E 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8717 (tptm) REVERT: U 104 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7072 (tm-30) REVERT: V 204 GLU cc_start: 0.8325 (pt0) cc_final: 0.7746 (pm20) REVERT: W 302 LYS cc_start: 0.8301 (tppp) cc_final: 0.7719 (tppp) REVERT: W 306 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7862 (mmmm) REVERT: F 2 LYS cc_start: 0.9090 (tttt) cc_final: 0.8422 (tmtt) REVERT: X 104 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7017 (tm-30) REVERT: X 106 LYS cc_start: 0.7894 (tppt) cc_final: 0.7561 (tppt) REVERT: Y 204 GLU cc_start: 0.8371 (pt0) cc_final: 0.7350 (pp20) REVERT: Z 306 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7335 (mmmm) REVERT: G 6 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7868 (ttmm) REVERT: i 102 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8357 (mmtt) REVERT: i 104 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7020 (tm-30) REVERT: i 106 LYS cc_start: 0.7678 (tppt) cc_final: 0.7407 (tppt) REVERT: j 204 GLU cc_start: 0.8071 (pt0) cc_final: 0.7744 (pm20) REVERT: k 304 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6755 (tm-30) REVERT: H 3 PHE cc_start: 0.8404 (m-80) cc_final: 0.8026 (m-80) REVERT: l 102 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8558 (mmtt) REVERT: m 204 GLU cc_start: 0.7905 (pt0) cc_final: 0.7370 (pm20) REVERT: m 205 PHE cc_start: 0.8286 (m-80) cc_final: 0.8052 (m-80) REVERT: n 306 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7577 (mmmm) REVERT: p 203 PHE cc_start: 0.7511 (t80) cc_final: 0.7309 (t80) REVERT: q 303 PHE cc_start: 0.8252 (t80) cc_final: 0.7808 (t80) REVERT: q 307 PHE cc_start: 0.7542 (t80) cc_final: 0.7293 (t80) REVERT: r 105 PHE cc_start: 0.9015 (p90) cc_final: 0.8791 (p90) REVERT: t 303 PHE cc_start: 0.8188 (t80) cc_final: 0.7770 (t80) REVERT: t 305 PHE cc_start: 0.7586 (t80) cc_final: 0.7183 (t80) REVERT: v 204 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7051 (tm-30) REVERT: w 302 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8490 (tmtt) REVERT: x 105 PHE cc_start: 0.8978 (p90) cc_final: 0.8358 (p90) REVERT: x 107 PHE cc_start: 0.8027 (t80) cc_final: 0.7191 (t80) REVERT: z 305 PHE cc_start: 0.7904 (t80) cc_final: 0.7476 (t80) REVERT: e 6 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8167 (ttmm) REVERT: e 7 PHE cc_start: 0.9053 (t80) cc_final: 0.8752 (t80) REVERT: 1 202 LYS cc_start: 0.8057 (tptp) cc_final: 0.7783 (tptp) REVERT: 2 305 PHE cc_start: 0.7995 (t80) cc_final: 0.7673 (t80) REVERT: f 7 PHE cc_start: 0.8908 (t80) cc_final: 0.8382 (t80) REVERT: 3 105 PHE cc_start: 0.8867 (p90) cc_final: 0.8660 (p90) REVERT: 3 106 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8356 (ttpp) REVERT: 4 204 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7088 (tm-30) REVERT: 5 303 PHE cc_start: 0.8146 (t80) cc_final: 0.7910 (t80) REVERT: g 2 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8492 (mmtt) REVERT: 6 106 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8435 (ttpp) REVERT: 7 204 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7069 (tm-30) REVERT: 8 302 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8593 (tmtt) REVERT: 8 307 PHE cc_start: 0.7753 (t80) cc_final: 0.7394 (t80) REVERT: 9 107 PHE cc_start: 0.7939 (t80) cc_final: 0.7557 (t80) outliers start: 8 outliers final: 0 residues processed: 164 average time/residue: 0.3601 time to fit residues: 67.0147 Evaluate side-chains 161 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain G residue 6 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.5980 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: 0.8358 moved from start: 0.9112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.478 5568 Z= 6.720 Angle : 6.059 58.626 7232 Z= 2.705 Chirality : 0.412 1.094 512 Planarity : 0.030 0.094 960 Dihedral : 24.743 81.773 652 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 201.05 Ramachandran Plot: Outliers : 10.16 % Allowed : 44.53 % Favored : 45.31 % Rotamer: Outliers : 14.84 % Allowed : 31.25 % Favored : 53.91 % Cbeta Deviations : 47.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -9.25 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.05 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.197 0.028 PHE 3 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 152 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 103 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: I 107 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8312 (m-10) REVERT: J 206 LYS cc_start: 0.9117 (tttm) cc_final: 0.7764 (ttpp) REVERT: K 302 LYS cc_start: 0.9008 (tppp) cc_final: 0.8743 (tppp) REVERT: K 306 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8224 (mmmm) REVERT: L 103 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: M 202 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8868 (ttmm) REVERT: M 206 LYS cc_start: 0.8635 (tttm) cc_final: 0.8055 (tttm) REVERT: N 302 LYS cc_start: 0.8796 (tppp) cc_final: 0.8519 (tppp) REVERT: N 304 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8027 (tm-30) REVERT: N 306 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8083 (mmmm) REVERT: N 307 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8458 (t80) REVERT: Q 302 LYS cc_start: 0.8820 (tppp) cc_final: 0.8181 (tppp) REVERT: Q 303 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: S 206 LYS cc_start: 0.8920 (tttm) cc_final: 0.7682 (ttpp) REVERT: T 304 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8171 (tm-30) REVERT: T 306 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8056 (mmmm) REVERT: E 6 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8402 (ttmm) REVERT: V 202 LYS cc_start: 0.9391 (ttmm) cc_final: 0.8765 (ttmm) REVERT: W 302 LYS cc_start: 0.8893 (tppp) cc_final: 0.8461 (tppp) REVERT: W 304 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7165 (tm-30) REVERT: Y 206 LYS cc_start: 0.8445 (tttm) cc_final: 0.8149 (tttm) REVERT: Z 304 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8187 (tm-30) REVERT: Z 306 LYS cc_start: 0.8547 (mmmm) cc_final: 0.8027 (mmmm) REVERT: Z 307 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: G 2 LYS cc_start: 0.9293 (tptt) cc_final: 0.8747 (tptm) REVERT: G 4 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7623 (mm-30) REVERT: G 6 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8433 (ttmm) REVERT: G 7 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: i 102 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8752 (mmmt) REVERT: i 106 LYS cc_start: 0.5094 (tppt) cc_final: 0.4263 (tptt) REVERT: j 206 LYS cc_start: 0.8832 (tttm) cc_final: 0.8202 (ttpp) REVERT: l 103 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: l 106 LYS cc_start: 0.8875 (tppt) cc_final: 0.8441 (tppt) REVERT: m 202 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8856 (ttmm) REVERT: m 206 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8363 (pttp) REVERT: n 302 LYS cc_start: 0.8954 (tppp) cc_final: 0.8696 (tppp) REVERT: n 306 LYS cc_start: 0.8769 (mmmm) cc_final: 0.8386 (mmmm) REVERT: n 307 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8541 (t80) REVERT: o 106 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8802 (ttmt) REVERT: p 203 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8121 (t80) REVERT: p 206 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8052 (tptp) REVERT: r 102 LYS cc_start: 0.9086 (tptp) cc_final: 0.8865 (tptp) REVERT: r 106 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8719 (ttmm) REVERT: s 202 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8776 (ttmm) REVERT: t 302 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8519 (tmtt) REVERT: t 306 LYS cc_start: 0.8769 (tmtt) cc_final: 0.7971 (tmtt) REVERT: c 2 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8598 (mmtt) REVERT: c 6 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8753 (ttmt) REVERT: u 106 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8200 (tmmt) REVERT: v 207 PHE cc_start: 0.8633 (t80) cc_final: 0.7962 (t80) REVERT: d 7 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8900 (t80) REVERT: 0 106 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8671 (ttpp) REVERT: 2 306 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8423 (tmtt) REVERT: 3 102 LYS cc_start: 0.9062 (tptp) cc_final: 0.8796 (tptp) REVERT: 3 103 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8271 (p90) REVERT: 3 107 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8442 (t80) REVERT: 5 307 PHE cc_start: 0.8920 (t80) cc_final: 0.8696 (t80) REVERT: g 2 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8473 (mmtt) REVERT: 7 202 LYS cc_start: 0.9162 (tptp) cc_final: 0.8827 (tptp) REVERT: 7 203 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8344 (t80) REVERT: 8 302 LYS cc_start: 0.9115 (tmtt) cc_final: 0.8580 (tmtt) REVERT: 8 307 PHE cc_start: 0.8622 (t80) cc_final: 0.8270 (t80) REVERT: BA 302 LYS cc_start: 0.9079 (tmtt) cc_final: 0.8538 (tmtt) REVERT: BA 307 PHE cc_start: 0.8865 (t80) cc_final: 0.8509 (t80) outliers start: 57 outliers final: 26 residues processed: 193 average time/residue: 0.3721 time to fit residues: 80.9484 Evaluate side-chains 197 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 147 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 106 LYS Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 206 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 2 residue 305 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 0.8338 moved from start: 0.9960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.155 0.483 5568 Z= 6.773 Angle : 6.160 59.459 7232 Z= 2.742 Chirality : 0.417 1.058 512 Planarity : 0.029 0.093 960 Dihedral : 24.925 89.475 648 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 199.03 Ramachandran Plot: Outliers : 3.52 % Allowed : 62.11 % Favored : 34.38 % Rotamer: Outliers : 23.18 % Allowed : 33.59 % Favored : 43.23 % Cbeta Deviations : 48.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.23 % 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: -9.72 (0.18), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.41 (0.14), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.178 0.026 PHE P 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 153 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9330 (tptt) cc_final: 0.9019 (tptt) REVERT: A 5 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: A 7 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8839 (m-10) REVERT: I 107 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8536 (m-10) REVERT: J 206 LYS cc_start: 0.8960 (tttm) cc_final: 0.8361 (ttpp) REVERT: K 302 LYS cc_start: 0.9007 (tppp) cc_final: 0.8719 (tppp) REVERT: K 306 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8281 (mmmm) REVERT: M 202 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8821 (ttmm) REVERT: M 206 LYS cc_start: 0.8655 (tttm) cc_final: 0.8401 (tttm) REVERT: N 302 LYS cc_start: 0.8979 (tppp) cc_final: 0.8745 (tppp) REVERT: N 304 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8119 (tm-30) REVERT: N 306 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8200 (mmmm) REVERT: N 307 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8357 (t80) REVERT: S 206 LYS cc_start: 0.8802 (tttm) cc_final: 0.7786 (ttpp) REVERT: T 304 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7422 (tm-30) REVERT: T 306 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8083 (mmtp) REVERT: U 106 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8259 (tppt) REVERT: V 202 LYS cc_start: 0.9399 (ttmm) cc_final: 0.9036 (ttmm) REVERT: X 103 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8648 (m-10) REVERT: Y 202 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8783 (ttmm) REVERT: Y 206 LYS cc_start: 0.8474 (tttm) cc_final: 0.8090 (tttm) REVERT: Z 302 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8374 (tppp) REVERT: Z 306 LYS cc_start: 0.8557 (mmmm) cc_final: 0.8028 (mmmm) REVERT: Z 307 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: G 2 LYS cc_start: 0.9290 (tptt) cc_final: 0.9083 (tptm) REVERT: G 5 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: G 6 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8423 (ttmm) REVERT: G 7 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: i 102 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8688 (mmmt) REVERT: i 103 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8820 (m-10) REVERT: H 6 LYS cc_start: 0.9325 (mmmm) cc_final: 0.9080 (mmmm) REVERT: l 102 LYS cc_start: 0.9416 (mmtt) cc_final: 0.9094 (mmtt) REVERT: l 103 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: l 106 LYS cc_start: 0.9047 (tppt) cc_final: 0.8661 (tppt) REVERT: m 202 LYS cc_start: 0.9223 (ttmm) cc_final: 0.8936 (ttmm) REVERT: n 302 LYS cc_start: 0.8929 (tppp) cc_final: 0.8654 (tppp) REVERT: n 304 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8054 (tm-30) REVERT: n 306 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8406 (mmmm) REVERT: a 2 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8331 (mmtt) REVERT: p 203 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8236 (t80) REVERT: q 306 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8728 (tttp) REVERT: q 307 PHE cc_start: 0.8865 (t80) cc_final: 0.8286 (t80) REVERT: r 106 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8686 (ttpp) REVERT: s 202 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8738 (ttmm) REVERT: c 6 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8769 (ttmt) REVERT: v 204 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8134 (tm-30) REVERT: d 7 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8983 (t80) REVERT: y 203 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8406 (t80) REVERT: z 302 LYS cc_start: 0.9171 (tmtt) cc_final: 0.8591 (tmtt) REVERT: 1 205 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8508 (t80) REVERT: 2 306 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8430 (tmtt) REVERT: 3 102 LYS cc_start: 0.9154 (tptp) cc_final: 0.8954 (tptp) REVERT: 3 103 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8504 (p90) REVERT: 3 107 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8495 (t80) REVERT: 5 306 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8241 (tttt) REVERT: 5 307 PHE cc_start: 0.8970 (t80) cc_final: 0.8442 (t80) REVERT: 7 203 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8388 (t80) REVERT: 8 307 PHE cc_start: 0.8601 (t80) cc_final: 0.8242 (t80) REVERT: 9 102 LYS cc_start: 0.9069 (tptp) cc_final: 0.8809 (tptp) REVERT: 9 104 GLU cc_start: 0.8807 (tm-30) cc_final: 0.7974 (tm-30) REVERT: BA 307 PHE cc_start: 0.8857 (t80) cc_final: 0.8419 (t80) outliers start: 89 outliers final: 47 residues processed: 209 average time/residue: 0.3692 time to fit residues: 87.3827 Evaluate side-chains 226 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 152 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 206 LYS Chi-restraints excluded: chain q residue 306 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 205 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 305 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 5 residue 306 LYS Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 1.0148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.155 0.488 5568 Z= 6.777 Angle : 6.178 59.687 7232 Z= 2.753 Chirality : 0.418 1.070 512 Planarity : 0.028 0.088 960 Dihedral : 25.126 86.399 648 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 198.49 Ramachandran Plot: Outliers : 4.30 % Allowed : 64.06 % Favored : 31.64 % Rotamer: Outliers : 27.34 % Allowed : 34.38 % Favored : 38.28 % Cbeta Deviations : 48.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.74 (0.19), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.42 (0.14), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.174 0.025 PHE P 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 154 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8111 (m-10) REVERT: A 7 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8839 (m-10) REVERT: I 107 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8523 (m-10) REVERT: J 206 LYS cc_start: 0.9035 (tttm) cc_final: 0.8440 (ttpp) REVERT: K 302 LYS cc_start: 0.9051 (tppp) cc_final: 0.8646 (tppp) REVERT: K 306 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8242 (mmmm) REVERT: L 103 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: M 202 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8830 (ttmm) REVERT: M 206 LYS cc_start: 0.8690 (tttm) cc_final: 0.8322 (tttm) REVERT: N 302 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8794 (tppp) REVERT: N 304 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8167 (tm-30) REVERT: N 306 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8185 (mmmm) REVERT: N 307 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8337 (t80) REVERT: Q 302 LYS cc_start: 0.8863 (tppp) cc_final: 0.8582 (mmmm) REVERT: Q 303 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: Q 306 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7834 (mmmm) REVERT: Q 307 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7849 (t80) REVERT: S 206 LYS cc_start: 0.8807 (tttm) cc_final: 0.8493 (ttpp) REVERT: T 304 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7379 (tm-30) REVERT: T 306 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8004 (mmtp) REVERT: U 106 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8391 (tppt) REVERT: V 202 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9028 (ttmm) REVERT: V 206 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7930 (ttpp) REVERT: W 302 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8572 (tppp) REVERT: X 103 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8694 (m-10) REVERT: Y 206 LYS cc_start: 0.8460 (tttm) cc_final: 0.8145 (tttm) REVERT: Z 302 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8450 (tppp) REVERT: Z 307 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: G 2 LYS cc_start: 0.9279 (tptt) cc_final: 0.8993 (tptm) REVERT: G 5 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: G 6 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8516 (ttmm) REVERT: G 7 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: i 102 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8643 (mmmt) REVERT: i 103 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8723 (m-10) REVERT: k 304 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7355 (tm-30) REVERT: H 6 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9069 (mmmm) REVERT: l 103 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: l 106 LYS cc_start: 0.9017 (tppt) cc_final: 0.8611 (tppt) REVERT: n 302 LYS cc_start: 0.8923 (tppp) cc_final: 0.8674 (tppp) REVERT: a 2 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8285 (mmtt) REVERT: o 107 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8108 (t80) REVERT: p 203 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8227 (t80) REVERT: q 306 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8748 (tttp) REVERT: q 307 PHE cc_start: 0.8853 (t80) cc_final: 0.8304 (t80) REVERT: r 104 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8742 (pp20) REVERT: r 106 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8725 (ttpp) REVERT: s 202 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8742 (ttmm) REVERT: s 207 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8271 (t80) REVERT: v 207 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8071 (t80) REVERT: x 103 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8737 (p90) REVERT: y 203 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8431 (t80) REVERT: z 302 LYS cc_start: 0.9170 (tmtt) cc_final: 0.8603 (tmtt) REVERT: 1 203 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8495 (t80) REVERT: 3 103 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8502 (p90) REVERT: 5 306 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8270 (tttt) REVERT: 5 307 PHE cc_start: 0.8966 (t80) cc_final: 0.8471 (t80) REVERT: g 2 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8448 (mmtt) REVERT: 8 307 PHE cc_start: 0.8629 (t80) cc_final: 0.8314 (t80) REVERT: 9 102 LYS cc_start: 0.8993 (tptp) cc_final: 0.8622 (tptp) REVERT: BA 307 PHE cc_start: 0.8908 (t80) cc_final: 0.8413 (t80) outliers start: 105 outliers final: 55 residues processed: 216 average time/residue: 0.3498 time to fit residues: 85.7460 Evaluate side-chains 243 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 154 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 202 LYS Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 305 PHE Chi-restraints excluded: chain q residue 306 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain x residue 102 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 305 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 5 residue 306 LYS Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 206 LYS Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 305 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 1.0281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.155 0.487 5568 Z= 6.782 Angle : 6.195 59.449 7232 Z= 2.753 Chirality : 0.420 1.093 512 Planarity : 0.028 0.092 960 Dihedral : 24.899 84.500 648 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 198.49 Ramachandran Plot: Outliers : 4.30 % Allowed : 65.62 % Favored : 30.08 % Rotamer: Outliers : 29.43 % Allowed : 36.46 % Favored : 34.11 % Cbeta Deviations : 48.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.64 (0.21), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.34 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.174 0.025 PHE P 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 153 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8085 (m-10) REVERT: A 7 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8844 (m-10) REVERT: I 107 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8534 (m-10) REVERT: J 206 LYS cc_start: 0.8994 (tttm) cc_final: 0.8425 (ttpp) REVERT: K 302 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8651 (tppp) REVERT: K 306 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8280 (mmmm) REVERT: M 202 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8808 (ttmm) REVERT: M 206 LYS cc_start: 0.8693 (tttm) cc_final: 0.8322 (tttm) REVERT: N 302 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8810 (tppp) REVERT: N 306 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8187 (mmmm) REVERT: N 307 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8343 (t80) REVERT: Q 302 LYS cc_start: 0.8852 (tppp) cc_final: 0.8598 (mmmm) REVERT: Q 303 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: Q 306 LYS cc_start: 0.8200 (mmmm) cc_final: 0.7795 (mmmm) REVERT: S 202 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8251 (ttpp) REVERT: S 206 LYS cc_start: 0.8709 (tttm) cc_final: 0.7846 (ttpp) REVERT: T 304 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7408 (tm-30) REVERT: T 306 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8020 (mmtp) REVERT: U 106 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8534 (tppt) REVERT: V 202 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9048 (ttmm) REVERT: V 206 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.7882 (ttpp) REVERT: W 302 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8599 (tppp) REVERT: Y 206 LYS cc_start: 0.8467 (tttm) cc_final: 0.8089 (tttm) REVERT: Z 302 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8254 (tppp) REVERT: Z 306 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8020 (mmmm) REVERT: Z 307 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: G 5 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: G 6 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8543 (ttmm) REVERT: G 7 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: i 102 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8623 (mmmt) REVERT: i 103 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8729 (m-10) REVERT: k 304 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7468 (tm-30) REVERT: H 6 LYS cc_start: 0.9343 (mmmm) cc_final: 0.9057 (mmmm) REVERT: l 102 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9138 (mmtm) REVERT: l 103 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: l 106 LYS cc_start: 0.9016 (tppt) cc_final: 0.8620 (tppt) REVERT: n 304 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7988 (tm-30) REVERT: n 306 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8465 (mmmm) REVERT: a 2 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8265 (mmtt) REVERT: o 107 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8254 (t80) REVERT: p 203 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8233 (t80) REVERT: q 306 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8725 (tttp) REVERT: q 307 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8384 (t80) REVERT: r 106 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8736 (ttpp) REVERT: s 203 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7703 (t80) REVERT: s 207 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8172 (t80) REVERT: c 3 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7837 (t80) REVERT: c 5 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8415 (t80) REVERT: v 207 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8072 (t80) REVERT: d 7 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8924 (t80) REVERT: x 103 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8672 (p90) REVERT: y 203 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8416 (t80) REVERT: z 302 LYS cc_start: 0.9161 (tmtt) cc_final: 0.8587 (tmtt) REVERT: 2 302 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8599 (tmtt) REVERT: 2 306 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8327 (tmtt) REVERT: 3 103 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8626 (p90) REVERT: 5 306 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8319 (tttt) REVERT: g 2 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8446 (mmtt) REVERT: 7 202 LYS cc_start: 0.9192 (tptp) cc_final: 0.8842 (tptp) REVERT: 7 203 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8439 (t80) REVERT: 8 307 PHE cc_start: 0.8711 (t80) cc_final: 0.8471 (t80) REVERT: 9 102 LYS cc_start: 0.8968 (tptp) cc_final: 0.8568 (tptp) REVERT: BA 307 PHE cc_start: 0.8906 (t80) cc_final: 0.8416 (t80) outliers start: 113 outliers final: 59 residues processed: 216 average time/residue: 0.3450 time to fit residues: 84.6574 Evaluate side-chains 252 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 154 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain n residue 306 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 202 LYS Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 305 PHE Chi-restraints excluded: chain q residue 306 LYS Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 203 PHE Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 202 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 102 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 302 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 305 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 102 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 5 residue 306 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 7 residue 206 LYS Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 305 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 1.0401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.155 0.488 5568 Z= 6.788 Angle : 6.200 59.671 7232 Z= 2.754 Chirality : 0.420 1.099 512 Planarity : 0.028 0.094 960 Dihedral : 24.873 82.992 648 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 198.76 Ramachandran Plot: Outliers : 3.91 % Allowed : 66.41 % Favored : 29.69 % Rotamer: Outliers : 30.47 % Allowed : 35.94 % Favored : 33.59 % Cbeta Deviations : 48.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.68 (0.20), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.37 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.174 0.025 PHE P 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 155 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8104 (m-10) REVERT: A 7 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8869 (m-10) REVERT: I 103 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8597 (m-80) REVERT: I 106 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8064 (tppt) REVERT: I 107 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8498 (m-10) REVERT: J 206 LYS cc_start: 0.9000 (tttm) cc_final: 0.8431 (ttpp) REVERT: K 302 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8673 (tppp) REVERT: K 306 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8318 (mmmm) REVERT: M 202 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8810 (ttmm) REVERT: M 206 LYS cc_start: 0.8714 (tttm) cc_final: 0.8324 (tttm) REVERT: N 302 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8810 (tppp) REVERT: N 306 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8186 (mmmm) REVERT: N 307 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8337 (t80) REVERT: O 102 LYS cc_start: 0.9301 (mmtm) cc_final: 0.9096 (mmtm) REVERT: Q 302 LYS cc_start: 0.8797 (tppp) cc_final: 0.8578 (mmmm) REVERT: Q 303 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: S 202 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8666 (ttpp) REVERT: S 206 LYS cc_start: 0.8725 (tttm) cc_final: 0.7866 (ttpp) REVERT: T 304 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7438 (tm-30) REVERT: T 306 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8001 (mmtp) REVERT: U 106 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8611 (tppt) REVERT: V 202 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.8376 (ttmm) REVERT: V 206 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8059 (ttpp) REVERT: W 302 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8167 (ttpp) REVERT: F 5 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: X 103 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8689 (m-10) REVERT: X 106 LYS cc_start: 0.8995 (tppt) cc_final: 0.8425 (tppt) REVERT: Y 206 LYS cc_start: 0.8403 (tttm) cc_final: 0.8040 (tttm) REVERT: Z 302 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8325 (tppp) REVERT: Z 306 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8007 (mmmm) REVERT: Z 307 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: G 5 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: G 6 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8610 (ttmm) REVERT: G 7 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: i 102 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8621 (mmmt) REVERT: i 103 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8732 (m-10) REVERT: k 304 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7508 (tm-30) REVERT: H 6 LYS cc_start: 0.9330 (mmmm) cc_final: 0.9029 (mmmm) REVERT: l 102 LYS cc_start: 0.9420 (mmtt) cc_final: 0.9194 (mmtm) REVERT: l 103 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: l 106 LYS cc_start: 0.8997 (tppt) cc_final: 0.8617 (tppt) REVERT: n 302 LYS cc_start: 0.8904 (tppp) cc_final: 0.8648 (tppp) REVERT: n 306 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8541 (mmmm) REVERT: a 2 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8254 (mmtt) REVERT: o 107 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8304 (t80) REVERT: p 203 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8219 (t80) REVERT: q 307 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8435 (t80) REVERT: r 106 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8695 (ttpp) REVERT: s 207 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8155 (t80) REVERT: c 3 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7915 (t80) REVERT: c 5 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8381 (t80) REVERT: v 207 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8007 (t80) REVERT: d 7 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8890 (t80) REVERT: y 203 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8407 (t80) REVERT: z 302 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8583 (tmtt) REVERT: 2 302 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8560 (tmtt) REVERT: 3 103 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8560 (p90) REVERT: 5 306 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8350 (tttt) REVERT: g 2 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8446 (mmtt) REVERT: 7 202 LYS cc_start: 0.9152 (tptp) cc_final: 0.8815 (tptp) REVERT: 7 203 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8243 (t80) REVERT: 9 102 LYS cc_start: 0.8920 (tptp) cc_final: 0.8521 (tptp) REVERT: BA 307 PHE cc_start: 0.8917 (t80) cc_final: 0.8450 (t80) outliers start: 117 outliers final: 61 residues processed: 220 average time/residue: 0.3426 time to fit residues: 85.7237 Evaluate side-chains 255 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 155 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain n residue 306 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 305 PHE Chi-restraints excluded: chain q residue 306 LYS Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 202 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 102 LYS Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 202 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 2 residue 302 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 305 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 5 residue 306 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 7 residue 206 LYS Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain 9 residue 103 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 305 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 1.0467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.155 0.484 5568 Z= 6.788 Angle : 6.219 59.601 7232 Z= 2.762 Chirality : 0.420 1.101 512 Planarity : 0.028 0.093 960 Dihedral : 24.892 83.617 648 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 198.78 Ramachandran Plot: Outliers : 3.91 % Allowed : 67.58 % Favored : 28.52 % Rotamer: Outliers : 31.25 % Allowed : 36.20 % Favored : 32.55 % Cbeta Deviations : 48.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.76 (0.19), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.44 (0.14), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.174 0.024 PHE P 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 156 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8096 (m-10) REVERT: A 7 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8869 (m-10) REVERT: I 103 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: I 106 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8093 (tppt) REVERT: I 107 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8513 (m-10) REVERT: J 206 LYS cc_start: 0.8997 (tttm) cc_final: 0.8418 (ttpp) REVERT: K 302 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8674 (tppp) REVERT: K 306 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8299 (mmmm) REVERT: M 202 LYS cc_start: 0.9200 (ttmm) cc_final: 0.8804 (ttmm) REVERT: M 206 LYS cc_start: 0.8732 (tttm) cc_final: 0.8245 (tttm) REVERT: N 302 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8808 (tppp) REVERT: N 306 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8211 (mmmm) REVERT: N 307 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8294 (t80) REVERT: O 102 LYS cc_start: 0.9334 (mmtm) cc_final: 0.9109 (mmtm) REVERT: Q 302 LYS cc_start: 0.8795 (tppp) cc_final: 0.8590 (mmmm) REVERT: Q 303 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: Q 306 LYS cc_start: 0.8269 (mmmm) cc_final: 0.7838 (mmmm) REVERT: S 202 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8631 (ttpp) REVERT: S 206 LYS cc_start: 0.8769 (tttm) cc_final: 0.7777 (ttpp) REVERT: T 304 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7390 (tm-30) REVERT: T 306 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7986 (mmtp) REVERT: U 106 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8677 (tppt) REVERT: V 202 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.8361 (ttmm) REVERT: V 206 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.7839 (ttpp) REVERT: W 302 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8203 (ttpp) REVERT: F 5 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: X 103 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8695 (m-10) REVERT: X 106 LYS cc_start: 0.8988 (tppt) cc_final: 0.8426 (tppt) REVERT: Y 206 LYS cc_start: 0.8385 (tttm) cc_final: 0.8055 (tttm) REVERT: Z 302 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8365 (tppp) REVERT: Z 306 LYS cc_start: 0.8501 (mmmm) cc_final: 0.7997 (mmmm) REVERT: Z 307 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: G 6 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8649 (ttmm) REVERT: G 7 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: i 102 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8620 (mmmt) REVERT: i 103 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8732 (m-10) REVERT: k 304 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7518 (tm-30) REVERT: H 6 LYS cc_start: 0.9333 (mmmm) cc_final: 0.8902 (mmmm) REVERT: l 102 LYS cc_start: 0.9413 (mmtt) cc_final: 0.9171 (mmtm) REVERT: l 103 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: l 106 LYS cc_start: 0.8992 (tppt) cc_final: 0.8589 (tppt) REVERT: m 206 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8271 (pttm) REVERT: n 302 LYS cc_start: 0.8973 (tppp) cc_final: 0.8708 (tppp) REVERT: a 2 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8442 (mtmm) REVERT: o 107 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8274 (t80) REVERT: p 203 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8216 (t80) REVERT: q 307 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8433 (t80) REVERT: b 3 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7521 (t80) REVERT: r 106 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8697 (ttpp) REVERT: s 203 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7657 (t80) REVERT: s 207 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8137 (t80) REVERT: c 3 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7857 (t80) REVERT: c 5 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (t80) REVERT: v 206 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8212 (tptp) REVERT: v 207 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7757 (t80) REVERT: d 7 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8887 (t80) REVERT: y 203 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8375 (t80) REVERT: z 302 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8582 (tmtt) REVERT: 2 302 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8568 (tmtt) REVERT: 2 306 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8190 (tmtt) REVERT: 3 103 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8601 (p90) REVERT: 5 306 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8337 (tttt) REVERT: 5 307 PHE cc_start: 0.9007 (t80) cc_final: 0.8792 (t80) REVERT: g 2 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8459 (mmtt) REVERT: 7 202 LYS cc_start: 0.9141 (tptp) cc_final: 0.8907 (tptp) REVERT: 7 203 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8424 (t80) REVERT: 8 307 PHE cc_start: 0.8818 (t80) cc_final: 0.8527 (t80) REVERT: 9 102 LYS cc_start: 0.8909 (tptp) cc_final: 0.8486 (tptp) REVERT: BA 307 PHE cc_start: 0.8949 (t80) cc_final: 0.8464 (t80) outliers start: 120 outliers final: 60 residues processed: 220 average time/residue: 0.3639 time to fit residues: 91.7041 Evaluate side-chains 259 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 157 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 305 PHE Chi-restraints excluded: chain q residue 306 LYS Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 203 PHE Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 202 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 102 LYS Chi-restraints excluded: chain y residue 202 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 302 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 305 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 102 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 5 residue 306 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 7 residue 206 LYS Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 103 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 305 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 1.0502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.155 0.487 5568 Z= 6.793 Angle : 6.222 59.672 7232 Z= 2.760 Chirality : 0.420 1.102 512 Planarity : 0.028 0.093 960 Dihedral : 24.993 85.593 648 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 199.88 Ramachandran Plot: Outliers : 3.91 % Allowed : 66.80 % Favored : 29.30 % Rotamer: Outliers : 30.47 % Allowed : 38.28 % Favored : 31.25 % Cbeta Deviations : 48.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.77 (0.19), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.45 (0.15), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.175 0.024 PHE P 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 156 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.8106 (m-10) REVERT: A 7 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8711 (m-10) REVERT: I 103 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: I 106 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8147 (tppt) REVERT: I 107 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8503 (m-10) REVERT: J 206 LYS cc_start: 0.9005 (tttm) cc_final: 0.8422 (ttpp) REVERT: K 302 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8683 (tppp) REVERT: K 306 LYS cc_start: 0.8721 (mmmm) cc_final: 0.8259 (mmmm) REVERT: L 106 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7751 (tppt) REVERT: M 202 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8774 (ttmm) REVERT: M 206 LYS cc_start: 0.8724 (tttm) cc_final: 0.8251 (tttm) REVERT: N 302 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8809 (tppp) REVERT: N 306 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8199 (mmmm) REVERT: N 307 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8357 (t80) REVERT: Q 303 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: Q 306 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7860 (mmmm) REVERT: S 202 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8671 (ttpp) REVERT: S 206 LYS cc_start: 0.8711 (tttm) cc_final: 0.7764 (ttpp) REVERT: T 304 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7343 (tm-30) REVERT: T 306 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7972 (mmtp) REVERT: U 106 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8673 (tppt) REVERT: V 202 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.8378 (ttmm) REVERT: V 206 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.7726 (ttpp) REVERT: W 302 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8195 (ttpp) REVERT: F 5 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: X 103 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8680 (m-10) REVERT: X 106 LYS cc_start: 0.8989 (tppt) cc_final: 0.8447 (tppt) REVERT: Y 206 LYS cc_start: 0.8398 (tttm) cc_final: 0.8061 (tttm) REVERT: Z 302 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8328 (tppp) REVERT: Z 306 LYS cc_start: 0.8496 (mmmm) cc_final: 0.7991 (mmmm) REVERT: Z 307 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: G 6 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8650 (ttmm) REVERT: G 7 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: i 102 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8620 (mmmt) REVERT: i 103 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8718 (m-10) REVERT: k 304 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7512 (tm-30) REVERT: H 6 LYS cc_start: 0.9337 (mmmm) cc_final: 0.9023 (mmmm) REVERT: l 102 LYS cc_start: 0.9411 (mmtm) cc_final: 0.9163 (mmtm) REVERT: l 103 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: l 106 LYS cc_start: 0.8991 (tppt) cc_final: 0.8604 (tppt) REVERT: m 206 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8274 (pttm) REVERT: n 302 LYS cc_start: 0.8911 (tppp) cc_final: 0.8693 (tppp) REVERT: a 2 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8499 (mtmm) REVERT: o 107 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8301 (t80) REVERT: p 203 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8242 (t80) REVERT: q 307 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8438 (t80) REVERT: b 3 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7565 (t80) REVERT: s 203 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7653 (t80) REVERT: s 207 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8128 (t80) REVERT: t 303 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7373 (t80) REVERT: c 3 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7854 (t80) REVERT: c 5 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8417 (t80) REVERT: v 207 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7930 (t80) REVERT: d 7 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8886 (t80) REVERT: x 104 GLU cc_start: 0.8706 (pp20) cc_final: 0.8412 (pp20) REVERT: y 203 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8376 (t80) REVERT: z 302 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8584 (tmtt) REVERT: 2 302 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8575 (tmtt) REVERT: 3 103 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8579 (p90) REVERT: 5 306 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8374 (tttt) REVERT: 5 307 PHE cc_start: 0.8960 (t80) cc_final: 0.8746 (t80) REVERT: g 2 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8460 (mmtt) REVERT: 8 307 PHE cc_start: 0.8815 (t80) cc_final: 0.8516 (t80) REVERT: 9 102 LYS cc_start: 0.8930 (tptp) cc_final: 0.8555 (tptp) REVERT: BA 307 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8427 (t80) outliers start: 117 outliers final: 60 residues processed: 220 average time/residue: 0.3483 time to fit residues: 87.0976 Evaluate side-chains 257 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 156 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 305 PHE Chi-restraints excluded: chain q residue 306 LYS Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 203 PHE Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 102 LYS Chi-restraints excluded: chain y residue 202 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain y residue 207 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 2 residue 302 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 305 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 102 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 5 residue 306 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 206 LYS Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain 9 residue 103 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 305 PHE Chi-restraints excluded: chain BA residue 306 LYS Chi-restraints excluded: chain BA residue 307 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: 0.8332 moved from start: 1.0540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.155 0.486 5568 Z= 6.791 Angle : 6.231 59.795 7232 Z= 2.763 Chirality : 0.420 1.103 512 Planarity : 0.028 0.093 960 Dihedral : 24.952 87.519 648 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 199.11 Ramachandran Plot: Outliers : 3.91 % Allowed : 66.80 % Favored : 29.30 % Rotamer: Outliers : 29.43 % Allowed : 39.06 % Favored : 31.51 % Cbeta Deviations : 48.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.78 (0.19), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.45 (0.15), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.175 0.024 PHE P 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 155 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.8106 (m-10) REVERT: A 7 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8872 (m-10) REVERT: I 103 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: I 106 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8079 (tppt) REVERT: I 107 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8510 (m-10) REVERT: J 206 LYS cc_start: 0.9006 (tttm) cc_final: 0.8428 (ttpp) REVERT: K 302 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8678 (tppp) REVERT: K 306 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8263 (mmmm) REVERT: M 202 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8770 (ttmm) REVERT: M 206 LYS cc_start: 0.8712 (tttm) cc_final: 0.8243 (tttm) REVERT: N 302 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8813 (tppp) REVERT: N 306 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8214 (mmmm) REVERT: N 307 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8291 (t80) REVERT: Q 303 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: S 202 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8641 (ttpp) REVERT: S 206 LYS cc_start: 0.8637 (tttm) cc_final: 0.7885 (ttpp) REVERT: T 304 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7348 (tm-30) REVERT: T 306 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7908 (mmtp) REVERT: T 307 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: U 106 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8657 (tppt) REVERT: V 202 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9135 (ttmm) REVERT: V 206 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8219 (ttpp) REVERT: W 302 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8622 (tppp) REVERT: W 307 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8080 (t80) REVERT: F 5 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: X 103 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8678 (m-10) REVERT: X 106 LYS cc_start: 0.8986 (tppt) cc_final: 0.8443 (tppt) REVERT: Y 206 LYS cc_start: 0.8392 (tttm) cc_final: 0.8064 (tttm) REVERT: Z 302 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8366 (tppp) REVERT: Z 306 LYS cc_start: 0.8497 (mmmm) cc_final: 0.7982 (mmmm) REVERT: Z 307 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: G 6 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8648 (ttmm) REVERT: G 7 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: i 102 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8624 (mmmt) REVERT: i 103 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8755 (m-10) REVERT: k 304 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7487 (tm-30) REVERT: H 6 LYS cc_start: 0.9337 (mmmm) cc_final: 0.9033 (mmmm) REVERT: l 102 LYS cc_start: 0.9407 (mmtm) cc_final: 0.9166 (mmtm) REVERT: l 103 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: l 106 LYS cc_start: 0.8976 (tppt) cc_final: 0.8595 (tppt) REVERT: m 206 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8302 (pttm) REVERT: n 302 LYS cc_start: 0.8923 (tppp) cc_final: 0.8717 (tppp) REVERT: a 2 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8488 (mtmm) REVERT: o 107 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8280 (t80) REVERT: p 203 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8257 (t80) REVERT: q 307 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8444 (t80) REVERT: b 3 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7505 (t80) REVERT: s 203 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7632 (t80) REVERT: s 207 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8163 (t80) REVERT: t 303 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7380 (t80) REVERT: c 3 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7847 (t80) REVERT: c 5 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8419 (t80) REVERT: v 206 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8178 (tptp) REVERT: v 207 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7741 (t80) REVERT: d 7 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8885 (t80) REVERT: x 104 GLU cc_start: 0.8690 (pp20) cc_final: 0.8362 (pp20) REVERT: y 203 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8383 (t80) REVERT: z 302 LYS cc_start: 0.9144 (tmtt) cc_final: 0.8584 (tmtt) REVERT: 2 302 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8568 (tmtt) REVERT: 3 103 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8620 (p90) REVERT: 5 306 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8421 (tttt) REVERT: g 2 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8451 (mmtt) REVERT: 7 202 LYS cc_start: 0.9223 (tptp) cc_final: 0.8807 (tptp) REVERT: 8 307 PHE cc_start: 0.8772 (t80) cc_final: 0.8491 (t80) REVERT: 9 102 LYS cc_start: 0.8914 (tptp) cc_final: 0.8538 (tptp) REVERT: BA 307 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8489 (t80) outliers start: 113 outliers final: 63 residues processed: 216 average time/residue: 0.3428 time to fit residues: 84.3053 Evaluate side-chains 262 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 156 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 307 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 202 LYS Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 305 PHE Chi-restraints excluded: chain q residue 306 LYS Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 203 PHE Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain t 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 c residue 5 PHE Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 102 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 202 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 302 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 305 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 102 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 5 residue 306 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 206 LYS Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain 9 residue 103 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 305 PHE Chi-restraints excluded: chain BA residue 306 LYS Chi-restraints excluded: chain BA residue 307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 1.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.155 0.487 5568 Z= 6.792 Angle : 6.244 59.913 7232 Z= 2.768 Chirality : 0.420 1.103 512 Planarity : 0.028 0.093 960 Dihedral : 24.990 89.950 648 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 200.74 Ramachandran Plot: Outliers : 3.91 % Allowed : 67.19 % Favored : 28.91 % Rotamer: Outliers : 27.86 % Allowed : 40.62 % Favored : 31.51 % Cbeta Deviations : 48.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.01 % 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: -9.78 (0.19), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.45 (0.15), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.175 0.025 PHE P 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 156 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8108 (m-10) REVERT: A 7 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8876 (m-10) REVERT: I 103 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: I 106 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8051 (tppt) REVERT: I 107 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8515 (m-10) REVERT: J 206 LYS cc_start: 0.9010 (tttm) cc_final: 0.8426 (ttpp) REVERT: K 302 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8681 (tppp) REVERT: K 306 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8280 (mmmm) REVERT: M 202 LYS cc_start: 0.9159 (ttmm) cc_final: 0.8769 (ttmm) REVERT: M 206 LYS cc_start: 0.8708 (tttm) cc_final: 0.8238 (tttm) REVERT: N 302 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8816 (tppp) REVERT: N 306 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8208 (mmmm) REVERT: N 307 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8299 (t80) REVERT: Q 303 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: S 202 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8681 (ttpp) REVERT: S 206 LYS cc_start: 0.8644 (tttm) cc_final: 0.7932 (ttpp) REVERT: T 304 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7341 (tm-30) REVERT: T 306 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7949 (mmtp) REVERT: T 307 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8487 (m-80) REVERT: U 106 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8642 (tppt) REVERT: V 202 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9098 (ttmm) REVERT: V 206 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8219 (ttpp) REVERT: W 302 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8616 (tppp) REVERT: F 5 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: X 103 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8696 (m-10) REVERT: X 106 LYS cc_start: 0.8985 (tppt) cc_final: 0.8449 (tppt) REVERT: Y 206 LYS cc_start: 0.8389 (tttm) cc_final: 0.8059 (tttm) REVERT: Z 302 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8362 (tppp) REVERT: Z 306 LYS cc_start: 0.8486 (mmmm) cc_final: 0.7978 (mmmm) REVERT: Z 307 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: G 6 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8643 (ttmm) REVERT: G 7 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: i 102 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8613 (mmmt) REVERT: i 103 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8676 (m-10) REVERT: k 304 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7516 (tm-30) REVERT: H 6 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9017 (mmmm) REVERT: l 102 LYS cc_start: 0.9407 (mmtm) cc_final: 0.9162 (mmtm) REVERT: l 103 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: l 106 LYS cc_start: 0.8986 (tppt) cc_final: 0.8602 (tppt) REVERT: m 206 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8262 (pttm) REVERT: n 302 LYS cc_start: 0.8915 (tppp) cc_final: 0.8714 (tppp) REVERT: a 2 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8495 (mtmm) REVERT: o 107 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8251 (t80) REVERT: p 203 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8255 (t80) REVERT: q 307 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8446 (t80) REVERT: b 3 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7604 (t80) REVERT: s 203 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7617 (t80) REVERT: s 207 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8125 (t80) REVERT: t 303 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7352 (t80) REVERT: c 3 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7849 (t80) REVERT: c 5 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8419 (t80) REVERT: v 207 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7949 (t80) REVERT: d 7 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8885 (t80) REVERT: x 104 GLU cc_start: 0.8700 (pp20) cc_final: 0.8351 (pp20) REVERT: y 203 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8384 (t80) REVERT: z 302 LYS cc_start: 0.9144 (tmtt) cc_final: 0.8582 (tmtt) REVERT: 2 302 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8572 (tmtt) REVERT: 3 103 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8611 (p90) REVERT: 5 306 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8261 (tttt) REVERT: 5 307 PHE cc_start: 0.8891 (t80) cc_final: 0.8039 (t80) REVERT: 7 202 LYS cc_start: 0.9245 (tptp) cc_final: 0.8830 (tptp) REVERT: 8 307 PHE cc_start: 0.8779 (t80) cc_final: 0.8524 (t80) REVERT: 9 102 LYS cc_start: 0.8912 (tptp) cc_final: 0.8536 (tptp) REVERT: BA 307 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8501 (t80) outliers start: 107 outliers final: 62 residues processed: 212 average time/residue: 0.3646 time to fit residues: 88.0008 Evaluate side-chains 258 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 155 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 305 PHE Chi-restraints excluded: chain q residue 306 LYS Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 203 PHE Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain t 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 c residue 5 PHE Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 102 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 202 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 302 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 305 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 102 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 5 residue 306 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 206 LYS Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain 9 residue 103 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 305 PHE Chi-restraints excluded: chain BA residue 306 LYS Chi-restraints excluded: chain BA residue 307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.054153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.046685 restraints weight = 19869.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.048549 restraints weight = 10842.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.049800 restraints weight = 6802.191| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 1.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.155 0.487 5568 Z= 6.799 Angle : 6.247 59.819 7232 Z= 2.768 Chirality : 0.421 1.101 512 Planarity : 0.028 0.093 960 Dihedral : 25.023 89.107 648 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 200.72 Ramachandran Plot: Outliers : 3.91 % Allowed : 67.19 % Favored : 28.91 % Rotamer: Outliers : 27.60 % Allowed : 41.15 % Favored : 31.25 % Cbeta Deviations : 49.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.01 % 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: -9.78 (0.19), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.45 (0.15), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.175 0.024 PHE P 205 =============================================================================== Job complete usr+sys time: 1340.47 seconds wall clock time: 25 minutes 33.48 seconds (1533.48 seconds total)