Starting phenix.real_space_refine on Sun Mar 10 23:30:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/03_2024/7lqe_23483_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/03_2024/7lqe_23483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/03_2024/7lqe_23483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/03_2024/7lqe_23483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/03_2024/7lqe_23483_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/03_2024/7lqe_23483_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4320 2.51 5 N 792 2.21 5 O 936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 304": "OE1" <-> "OE2" Residue "L PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 204": "OE1" <-> "OE2" Residue "N PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 304": "OE1" <-> "OE2" Residue "O PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 204": "OE1" <-> "OE2" Residue "Q PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 304": "OE1" <-> "OE2" Residue "R PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 204": "OE1" <-> "OE2" Residue "T PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 304": "OE1" <-> "OE2" Residue "U PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 204": "OE1" <-> "OE2" Residue "W PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 304": "OE1" <-> "OE2" Residue "X PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 204": "OE1" <-> "OE2" Residue "Z PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 304": "OE1" <-> "OE2" Residue "j PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 204": "OE1" <-> "OE2" Residue "l PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 304": "OE1" <-> "OE2" Residue "m PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 204": "OE1" <-> "OE2" Residue "o PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 304": "OE1" <-> "OE2" Residue "p PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 204": "OE1" <-> "OE2" Residue "r PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 304": "OE1" <-> "OE2" Residue "s PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 204": "OE1" <-> "OE2" Residue "u PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 304": "OE1" <-> "OE2" Residue "b PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 204": "OE1" <-> "OE2" Residue "x PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 304": "OE1" <-> "OE2" Residue "c PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 204": "OE1" <-> "OE2" Residue "0 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 304": "OE1" <-> "OE2" Residue "d PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 204": "OE1" <-> "OE2" Residue "3 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 304": "OE1" <-> "OE2" Residue "e PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 204": "OE1" <-> "OE2" Residue "6 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 304": "OE1" <-> "OE2" Residue "f PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 204": "OE1" <-> "OE2" Residue "9 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA GLU 304": "OE1" <-> "OE2" Residue "g PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 204": "OE1" <-> "OE2" Residue "CA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 304": "OE1" <-> "OE2" Residue "h PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA GLU 204": "OE1" <-> "OE2" Residue "FA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA GLU 304": "OE1" <-> "OE2" Residue "i PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA GLU 204": "OE1" <-> "OE2" Residue "IA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA 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: 6048 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.75, per 1000 atoms: 0.45 Number of scatterers: 6048 At special positions: 0 Unit cell: (87.48, 77.76, 106.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 936 8.00 N 792 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.77 Conformation dependent library (CDL) restraints added in 450.6 milliseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... 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: 0.72 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: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 773 1.26 - 1.33: 667 1.33 - 1.41: 1800 1.41 - 1.48: 651 1.48 - 1.56: 2373 Bond restraints: 6264 Sorted by residual: bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.44e+01 ... (remaining 6259 not shown) Histogram of bond angle deviations from ideal: 105.43 - 109.76: 572 109.76 - 114.08: 2036 114.08 - 118.41: 1064 118.41 - 122.73: 3735 122.73 - 127.06: 729 Bond angle restraints: 8136 Sorted by residual: angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.82 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " pdb=" CAA 5CR h 1 " ideal model delta sigma weight residual 114.91 124.78 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 ... (remaining 8131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 2422 15.26 - 30.52: 395 30.52 - 45.78: 171 45.78 - 61.04: 99 61.04 - 76.30: 9 Dihedral angle restraints: 3096 sinusoidal: 1440 harmonic: 1656 Sorted by residual: dihedral pdb=" CA LYS q 106 " pdb=" CB LYS q 106 " pdb=" CG LYS q 106 " pdb=" CD LYS q 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS Y 106 " pdb=" CB LYS Y 106 " pdb=" CG LYS Y 106 " pdb=" CD LYS Y 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS M 106 " pdb=" CB LYS M 106 " pdb=" CG LYS M 106 " pdb=" CD LYS M 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.32 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 191 0.017 - 0.035: 166 0.035 - 0.052: 150 0.052 - 0.070: 53 0.070 - 0.087: 16 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA LYS W 202 " pdb=" N LYS W 202 " pdb=" C LYS W 202 " pdb=" CB LYS W 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.91e-01 chirality pdb=" CA LYS Q 202 " pdb=" N LYS Q 202 " pdb=" C LYS Q 202 " pdb=" CB LYS Q 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.90e-01 chirality pdb=" CA LYS N 202 " pdb=" N LYS N 202 " pdb=" C LYS N 202 " pdb=" CB LYS N 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.87e-01 ... (remaining 573 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE u 205 " -0.009 2.00e-02 2.50e+03 6.94e-03 8.42e-01 pdb=" CG PHE u 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE u 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 205 " -0.009 2.00e-02 2.50e+03 6.93e-03 8.39e-01 pdb=" CG PHE 6 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 6 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE x 205 " -0.009 2.00e-02 2.50e+03 6.90e-03 8.33e-01 pdb=" CG PHE x 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE x 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE x 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE x 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2594 2.92 - 3.41: 5484 3.41 - 3.91: 10054 3.91 - 4.40: 12584 4.40 - 4.90: 20852 Nonbonded interactions: 51568 Sorted by model distance: nonbonded pdb=" N GLU D 4 " pdb=" OE1 GLU D 4 " model vdw 2.423 2.520 nonbonded pdb=" N GLU E 4 " pdb=" OE1 GLU E 4 " model vdw 2.423 2.520 nonbonded pdb=" N GLU B 4 " pdb=" OE1 GLU B 4 " model vdw 2.423 2.520 nonbonded pdb=" N GLU F 4 " pdb=" OE1 GLU F 4 " model vdw 2.423 2.520 nonbonded pdb=" N GLU A 4 " pdb=" OE1 GLU A 4 " model vdw 2.423 2.520 ... (remaining 51563 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 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 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: 7.100 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 16.740 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.118 6264 Z= 0.782 Angle : 1.417 9.910 8136 Z= 0.592 Chirality : 0.035 0.087 576 Planarity : 0.002 0.009 1080 Dihedral : 20.718 76.296 1944 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE u 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 143 time to evaluate : 0.666 Fit side-chains REVERT: A 2 LYS cc_start: 0.8975 (tttt) cc_final: 0.8577 (tptt) REVERT: J 102 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8362 (mtpt) REVERT: K 202 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8709 (ttmt) REVERT: K 206 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8037 (ttmm) REVERT: L 304 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6841 (mm-30) REVERT: L 306 LYS cc_start: 0.8718 (tttt) cc_final: 0.8208 (mmmm) REVERT: B 2 LYS cc_start: 0.8950 (tttt) cc_final: 0.8747 (tttp) REVERT: M 102 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8316 (ttmm) REVERT: N 202 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8696 (ttmm) REVERT: N 204 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7046 (mt-10) REVERT: O 306 LYS cc_start: 0.8895 (tttt) cc_final: 0.8380 (mmmm) REVERT: C 2 LYS cc_start: 0.8858 (tttt) cc_final: 0.8520 (ttmm) REVERT: P 102 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (ttmt) REVERT: P 104 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6835 (mm-30) REVERT: Q 204 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7270 (mt-10) REVERT: R 304 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6963 (mm-30) REVERT: R 306 LYS cc_start: 0.8731 (tttt) cc_final: 0.8294 (mmmm) REVERT: D 2 LYS cc_start: 0.8945 (tttt) cc_final: 0.8716 (ttmm) REVERT: S 102 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8641 (ttmt) REVERT: U 304 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6582 (mm-30) REVERT: U 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8235 (mmmm) REVERT: E 4 GLU cc_start: 0.7580 (mp0) cc_final: 0.5848 (mp0) REVERT: V 102 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8592 (ttmt) REVERT: V 104 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6989 (mm-30) REVERT: W 202 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8626 (ttmm) REVERT: W 204 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7274 (mt-10) REVERT: W 206 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8144 (ttmm) REVERT: X 304 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7245 (mm-30) REVERT: X 306 LYS cc_start: 0.8889 (tttt) cc_final: 0.8236 (mmmm) REVERT: F 2 LYS cc_start: 0.8964 (tttt) cc_final: 0.8518 (tttm) REVERT: F 4 GLU cc_start: 0.7595 (mp0) cc_final: 0.7012 (mp0) REVERT: Y 102 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8225 (ttpt) REVERT: Z 202 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8683 (ttmm) REVERT: Z 206 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8130 (ttmm) REVERT: j 304 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7285 (mm-30) REVERT: j 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8240 (mmmm) REVERT: G 2 LYS cc_start: 0.8756 (tttt) cc_final: 0.8452 (tttm) REVERT: G 4 GLU cc_start: 0.7496 (mp0) cc_final: 0.6174 (mp0) REVERT: G 6 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7922 (mtmt) REVERT: k 102 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8561 (mtpt) REVERT: l 202 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8598 (ttmt) REVERT: l 206 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7935 (ttmm) REVERT: m 302 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8498 (mtmt) REVERT: m 304 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7248 (mm-30) REVERT: m 306 LYS cc_start: 0.8693 (tttt) cc_final: 0.8127 (mmmm) REVERT: H 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8810 (ttmt) REVERT: n 102 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8275 (mtpt) REVERT: p 306 LYS cc_start: 0.8809 (tttt) cc_final: 0.8244 (mmmm) REVERT: r 202 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8843 (ttmt) REVERT: s 302 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8303 (mmtt) REVERT: s 306 LYS cc_start: 0.8710 (tttt) cc_final: 0.8340 (tppt) REVERT: a 6 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: w 104 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: z 105 PHE cc_start: 0.8273 (t80) cc_final: 0.7515 (t80) REVERT: 2 105 PHE cc_start: 0.8345 (t80) cc_final: 0.7759 (t80) REVERT: 4 303 PHE cc_start: 0.8424 (t80) cc_final: 0.8200 (t80) REVERT: 4 307 PHE cc_start: 0.7856 (t80) cc_final: 0.7604 (t80) REVERT: HA 104 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: HA 105 PHE cc_start: 0.8203 (t80) cc_final: 0.7558 (t80) REVERT: JA 303 PHE cc_start: 0.8181 (t80) cc_final: 0.7871 (t80) REVERT: JA 307 PHE cc_start: 0.7572 (t80) cc_final: 0.7215 (t80) outliers start: 63 outliers final: 25 residues processed: 178 average time/residue: 0.3700 time to fit residues: 75.3769 Evaluate side-chains 175 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain S residue 102 LYS Chi-restraints excluded: chain S residue 106 LYS Chi-restraints excluded: chain V residue 102 LYS Chi-restraints excluded: chain V residue 106 LYS Chi-restraints excluded: chain Y residue 102 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain k residue 102 LYS Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain m residue 302 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 104 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.8109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.427 6264 Z= 6.521 Angle : 4.967 41.836 8136 Z= 2.304 Chirality : 0.384 0.991 576 Planarity : 0.023 0.081 1080 Dihedral : 24.124 115.753 861 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 125.46 Ramachandran Plot: Outliers : 7.99 % Allowed : 37.85 % Favored : 54.17 % Rotamer: Outliers : 17.13 % Allowed : 23.15 % Favored : 59.72 % Cbeta Deviations : 38.54 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.78 % 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: -8.42 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.42 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.175 0.026 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 150 time to evaluate : 0.642 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 4 GLU cc_start: 0.8388 (mp0) cc_final: 0.7564 (mp0) REVERT: J 104 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7863 (mm-30) REVERT: K 206 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8759 (ttmm) REVERT: L 304 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8412 (mm-30) REVERT: L 306 LYS cc_start: 0.9125 (tttt) cc_final: 0.8877 (mmmm) REVERT: B 2 LYS cc_start: 0.9275 (tttt) cc_final: 0.8790 (tttm) REVERT: M 104 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8077 (mm-30) REVERT: M 106 LYS cc_start: 0.9098 (mmmm) cc_final: 0.8740 (mmmm) REVERT: N 204 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7948 (mt-10) REVERT: O 306 LYS cc_start: 0.9067 (tttt) cc_final: 0.8862 (tttt) REVERT: O 307 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8479 (t80) REVERT: C 2 LYS cc_start: 0.9155 (tttt) cc_final: 0.8772 (ttmm) REVERT: P 102 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8919 (ttpt) REVERT: P 104 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8061 (mm-30) REVERT: P 106 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8555 (mmmm) REVERT: D 2 LYS cc_start: 0.9412 (tttt) cc_final: 0.9180 (ttmm) REVERT: D 4 GLU cc_start: 0.8731 (mp0) cc_final: 0.7445 (mp0) REVERT: S 106 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8580 (mmmm) REVERT: U 306 LYS cc_start: 0.8979 (tttt) cc_final: 0.8532 (ttmm) REVERT: E 4 GLU cc_start: 0.8347 (mp0) cc_final: 0.7531 (mp0) REVERT: V 104 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8762 (mp0) REVERT: W 205 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8726 (m-10) REVERT: X 307 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8488 (t80) REVERT: F 2 LYS cc_start: 0.9369 (tttt) cc_final: 0.8941 (tttp) REVERT: Y 104 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7988 (mm-30) REVERT: G 4 GLU cc_start: 0.8379 (mp0) cc_final: 0.8075 (mp0) REVERT: k 104 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8287 (mm-30) REVERT: k 106 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8495 (mmmm) REVERT: H 2 LYS cc_start: 0.9407 (tttt) cc_final: 0.9123 (tttp) REVERT: n 106 LYS cc_start: 0.8962 (tptm) cc_final: 0.8586 (tptm) REVERT: n 107 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9114 (m-80) REVERT: p 306 LYS cc_start: 0.9099 (mttt) cc_final: 0.8769 (mmmm) REVERT: I 6 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8609 (mtmt) REVERT: q 107 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8844 (m-80) REVERT: s 302 LYS cc_start: 0.9317 (tttt) cc_final: 0.8648 (tptt) REVERT: s 306 LYS cc_start: 0.9171 (tttt) cc_final: 0.8798 (tptt) REVERT: a 2 LYS cc_start: 0.8981 (ptpt) cc_final: 0.8623 (ptpt) REVERT: u 206 LYS cc_start: 0.9122 (tttt) cc_final: 0.8853 (tttt) REVERT: 9 202 LYS cc_start: 0.9076 (tttm) cc_final: 0.8727 (mtpp) REVERT: AA 305 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8064 (t80) REVERT: BA 103 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8780 (t80) REVERT: BA 107 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.9005 (t80) REVERT: CA 202 LYS cc_start: 0.8949 (tttm) cc_final: 0.8535 (ttmt) REVERT: CA 206 LYS cc_start: 0.9145 (tttt) cc_final: 0.8913 (tttt) REVERT: FA 206 LYS cc_start: 0.9102 (tttt) cc_final: 0.8615 (pptt) REVERT: GA 302 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8334 (tptp) REVERT: JA 305 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8295 (t80) outliers start: 74 outliers final: 45 residues processed: 199 average time/residue: 0.3803 time to fit residues: 86.0258 Evaluate side-chains 205 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 149 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain r residue 206 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain u residue 204 GLU Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain y residue 305 PHE Chi-restraints excluded: chain y residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain CA residue 204 GLU Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 302 LYS Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 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: 0.8568 moved from start: 0.8691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.150 0.425 6264 Z= 6.560 Angle : 4.989 36.911 8136 Z= 2.313 Chirality : 0.385 1.090 576 Planarity : 0.023 0.079 1080 Dihedral : 23.617 87.976 763 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 130.05 Ramachandran Plot: Outliers : 1.04 % Allowed : 56.25 % Favored : 42.71 % Rotamer: Outliers : 17.36 % Allowed : 34.95 % Favored : 47.69 % Cbeta Deviations : 41.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.38 % 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: -8.59 (0.26), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.54 (0.20), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.170 0.024 PHE 5 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 146 time to evaluate : 0.663 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 4 GLU cc_start: 0.8282 (mp0) cc_final: 0.7392 (mp0) REVERT: J 104 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7214 (mm-30) REVERT: J 107 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8375 (t80) REVERT: K 204 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8571 (mm-30) REVERT: K 206 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8895 (ttmm) REVERT: L 304 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8206 (mm-30) REVERT: L 306 LYS cc_start: 0.9172 (tttt) cc_final: 0.8902 (mmmm) REVERT: B 6 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8623 (mtmt) REVERT: M 106 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8751 (mmmm) REVERT: N 204 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8034 (tt0) REVERT: O 306 LYS cc_start: 0.9062 (tttt) cc_final: 0.8842 (tttt) REVERT: O 307 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8516 (t80) REVERT: C 2 LYS cc_start: 0.9136 (tttt) cc_final: 0.8908 (tttm) REVERT: C 4 GLU cc_start: 0.8248 (mp0) cc_final: 0.7223 (mp0) REVERT: P 102 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8995 (ttpt) REVERT: P 104 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8087 (mm-30) REVERT: P 106 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8543 (mmmm) REVERT: D 2 LYS cc_start: 0.9342 (tttt) cc_final: 0.9096 (ttmm) REVERT: D 4 GLU cc_start: 0.8810 (mp0) cc_final: 0.8093 (mp0) REVERT: S 104 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8129 (mm-30) REVERT: S 106 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8477 (mmmm) REVERT: U 304 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7624 (mm-30) REVERT: U 306 LYS cc_start: 0.8990 (tttt) cc_final: 0.8517 (ttmm) REVERT: E 6 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8601 (mtmt) REVERT: V 104 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8903 (mm-30) REVERT: V 106 LYS cc_start: 0.9105 (tptm) cc_final: 0.8820 (tptm) REVERT: W 205 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8685 (m-10) REVERT: X 307 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8616 (t80) REVERT: F 2 LYS cc_start: 0.9405 (tttt) cc_final: 0.9037 (tttp) REVERT: F 6 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8629 (mmmt) REVERT: Y 104 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8334 (mm-30) REVERT: Z 203 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: Z 206 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8848 (ttmm) REVERT: j 306 LYS cc_start: 0.9131 (mttt) cc_final: 0.8809 (mmmm) REVERT: j 307 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8073 (t80) REVERT: G 4 GLU cc_start: 0.8507 (mp0) cc_final: 0.8149 (mp0) REVERT: k 106 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8561 (mmmm) REVERT: k 107 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.7828 (t80) REVERT: m 306 LYS cc_start: 0.9197 (tttt) cc_final: 0.8767 (mmmm) REVERT: H 2 LYS cc_start: 0.9416 (tttt) cc_final: 0.9168 (tttp) REVERT: n 106 LYS cc_start: 0.8930 (tptm) cc_final: 0.8582 (tptm) REVERT: n 107 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9151 (m-80) REVERT: o 207 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8427 (t80) REVERT: p 306 LYS cc_start: 0.9187 (mttt) cc_final: 0.8783 (mmmm) REVERT: q 107 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8769 (m-80) REVERT: s 302 LYS cc_start: 0.9278 (tttt) cc_final: 0.8555 (tptt) REVERT: s 306 LYS cc_start: 0.9218 (tttt) cc_final: 0.8837 (tptt) REVERT: a 2 LYS cc_start: 0.8933 (ptpt) cc_final: 0.8605 (ptpt) REVERT: b 7 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.9134 (t80) REVERT: z 105 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8281 (t80) REVERT: d 2 LYS cc_start: 0.8957 (ptpt) cc_final: 0.8608 (ptpt) REVERT: f 4 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7966 (tp30) REVERT: 9 204 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7991 (tm-30) REVERT: CA 206 LYS cc_start: 0.9192 (tttt) cc_final: 0.8748 (tttp) REVERT: FA 206 LYS cc_start: 0.9101 (tttt) cc_final: 0.8627 (pptt) REVERT: GA 302 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8414 (tptp) outliers start: 75 outliers final: 39 residues processed: 201 average time/residue: 0.4088 time to fit residues: 94.5076 Evaluate side-chains 205 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 148 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain k residue 107 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain u residue 204 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain z residue 107 PHE Chi-restraints excluded: chain 0 residue 204 GLU Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 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: 0.8579 moved from start: 0.9003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.423 6264 Z= 6.586 Angle : 5.047 43.884 8136 Z= 2.325 Chirality : 0.386 1.077 576 Planarity : 0.023 0.083 1080 Dihedral : 23.325 88.093 755 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 128.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 59.03 % Favored : 40.62 % Rotamer: Outliers : 21.99 % Allowed : 36.81 % Favored : 41.20 % Cbeta Deviations : 41.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.38 % 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: -8.66 (0.27), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.59 (0.20), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.187 0.023 PHE 5 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 143 time to evaluate : 0.643 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: A 4 GLU cc_start: 0.8107 (mp0) cc_final: 0.7830 (mp0) REVERT: A 6 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8691 (mtmt) REVERT: J 106 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8720 (mmmm) REVERT: J 107 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8358 (t80) REVERT: K 204 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8614 (mm-30) REVERT: L 304 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8164 (mm-30) REVERT: L 306 LYS cc_start: 0.9173 (tttt) cc_final: 0.8911 (mmmm) REVERT: M 106 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8821 (mmmm) REVERT: N 204 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8100 (tt0) REVERT: N 205 PHE cc_start: 0.9444 (OUTLIER) cc_final: 0.9149 (m-10) REVERT: O 306 LYS cc_start: 0.9046 (tttt) cc_final: 0.8786 (tttt) REVERT: O 307 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8514 (t80) REVERT: C 2 LYS cc_start: 0.9127 (tttt) cc_final: 0.8881 (tttm) REVERT: C 4 GLU cc_start: 0.8177 (mp0) cc_final: 0.7419 (mp0) REVERT: P 102 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9005 (ttpt) REVERT: P 104 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7944 (mm-30) REVERT: P 106 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8539 (mmmm) REVERT: D 2 LYS cc_start: 0.9370 (tttt) cc_final: 0.9124 (ttmm) REVERT: D 4 GLU cc_start: 0.8838 (mp0) cc_final: 0.8214 (mp0) REVERT: S 106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8532 (mmmm) REVERT: U 304 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7838 (mm-30) REVERT: U 306 LYS cc_start: 0.8943 (tttt) cc_final: 0.8474 (ttmm) REVERT: V 106 LYS cc_start: 0.9128 (tptm) cc_final: 0.8881 (ttmm) REVERT: W 205 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8782 (m-80) REVERT: X 307 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8621 (t80) REVERT: F 6 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8641 (mmmt) REVERT: Y 104 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8383 (mm-30) REVERT: Z 202 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8864 (tttt) REVERT: Z 203 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8296 (m-80) REVERT: Z 204 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: j 306 LYS cc_start: 0.9139 (mttt) cc_final: 0.8875 (mmmm) REVERT: j 307 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8035 (t80) REVERT: G 4 GLU cc_start: 0.8533 (mp0) cc_final: 0.8295 (mp0) REVERT: k 107 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8117 (t80) REVERT: m 306 LYS cc_start: 0.9188 (mttt) cc_final: 0.8800 (mmmm) REVERT: n 106 LYS cc_start: 0.8908 (tptm) cc_final: 0.8587 (tptm) REVERT: n 107 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9150 (m-80) REVERT: o 207 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8336 (t80) REVERT: I 4 GLU cc_start: 0.8561 (mp0) cc_final: 0.7866 (mp0) REVERT: q 107 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8737 (m-80) REVERT: s 302 LYS cc_start: 0.9289 (tttt) cc_final: 0.8532 (tptt) REVERT: s 306 LYS cc_start: 0.9277 (tttt) cc_final: 0.8876 (tppt) REVERT: a 2 LYS cc_start: 0.8930 (ptpt) cc_final: 0.8595 (ptpt) REVERT: a 7 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8603 (t80) REVERT: w 103 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8972 (t80) REVERT: z 105 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8342 (t80) REVERT: 1 305 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8457 (t80) REVERT: 7 302 LYS cc_start: 0.9020 (tptp) cc_final: 0.8750 (tptp) REVERT: f 4 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: 8 104 GLU cc_start: 0.8527 (tm-30) cc_final: 0.7907 (tm-30) REVERT: g 7 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8725 (t80) REVERT: BA 102 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8655 (mmmm) REVERT: BA 107 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8917 (t80) REVERT: FA 206 LYS cc_start: 0.9104 (tttt) cc_final: 0.8623 (pptt) REVERT: GA 302 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8407 (tptp) outliers start: 95 outliers final: 54 residues processed: 208 average time/residue: 0.3674 time to fit residues: 87.3120 Evaluate side-chains 224 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 143 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain W residue 206 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain k residue 107 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 7 PHE Chi-restraints excluded: chain u residue 204 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain y residue 307 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain z residue 107 PHE Chi-restraints excluded: chain 0 residue 204 GLU Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 2 residue 107 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain BA residue 102 LYS Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain CA residue 204 GLU Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU 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: 0.8582 moved from start: 0.9149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.429 6264 Z= 6.601 Angle : 5.023 40.306 8136 Z= 2.318 Chirality : 0.388 1.089 576 Planarity : 0.023 0.082 1080 Dihedral : 23.180 87.523 751 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 131.21 Ramachandran Plot: Outliers : 1.04 % Allowed : 60.42 % Favored : 38.54 % Rotamer: Outliers : 21.76 % Allowed : 40.28 % Favored : 37.96 % Cbeta Deviations : 42.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -8.76 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.68 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.178 0.023 PHE 5 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 143 time to evaluate : 0.618 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: A 4 GLU cc_start: 0.8116 (mp0) cc_final: 0.7740 (mp0) REVERT: A 6 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8726 (mtmt) REVERT: J 106 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8669 (mmmm) REVERT: J 107 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8441 (t80) REVERT: L 306 LYS cc_start: 0.9193 (mttt) cc_final: 0.8918 (mmmm) REVERT: M 106 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8808 (mmmm) REVERT: N 204 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8161 (tt0) REVERT: N 205 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.9114 (m-80) REVERT: O 306 LYS cc_start: 0.9032 (tttt) cc_final: 0.8787 (tttt) REVERT: O 307 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8521 (t80) REVERT: C 2 LYS cc_start: 0.9130 (tttt) cc_final: 0.8748 (tttm) REVERT: C 4 GLU cc_start: 0.8216 (mp0) cc_final: 0.7496 (mp0) REVERT: P 102 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8949 (ttpt) REVERT: P 106 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8469 (mmmm) REVERT: D 2 LYS cc_start: 0.9401 (tttt) cc_final: 0.9145 (ttmm) REVERT: D 4 GLU cc_start: 0.8830 (mp0) cc_final: 0.8299 (mp0) REVERT: S 106 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8588 (mmmm) REVERT: U 302 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9096 (mttt) REVERT: U 304 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7940 (mm-30) REVERT: U 306 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8460 (ttmm) REVERT: V 106 LYS cc_start: 0.9156 (tptm) cc_final: 0.8901 (ttmm) REVERT: W 205 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8854 (m-80) REVERT: X 307 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8610 (t80) REVERT: F 2 LYS cc_start: 0.9393 (tttt) cc_final: 0.9087 (tttp) REVERT: F 6 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8663 (mmmt) REVERT: Y 104 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8405 (mm-30) REVERT: Z 202 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8863 (tttt) REVERT: Z 203 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: j 306 LYS cc_start: 0.9140 (mttt) cc_final: 0.8863 (mmmm) REVERT: j 307 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8051 (t80) REVERT: k 106 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8540 (mmmm) REVERT: k 107 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.7912 (t80) REVERT: m 306 LYS cc_start: 0.9198 (mttt) cc_final: 0.8793 (mmmm) REVERT: H 2 LYS cc_start: 0.9421 (tttt) cc_final: 0.9172 (tttp) REVERT: n 106 LYS cc_start: 0.8916 (tptm) cc_final: 0.8595 (tptm) REVERT: n 107 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9133 (m-80) REVERT: o 207 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8388 (t80) REVERT: p 303 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: I 4 GLU cc_start: 0.8492 (mp0) cc_final: 0.7593 (mp0) REVERT: q 104 GLU cc_start: 0.8665 (tp30) cc_final: 0.8373 (tp30) REVERT: s 302 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8530 (tptt) REVERT: s 306 LYS cc_start: 0.9286 (tttt) cc_final: 0.8912 (tptt) REVERT: a 2 LYS cc_start: 0.8932 (ptpt) cc_final: 0.8604 (ptpt) REVERT: a 7 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8637 (t80) REVERT: v 307 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8104 (p90) REVERT: b 7 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9101 (t80) REVERT: z 105 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8327 (t80) REVERT: d 2 LYS cc_start: 0.8939 (ptpt) cc_final: 0.8609 (ptpt) REVERT: 2 107 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.9056 (t80) REVERT: f 4 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: 8 104 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7948 (tm-30) REVERT: g 7 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8587 (t80) REVERT: BA 102 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8811 (mmmm) REVERT: BA 107 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8875 (t80) REVERT: DA 303 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8725 (t80) REVERT: FA 206 LYS cc_start: 0.9094 (tttt) cc_final: 0.8621 (pptt) REVERT: GA 302 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8425 (tptp) outliers start: 94 outliers final: 55 residues processed: 206 average time/residue: 0.3820 time to fit residues: 89.8233 Evaluate side-chains 228 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 143 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain U residue 302 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain W residue 206 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain k residue 107 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 7 PHE Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 204 GLU Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain y residue 307 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain z residue 107 PHE Chi-restraints excluded: chain 0 residue 204 GLU Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 2 residue 107 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain BA residue 102 LYS Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain CA residue 204 GLU Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain HA residue 104 GLU 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: 0.8584 moved from start: 0.9236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.426 6264 Z= 6.602 Angle : 5.027 41.172 8136 Z= 2.322 Chirality : 0.388 1.082 576 Planarity : 0.023 0.079 1080 Dihedral : 22.932 88.090 748 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 132.73 Ramachandran Plot: Outliers : 0.69 % Allowed : 59.72 % Favored : 39.58 % Rotamer: Outliers : 23.84 % Allowed : 40.51 % Favored : 35.65 % Cbeta Deviations : 42.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % 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: -8.74 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.66 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.171 0.022 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 145 time to evaluate : 1.123 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: A 6 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8732 (mtmt) REVERT: J 106 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8647 (mmmm) REVERT: J 107 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8325 (t80) REVERT: L 306 LYS cc_start: 0.9172 (mttt) cc_final: 0.8918 (mmmm) REVERT: M 106 LYS cc_start: 0.9109 (mmmm) cc_final: 0.8797 (mmmm) REVERT: N 204 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8232 (tt0) REVERT: N 205 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.9115 (m-80) REVERT: O 306 LYS cc_start: 0.9046 (tttt) cc_final: 0.8765 (tttt) REVERT: O 307 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8532 (t80) REVERT: C 2 LYS cc_start: 0.9132 (tttt) cc_final: 0.8760 (tttm) REVERT: C 4 GLU cc_start: 0.8206 (mp0) cc_final: 0.7463 (mp0) REVERT: P 102 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8952 (ttpt) REVERT: P 106 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8516 (mmmm) REVERT: Q 206 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8821 (ttmm) REVERT: D 2 LYS cc_start: 0.9392 (tttt) cc_final: 0.9138 (ttmm) REVERT: D 4 GLU cc_start: 0.8822 (mp0) cc_final: 0.8204 (mp0) REVERT: S 106 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8591 (mmmm) REVERT: U 304 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8026 (mm-30) REVERT: U 306 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8461 (ttmm) REVERT: V 106 LYS cc_start: 0.9170 (tptm) cc_final: 0.8899 (ttmm) REVERT: W 205 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8853 (m-80) REVERT: X 306 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8701 (mmmm) REVERT: X 307 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8613 (t80) REVERT: F 6 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8643 (mmmt) REVERT: Y 104 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8384 (mm-30) REVERT: Z 202 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8859 (tttt) REVERT: Z 203 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: j 306 LYS cc_start: 0.9144 (mttt) cc_final: 0.8864 (mmmm) REVERT: j 307 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8024 (t80) REVERT: G 6 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8468 (mmmt) REVERT: k 107 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8135 (t80) REVERT: m 306 LYS cc_start: 0.9192 (mttt) cc_final: 0.8877 (mmmm) REVERT: H 2 LYS cc_start: 0.9407 (tttt) cc_final: 0.9160 (tttp) REVERT: H 4 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6058 (pm20) REVERT: n 106 LYS cc_start: 0.8920 (tptm) cc_final: 0.8602 (tptm) REVERT: n 107 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.9152 (m-80) REVERT: o 207 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8398 (t80) REVERT: I 4 GLU cc_start: 0.8524 (mp0) cc_final: 0.7914 (mp0) REVERT: q 107 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: s 302 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8536 (tptt) REVERT: s 306 LYS cc_start: 0.9287 (tttt) cc_final: 0.8918 (tptt) REVERT: a 2 LYS cc_start: 0.8931 (ptpt) cc_final: 0.8598 (ptpt) REVERT: a 7 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8637 (t80) REVERT: b 7 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9103 (t80) REVERT: z 105 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8327 (t80) REVERT: d 2 LYS cc_start: 0.8941 (ptpt) cc_final: 0.8613 (ptpt) REVERT: 2 107 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.9127 (t80) REVERT: f 4 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: 8 104 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7981 (tm-30) REVERT: g 7 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8658 (t80) REVERT: BA 102 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8670 (mmmm) REVERT: BA 107 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.8884 (t80) REVERT: FA 202 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8788 (mttm) REVERT: FA 206 LYS cc_start: 0.9100 (tttt) cc_final: 0.8632 (pptt) REVERT: GA 302 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8538 (tptp) REVERT: JA 302 LYS cc_start: 0.9129 (tptp) cc_final: 0.8875 (tptp) outliers start: 103 outliers final: 66 residues processed: 214 average time/residue: 0.3658 time to fit residues: 90.1279 Evaluate side-chains 241 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 144 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain k residue 107 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 7 PHE Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 204 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain y residue 307 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain z residue 107 PHE Chi-restraints excluded: chain 0 residue 204 GLU Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 2 residue 107 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain BA residue 102 LYS Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain CA residue 204 GLU Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain FA residue 202 LYS Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain HA residue 104 GLU 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: 0.8585 moved from start: 0.9303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.428 6264 Z= 6.607 Angle : 5.037 41.423 8136 Z= 2.327 Chirality : 0.389 1.084 576 Planarity : 0.023 0.080 1080 Dihedral : 22.958 89.215 748 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 130.99 Ramachandran Plot: Outliers : 0.69 % Allowed : 59.72 % Favored : 39.58 % Rotamer: Outliers : 24.31 % Allowed : 40.28 % Favored : 35.42 % Cbeta Deviations : 43.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % 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: -8.74 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.66 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.170 0.022 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 144 time to evaluate : 0.626 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 6 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8731 (mtmt) REVERT: J 106 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8644 (mmmm) REVERT: J 107 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8359 (t80) REVERT: L 306 LYS cc_start: 0.9178 (mttt) cc_final: 0.8896 (mmmm) REVERT: M 106 LYS cc_start: 0.9098 (mmmm) cc_final: 0.8829 (mmmm) REVERT: N 204 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8282 (tt0) REVERT: N 205 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.9100 (m-80) REVERT: O 303 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8563 (m-10) REVERT: O 306 LYS cc_start: 0.9057 (tttt) cc_final: 0.8770 (tttt) REVERT: O 307 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8531 (t80) REVERT: C 2 LYS cc_start: 0.9124 (tttt) cc_final: 0.8748 (tttm) REVERT: C 4 GLU cc_start: 0.8216 (mp0) cc_final: 0.7481 (mp0) REVERT: P 102 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8954 (ttpt) REVERT: P 106 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8525 (mmmm) REVERT: Q 207 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8176 (t80) REVERT: D 2 LYS cc_start: 0.9390 (tttt) cc_final: 0.9130 (ttmm) REVERT: D 4 GLU cc_start: 0.8818 (mp0) cc_final: 0.8214 (mp0) REVERT: S 106 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8610 (mmmm) REVERT: U 302 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9085 (mttt) REVERT: U 304 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8018 (mm-30) REVERT: U 306 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8455 (ttmm) REVERT: V 106 LYS cc_start: 0.9173 (tptm) cc_final: 0.8920 (ttmm) REVERT: W 205 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: X 307 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8617 (t80) REVERT: F 6 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8660 (mmmt) REVERT: Y 104 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8382 (mm-30) REVERT: Z 202 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8852 (tttt) REVERT: Z 203 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: j 306 LYS cc_start: 0.9137 (mttt) cc_final: 0.8865 (mmmm) REVERT: j 307 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8024 (t80) REVERT: k 107 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8147 (t80) REVERT: m 306 LYS cc_start: 0.9191 (mttt) cc_final: 0.8878 (mmmm) REVERT: H 2 LYS cc_start: 0.9412 (tttt) cc_final: 0.9201 (tttp) REVERT: H 4 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6047 (pm20) REVERT: H 7 PHE cc_start: 0.9473 (OUTLIER) cc_final: 0.8746 (t80) REVERT: n 106 LYS cc_start: 0.8916 (tptm) cc_final: 0.8598 (tptm) REVERT: n 107 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.9127 (m-80) REVERT: o 207 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8392 (t80) REVERT: p 303 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: I 4 GLU cc_start: 0.8469 (mp0) cc_final: 0.7857 (mp0) REVERT: q 104 GLU cc_start: 0.8473 (tp30) cc_final: 0.8272 (tp30) REVERT: q 107 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8678 (m-80) REVERT: s 302 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8522 (tptt) REVERT: s 306 LYS cc_start: 0.9284 (tttt) cc_final: 0.8905 (tptt) REVERT: a 2 LYS cc_start: 0.8939 (ptpt) cc_final: 0.8605 (ptpt) REVERT: a 7 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8637 (t80) REVERT: u 206 LYS cc_start: 0.9157 (tttm) cc_final: 0.8848 (tttt) REVERT: v 306 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8025 (tptp) REVERT: b 7 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.9102 (t80) REVERT: z 105 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8307 (t80) REVERT: d 2 LYS cc_start: 0.8962 (ptpt) cc_final: 0.8622 (ptpt) REVERT: 2 107 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.9129 (t80) REVERT: f 4 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: 8 104 GLU cc_start: 0.8527 (tm-30) cc_final: 0.7979 (tm-30) REVERT: 9 204 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7923 (tm-30) REVERT: g 7 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8662 (t80) REVERT: BA 102 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8809 (mmmm) REVERT: FA 206 LYS cc_start: 0.9104 (tttt) cc_final: 0.8619 (pptt) REVERT: GA 302 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8632 (tptp) REVERT: JA 302 LYS cc_start: 0.9125 (tptp) cc_final: 0.8880 (tptp) outliers start: 105 outliers final: 66 residues processed: 216 average time/residue: 0.3552 time to fit residues: 87.8853 Evaluate side-chains 243 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 144 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain M residue 107 PHE Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain U residue 302 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain k residue 107 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 7 PHE Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 204 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain y residue 307 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain z residue 107 PHE Chi-restraints excluded: chain 0 residue 204 GLU Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 2 residue 107 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain BA residue 102 LYS Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain CA residue 204 GLU Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.9342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.430 6264 Z= 6.614 Angle : 5.038 40.971 8136 Z= 2.326 Chirality : 0.389 1.083 576 Planarity : 0.023 0.079 1080 Dihedral : 22.955 89.757 748 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 131.76 Ramachandran Plot: Outliers : 0.69 % Allowed : 60.42 % Favored : 38.89 % Rotamer: Outliers : 25.00 % Allowed : 40.51 % Favored : 34.49 % Cbeta Deviations : 43.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % 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: -8.71 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.63 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.170 0.022 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 145 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8750 (mtmt) REVERT: J 106 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8648 (mmmm) REVERT: J 107 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8362 (t80) REVERT: L 304 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8040 (mp0) REVERT: L 306 LYS cc_start: 0.9177 (mttt) cc_final: 0.8912 (mmmm) REVERT: M 106 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8790 (mmmm) REVERT: N 204 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8295 (tt0) REVERT: N 205 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9096 (m-80) REVERT: O 303 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8569 (m-10) REVERT: O 306 LYS cc_start: 0.9057 (tttt) cc_final: 0.8772 (tttt) REVERT: O 307 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8531 (t80) REVERT: C 2 LYS cc_start: 0.9126 (tttt) cc_final: 0.8756 (tttm) REVERT: C 4 GLU cc_start: 0.8217 (mp0) cc_final: 0.7498 (mp0) REVERT: P 102 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8951 (ttpt) REVERT: P 106 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8538 (mmmm) REVERT: Q 207 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8156 (t80) REVERT: R 304 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7566 (mm-30) REVERT: D 2 LYS cc_start: 0.9390 (tttt) cc_final: 0.9131 (ttmm) REVERT: D 4 GLU cc_start: 0.8818 (mp0) cc_final: 0.8207 (mp0) REVERT: S 106 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8597 (mmmm) REVERT: U 304 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8033 (mm-30) REVERT: U 306 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8453 (ttmm) REVERT: V 106 LYS cc_start: 0.9184 (tptm) cc_final: 0.8939 (ttmm) REVERT: W 205 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8785 (m-80) REVERT: W 206 LYS cc_start: 0.8973 (ptmm) cc_final: 0.8654 (ptmm) REVERT: X 306 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8799 (mmmm) REVERT: X 307 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8593 (t80) REVERT: F 6 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8649 (mmmt) REVERT: Y 104 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8381 (mm-30) REVERT: Z 202 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8866 (tttt) REVERT: Z 203 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: Z 204 GLU cc_start: 0.8498 (tt0) cc_final: 0.7580 (tm-30) REVERT: j 306 LYS cc_start: 0.9134 (mttt) cc_final: 0.8865 (mmmm) REVERT: j 307 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8015 (t80) REVERT: k 107 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8147 (t80) REVERT: m 306 LYS cc_start: 0.9191 (mttt) cc_final: 0.8878 (mmmm) REVERT: H 2 LYS cc_start: 0.9407 (tttt) cc_final: 0.9186 (tttp) REVERT: H 4 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6053 (pm20) REVERT: H 7 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.8803 (t80) REVERT: n 106 LYS cc_start: 0.8920 (tptm) cc_final: 0.8602 (tptm) REVERT: n 107 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.9105 (m-80) REVERT: o 207 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8389 (t80) REVERT: p 303 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: I 4 GLU cc_start: 0.8488 (mp0) cc_final: 0.7883 (mp0) REVERT: q 104 GLU cc_start: 0.8493 (tp30) cc_final: 0.8266 (tp30) REVERT: q 107 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: s 302 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8522 (tptt) REVERT: s 306 LYS cc_start: 0.9286 (tttt) cc_final: 0.8923 (tptt) REVERT: a 2 LYS cc_start: 0.8937 (ptpt) cc_final: 0.8606 (ptpt) REVERT: a 7 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8635 (t80) REVERT: v 306 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8032 (tptp) REVERT: b 7 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9101 (t80) REVERT: z 105 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8309 (t80) REVERT: d 2 LYS cc_start: 0.8965 (ptpt) cc_final: 0.8617 (ptpt) REVERT: 2 107 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.9128 (t80) REVERT: f 4 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: 8 104 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7975 (tm-30) REVERT: 9 204 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7994 (tm-30) REVERT: g 7 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.8667 (t80) REVERT: BA 102 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8807 (mmmm) REVERT: FA 202 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8799 (mttm) REVERT: FA 206 LYS cc_start: 0.9073 (tttt) cc_final: 0.8536 (pptt) REVERT: JA 302 LYS cc_start: 0.9136 (tptp) cc_final: 0.8899 (tptp) outliers start: 108 outliers final: 67 residues processed: 217 average time/residue: 0.3557 time to fit residues: 88.4182 Evaluate side-chains 245 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 145 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain k residue 107 PHE Chi-restraints excluded: chain m residue 304 GLU Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 7 PHE Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 204 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain y residue 307 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain z residue 107 PHE Chi-restraints excluded: chain 0 residue 204 GLU Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 2 residue 107 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain BA residue 102 LYS Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain CA residue 204 GLU Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain FA residue 202 LYS Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.9378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.428 6264 Z= 6.612 Angle : 5.037 40.680 8136 Z= 2.324 Chirality : 0.389 1.086 576 Planarity : 0.023 0.079 1080 Dihedral : 22.981 88.848 748 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 132.83 Ramachandran Plot: Outliers : 0.69 % Allowed : 60.76 % Favored : 38.54 % Rotamer: Outliers : 25.00 % Allowed : 40.97 % Favored : 34.03 % Cbeta Deviations : 43.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.78 % 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: -8.77 (0.24), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.68 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.169 0.022 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 143 time to evaluate : 0.594 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 6 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8724 (mtmt) REVERT: J 106 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8648 (mmmm) REVERT: J 107 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8364 (t80) REVERT: L 306 LYS cc_start: 0.9172 (mttt) cc_final: 0.8868 (mmmm) REVERT: M 106 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8817 (mmmm) REVERT: N 204 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8293 (tt0) REVERT: N 205 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.9095 (m-80) REVERT: O 303 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8556 (m-10) REVERT: O 306 LYS cc_start: 0.9058 (tttt) cc_final: 0.8765 (tttt) REVERT: O 307 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8529 (t80) REVERT: C 2 LYS cc_start: 0.9128 (tttt) cc_final: 0.8746 (tttm) REVERT: C 4 GLU cc_start: 0.8219 (mp0) cc_final: 0.7502 (mp0) REVERT: P 102 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8952 (ttpt) REVERT: P 106 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8541 (mmmm) REVERT: Q 207 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8154 (t80) REVERT: R 304 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7409 (mm-30) REVERT: R 306 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8747 (ttpt) REVERT: D 2 LYS cc_start: 0.9389 (tttt) cc_final: 0.9128 (ttmm) REVERT: D 4 GLU cc_start: 0.8813 (mp0) cc_final: 0.8212 (mp0) REVERT: S 106 LYS cc_start: 0.9061 (mmmm) cc_final: 0.8621 (mmmm) REVERT: U 302 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9076 (mttt) REVERT: U 304 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8032 (mm-30) REVERT: U 306 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8451 (ttmm) REVERT: V 106 LYS cc_start: 0.9173 (tptm) cc_final: 0.8941 (ttmm) REVERT: W 205 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8798 (m-10) REVERT: W 206 LYS cc_start: 0.8983 (ptmm) cc_final: 0.8652 (ptmm) REVERT: X 307 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8619 (t80) REVERT: F 6 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8646 (mmmt) REVERT: Y 104 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8383 (mm-30) REVERT: Z 202 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9022 (tttt) REVERT: Z 203 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.8704 (m-10) REVERT: Z 204 GLU cc_start: 0.8503 (tt0) cc_final: 0.7589 (tm-30) REVERT: j 306 LYS cc_start: 0.9139 (mttt) cc_final: 0.8854 (mmmm) REVERT: j 307 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8015 (t80) REVERT: k 107 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8144 (t80) REVERT: m 306 LYS cc_start: 0.9189 (mttt) cc_final: 0.8874 (mmmm) REVERT: H 2 LYS cc_start: 0.9409 (tttt) cc_final: 0.9194 (tttp) REVERT: H 4 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6062 (pm20) REVERT: H 7 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.8852 (t80) REVERT: n 106 LYS cc_start: 0.8877 (tptm) cc_final: 0.8558 (tptm) REVERT: n 107 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.9085 (m-80) REVERT: o 207 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8384 (t80) REVERT: p 303 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: I 4 GLU cc_start: 0.8487 (mp0) cc_final: 0.7894 (mp0) REVERT: q 104 GLU cc_start: 0.8543 (tp30) cc_final: 0.7844 (tm-30) REVERT: q 107 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: s 302 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8522 (tptt) REVERT: s 306 LYS cc_start: 0.9285 (tttt) cc_final: 0.8903 (tptt) REVERT: a 2 LYS cc_start: 0.8936 (ptpt) cc_final: 0.8604 (ptpt) REVERT: a 7 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8636 (t80) REVERT: u 206 LYS cc_start: 0.9173 (tptm) cc_final: 0.8775 (tptm) REVERT: v 306 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8028 (tptp) REVERT: b 7 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.9101 (t80) REVERT: z 105 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8312 (t80) REVERT: 0 202 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8760 (ttmm) REVERT: d 2 LYS cc_start: 0.8974 (ptpt) cc_final: 0.8619 (ptpt) REVERT: 2 107 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.9131 (t80) REVERT: f 4 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: 8 104 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7979 (tm-30) REVERT: 9 204 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8077 (tm-30) REVERT: 9 206 LYS cc_start: 0.9157 (tttt) cc_final: 0.8940 (pttt) REVERT: g 7 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.8674 (t80) REVERT: BA 102 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8729 (mmmm) REVERT: FA 202 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8797 (mttm) REVERT: FA 206 LYS cc_start: 0.9070 (tttt) cc_final: 0.8542 (pptt) REVERT: JA 302 LYS cc_start: 0.9132 (tptp) cc_final: 0.8882 (tptp) outliers start: 108 outliers final: 70 residues processed: 217 average time/residue: 0.3583 time to fit residues: 89.2300 Evaluate side-chains 248 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 143 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain M residue 107 PHE Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain U residue 302 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain Z residue 206 LYS Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain k residue 107 PHE Chi-restraints excluded: chain m residue 304 GLU Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 7 PHE Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 204 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain y residue 307 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain z residue 107 PHE Chi-restraints excluded: chain 0 residue 202 LYS Chi-restraints excluded: chain 0 residue 203 PHE Chi-restraints excluded: chain 0 residue 204 GLU Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 2 residue 107 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain BA residue 102 LYS Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain CA residue 204 GLU Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain FA residue 202 LYS Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.9399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.430 6264 Z= 6.614 Angle : 5.032 40.556 8136 Z= 2.322 Chirality : 0.389 1.082 576 Planarity : 0.023 0.078 1080 Dihedral : 23.011 88.391 748 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 131.01 Ramachandran Plot: Outliers : 1.04 % Allowed : 60.07 % Favored : 38.89 % Rotamer: Outliers : 25.46 % Allowed : 40.28 % Favored : 34.26 % Cbeta Deviations : 43.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.78 % 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: -8.74 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.66 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.169 0.022 PHE 7 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 143 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: A 6 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8757 (mtmt) REVERT: J 106 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8691 (mmmm) REVERT: J 107 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8360 (t80) REVERT: L 306 LYS cc_start: 0.9168 (mttt) cc_final: 0.8928 (mmmm) REVERT: M 106 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8803 (mmmm) REVERT: N 204 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8292 (tt0) REVERT: N 205 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9095 (m-80) REVERT: O 303 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8550 (m-10) REVERT: O 306 LYS cc_start: 0.9059 (tttt) cc_final: 0.8774 (tttt) REVERT: O 307 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8530 (t80) REVERT: C 2 LYS cc_start: 0.9130 (tttt) cc_final: 0.8761 (tttm) REVERT: C 4 GLU cc_start: 0.8220 (mp0) cc_final: 0.7497 (mp0) REVERT: P 102 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8957 (ttpt) REVERT: P 106 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8550 (mmmm) REVERT: Q 207 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8145 (t80) REVERT: R 304 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7622 (mm-30) REVERT: D 2 LYS cc_start: 0.9389 (tttt) cc_final: 0.9126 (ttmm) REVERT: D 4 GLU cc_start: 0.8813 (mp0) cc_final: 0.8209 (mp0) REVERT: S 106 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8619 (mmmm) REVERT: U 302 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9074 (mttt) REVERT: U 304 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8031 (mm-30) REVERT: U 306 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8450 (ttmm) REVERT: V 106 LYS cc_start: 0.9181 (tptm) cc_final: 0.8918 (ttmm) REVERT: W 205 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8678 (m-10) REVERT: W 206 LYS cc_start: 0.8988 (ptmm) cc_final: 0.8656 (ptmm) REVERT: X 307 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8618 (t80) REVERT: F 6 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8648 (mmmt) REVERT: Y 104 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8378 (mm-30) REVERT: Z 202 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8858 (tttt) REVERT: Z 203 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: Z 204 GLU cc_start: 0.8496 (tt0) cc_final: 0.7392 (tm-30) REVERT: j 306 LYS cc_start: 0.9129 (mttt) cc_final: 0.8854 (mmmm) REVERT: j 307 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8015 (t80) REVERT: G 6 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8464 (mmmt) REVERT: k 107 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8138 (t80) REVERT: m 306 LYS cc_start: 0.9189 (mttt) cc_final: 0.8874 (mmmm) REVERT: H 2 LYS cc_start: 0.9407 (tttt) cc_final: 0.9188 (tttp) REVERT: H 4 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6068 (pm20) REVERT: H 7 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.8853 (t80) REVERT: n 106 LYS cc_start: 0.8923 (tptm) cc_final: 0.8623 (tptm) REVERT: n 107 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.9124 (m-80) REVERT: o 207 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8383 (t80) REVERT: p 303 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: I 4 GLU cc_start: 0.8489 (mp0) cc_final: 0.7885 (mp0) REVERT: q 107 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: s 302 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8521 (tptt) REVERT: s 306 LYS cc_start: 0.9285 (tttt) cc_final: 0.8920 (tptt) REVERT: a 2 LYS cc_start: 0.8934 (ptpt) cc_final: 0.8598 (ptpt) REVERT: a 7 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8638 (t80) REVERT: v 306 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8035 (tptp) REVERT: b 7 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9101 (t80) REVERT: z 105 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8312 (t80) REVERT: 0 202 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8744 (ttmm) REVERT: d 2 LYS cc_start: 0.8971 (ptpt) cc_final: 0.8617 (ptpt) REVERT: 2 107 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.9130 (t80) REVERT: f 4 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: 8 104 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7977 (tm-30) REVERT: 9 204 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8169 (tm-30) REVERT: g 7 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8671 (t80) REVERT: BA 102 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8730 (mmmm) REVERT: FA 202 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8799 (mttm) REVERT: FA 206 LYS cc_start: 0.9072 (tttt) cc_final: 0.8543 (pptt) outliers start: 110 outliers final: 72 residues processed: 218 average time/residue: 0.3651 time to fit residues: 90.9937 Evaluate side-chains 250 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 143 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain U residue 302 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain Z residue 205 PHE Chi-restraints excluded: chain Z residue 206 LYS Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain k residue 107 PHE Chi-restraints excluded: chain m residue 304 GLU Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 7 PHE Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 204 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain y residue 307 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain z residue 107 PHE Chi-restraints excluded: chain 0 residue 202 LYS Chi-restraints excluded: chain 0 residue 203 PHE Chi-restraints excluded: chain 0 residue 204 GLU Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 2 residue 107 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain BA residue 102 LYS Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain CA residue 204 GLU Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain FA residue 202 LYS Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.049272 restraints weight = 19092.060| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.22 r_work: 0.2515 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.9420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.428 6264 Z= 6.615 Angle : 5.030 40.491 8136 Z= 2.322 Chirality : 0.389 1.083 576 Planarity : 0.023 0.079 1080 Dihedral : 23.075 88.192 748 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 131.43 Ramachandran Plot: Outliers : 0.69 % Allowed : 60.76 % Favored : 38.54 % Rotamer: Outliers : 25.93 % Allowed : 39.81 % Favored : 34.26 % Cbeta Deviations : 42.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -8.74 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.66 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.170 0.022 PHE 7 303 =============================================================================== Job complete usr+sys time: 1519.20 seconds wall clock time: 28 minutes 30.02 seconds (1710.02 seconds total)