Starting phenix.real_space_refine on Fri Mar 15 07:14:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bky_16098/03_2024/8bky_16098.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bky_16098/03_2024/8bky_16098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bky_16098/03_2024/8bky_16098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bky_16098/03_2024/8bky_16098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bky_16098/03_2024/8bky_16098.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bky_16098/03_2024/8bky_16098.pdb" } resolution = 3.6 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 43560 2.51 5 N 11952 2.21 5 O 12600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 58": "OD1" <-> "OD2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ASP 275": "OD1" <-> "OD2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C ASP 295": "OD1" <-> "OD2" Residue "C ASP 301": "OD1" <-> "OD2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D ASP 255": "OD1" <-> "OD2" Residue "D ASP 275": "OD1" <-> "OD2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E ASP 255": "OD1" <-> "OD2" Residue "E ASP 275": "OD1" <-> "OD2" Residue "E ASP 295": "OD1" <-> "OD2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F ASP 58": "OD1" <-> "OD2" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 275": "OD1" <-> "OD2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F ASP 295": "OD1" <-> "OD2" Residue "F ASP 301": "OD1" <-> "OD2" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "G ASP 58": "OD1" <-> "OD2" Residue "G ASP 255": "OD1" <-> "OD2" Residue "G ASP 275": "OD1" <-> "OD2" Residue "G ASP 295": "OD1" <-> "OD2" Residue "G ASP 301": "OD1" <-> "OD2" Residue "G GLU 317": "OE1" <-> "OE2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H ASP 275": "OD1" <-> "OD2" Residue "H ASP 295": "OD1" <-> "OD2" Residue "H ASP 301": "OD1" <-> "OD2" Residue "H GLU 317": "OE1" <-> "OE2" Residue "H GLU 372": "OE1" <-> "OE2" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I ASP 255": "OD1" <-> "OD2" Residue "I ASP 275": "OD1" <-> "OD2" Residue "I ASP 295": "OD1" <-> "OD2" Residue "I ASP 301": "OD1" <-> "OD2" Residue "I GLU 317": "OE1" <-> "OE2" Residue "I GLU 372": "OE1" <-> "OE2" Residue "J ASP 58": "OD1" <-> "OD2" Residue "J ASP 255": "OD1" <-> "OD2" Residue "J ASP 275": "OD1" <-> "OD2" Residue "J GLU 291": "OE1" <-> "OE2" Residue "J ASP 295": "OD1" <-> "OD2" Residue "J ASP 301": "OD1" <-> "OD2" Residue "J GLU 317": "OE1" <-> "OE2" Residue "J GLU 372": "OE1" <-> "OE2" Residue "K ASP 58": "OD1" <-> "OD2" Residue "K ASP 255": "OD1" <-> "OD2" Residue "K ASP 275": "OD1" <-> "OD2" Residue "K GLU 291": "OE1" <-> "OE2" Residue "K ASP 295": "OD1" <-> "OD2" Residue "K ASP 301": "OD1" <-> "OD2" Residue "K GLU 317": "OE1" <-> "OE2" Residue "K GLU 372": "OE1" <-> "OE2" Residue "L ASP 58": "OD1" <-> "OD2" Residue "L ASP 255": "OD1" <-> "OD2" Residue "L ASP 275": "OD1" <-> "OD2" Residue "L ASP 295": "OD1" <-> "OD2" Residue "L ASP 301": "OD1" <-> "OD2" Residue "L GLU 317": "OE1" <-> "OE2" Residue "L GLU 372": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M ASP 275": "OD1" <-> "OD2" Residue "M ASP 295": "OD1" <-> "OD2" Residue "M ASP 301": "OD1" <-> "OD2" Residue "M GLU 317": "OE1" <-> "OE2" Residue "M GLU 372": "OE1" <-> "OE2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N ASP 255": "OD1" <-> "OD2" Residue "N ASP 275": "OD1" <-> "OD2" Residue "N ASP 295": "OD1" <-> "OD2" Residue "N ASP 301": "OD1" <-> "OD2" Residue "N GLU 317": "OE1" <-> "OE2" Residue "N GLU 372": "OE1" <-> "OE2" Residue "O ASP 58": "OD1" <-> "OD2" Residue "O ASP 255": "OD1" <-> "OD2" Residue "O ASP 275": "OD1" <-> "OD2" Residue "O ASP 295": "OD1" <-> "OD2" Residue "O ASP 301": "OD1" <-> "OD2" Residue "O GLU 317": "OE1" <-> "OE2" Residue "O GLU 372": "OE1" <-> "OE2" Residue "P ASP 58": "OD1" <-> "OD2" Residue "P ASP 255": "OD1" <-> "OD2" Residue "P ASP 275": "OD1" <-> "OD2" Residue "P ASP 295": "OD1" <-> "OD2" Residue "P ASP 301": "OD1" <-> "OD2" Residue "P GLU 317": "OE1" <-> "OE2" Residue "P GLU 372": "OE1" <-> "OE2" Residue "Q ASP 58": "OD1" <-> "OD2" Residue "Q ASP 255": "OD1" <-> "OD2" Residue "Q ASP 275": "OD1" <-> "OD2" Residue "Q ASP 295": "OD1" <-> "OD2" Residue "Q ASP 301": "OD1" <-> "OD2" Residue "Q GLU 317": "OE1" <-> "OE2" Residue "Q GLU 372": "OE1" <-> "OE2" Residue "R ASP 58": "OD1" <-> "OD2" Residue "R ASP 255": "OD1" <-> "OD2" Residue "R ASP 275": "OD1" <-> "OD2" Residue "R ASP 295": "OD1" <-> "OD2" Residue "R ASP 301": "OD1" <-> "OD2" Residue "R GLU 317": "OE1" <-> "OE2" Residue "R GLU 372": "OE1" <-> "OE2" Residue "S ASP 58": "OD1" <-> "OD2" Residue "S ASP 255": "OD1" <-> "OD2" Residue "S ASP 275": "OD1" <-> "OD2" Residue "S ASP 295": "OD1" <-> "OD2" Residue "S ASP 301": "OD1" <-> "OD2" Residue "S GLU 317": "OE1" <-> "OE2" Residue "S GLU 372": "OE1" <-> "OE2" Residue "T ASP 58": "OD1" <-> "OD2" Residue "T ASP 255": "OD1" <-> "OD2" Residue "T ASP 275": "OD1" <-> "OD2" Residue "T ASP 295": "OD1" <-> "OD2" Residue "T ASP 301": "OD1" <-> "OD2" Residue "T GLU 317": "OE1" <-> "OE2" Residue "T GLU 372": "OE1" <-> "OE2" Residue "U ASP 58": "OD1" <-> "OD2" Residue "U ASP 255": "OD1" <-> "OD2" Residue "U ASP 275": "OD1" <-> "OD2" Residue "U ASP 295": "OD1" <-> "OD2" Residue "U ASP 301": "OD1" <-> "OD2" Residue "U GLU 317": "OE1" <-> "OE2" Residue "U GLU 372": "OE1" <-> "OE2" Residue "V ASP 58": "OD1" <-> "OD2" Residue "V ASP 255": "OD1" <-> "OD2" Residue "V ASP 275": "OD1" <-> "OD2" Residue "V ASP 295": "OD1" <-> "OD2" Residue "V ASP 301": "OD1" <-> "OD2" Residue "V GLU 317": "OE1" <-> "OE2" Residue "V GLU 372": "OE1" <-> "OE2" Residue "W ASP 58": "OD1" <-> "OD2" Residue "W ASP 255": "OD1" <-> "OD2" Residue "W ASP 275": "OD1" <-> "OD2" Residue "W ASP 295": "OD1" <-> "OD2" Residue "W ASP 301": "OD1" <-> "OD2" Residue "W GLU 317": "OE1" <-> "OE2" Residue "W GLU 372": "OE1" <-> "OE2" Residue "X ASP 58": "OD1" <-> "OD2" Residue "X ASP 255": "OD1" <-> "OD2" Residue "X ASP 275": "OD1" <-> "OD2" Residue "X ASP 295": "OD1" <-> "OD2" Residue "X ASP 301": "OD1" <-> "OD2" Residue "X GLU 317": "OE1" <-> "OE2" Residue "X GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68280 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 23, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 26.60, per 1000 atoms: 0.39 Number of scatterers: 68280 At special positions: 0 Unit cell: (247.8, 245, 112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 12600 8.00 N 11952 7.00 C 43560 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: 19.99 Conformation dependent library (CDL) restraints added in 10.0 seconds 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15888 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 96 sheets defined 40.1% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG A 423 " --> pdb=" O PRO A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL A 446 " --> pdb=" O GLN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 471 Processing helix chain 'A' and resid 479 through 482 Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 63 through 75 removed outlier: 4.404A pdb=" N HIS B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA B 253 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG B 423 " --> pdb=" O PRO B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL B 446 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 471 Processing helix chain 'B' and resid 479 through 482 Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS C 67 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA C 253 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 294 removed outlier: 4.143A pdb=" N ALA C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL C 279 " --> pdb=" O ASP C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA C 353 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 393 Processing helix chain 'C' and resid 419 through 423 removed outlier: 3.946A pdb=" N ARG C 423 " --> pdb=" O PRO C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG C 428 " --> pdb=" O TYR C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL C 446 " --> pdb=" O GLN C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 471 Processing helix chain 'C' and resid 479 through 482 Processing helix chain 'C' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU C 500 " --> pdb=" O GLU C 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA D 253 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL D 279 " --> pdb=" O ASP D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 315 Processing helix chain 'D' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA D 353 " --> pdb=" O SER D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG D 423 " --> pdb=" O PRO D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG D 428 " --> pdb=" O TYR D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL D 446 " --> pdb=" O GLN D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 471 Processing helix chain 'D' and resid 479 through 482 Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU D 500 " --> pdb=" O GLU D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 63 through 75 removed outlier: 4.404A pdb=" N HIS E 67 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA E 253 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL E 279 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA E 353 " --> pdb=" O SER E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 393 Processing helix chain 'E' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG E 423 " --> pdb=" O PRO E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG E 428 " --> pdb=" O TYR E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL E 446 " --> pdb=" O GLN E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 471 Processing helix chain 'E' and resid 479 through 482 Processing helix chain 'E' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU E 500 " --> pdb=" O GLU E 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS F 67 " --> pdb=" O TYR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA F 253 " --> pdb=" O GLY F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR F 269 " --> pdb=" O LEU F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 294 removed outlier: 4.143A pdb=" N ALA F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL F 279 " --> pdb=" O ASP F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 315 Processing helix chain 'F' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA F 353 " --> pdb=" O SER F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 393 Processing helix chain 'F' and resid 419 through 423 removed outlier: 3.946A pdb=" N ARG F 423 " --> pdb=" O PRO F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG F 428 " --> pdb=" O TYR F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL F 446 " --> pdb=" O GLN F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 471 Processing helix chain 'F' and resid 479 through 482 Processing helix chain 'F' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU F 500 " --> pdb=" O GLU F 496 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 63 through 75 removed outlier: 4.404A pdb=" N HIS G 67 " --> pdb=" O TYR G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA G 253 " --> pdb=" O GLY G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR G 269 " --> pdb=" O LEU G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA G 278 " --> pdb=" O ILE G 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL G 279 " --> pdb=" O ASP G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 315 Processing helix chain 'G' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA G 353 " --> pdb=" O SER G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 393 Processing helix chain 'G' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG G 423 " --> pdb=" O PRO G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG G 428 " --> pdb=" O TYR G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL G 446 " --> pdb=" O GLN G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 471 Processing helix chain 'G' and resid 479 through 482 Processing helix chain 'G' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU G 500 " --> pdb=" O GLU G 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS H 67 " --> pdb=" O TYR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA H 253 " --> pdb=" O GLY H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA H 278 " --> pdb=" O ILE H 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL H 279 " --> pdb=" O ASP H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 315 Processing helix chain 'H' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA H 353 " --> pdb=" O SER H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 393 Processing helix chain 'H' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG H 423 " --> pdb=" O PRO H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 424 through 441 removed outlier: 3.824A pdb=" N ARG H 428 " --> pdb=" O TYR H 424 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL H 446 " --> pdb=" O GLN H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 471 Processing helix chain 'H' and resid 479 through 482 Processing helix chain 'H' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU H 500 " --> pdb=" O GLU H 496 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS I 67 " --> pdb=" O TYR I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA I 253 " --> pdb=" O GLY I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR I 269 " --> pdb=" O LEU I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA I 278 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL I 279 " --> pdb=" O ASP I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 315 Processing helix chain 'I' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA I 353 " --> pdb=" O SER I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 393 Processing helix chain 'I' and resid 419 through 423 removed outlier: 3.946A pdb=" N ARG I 423 " --> pdb=" O PRO I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG I 428 " --> pdb=" O TYR I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL I 446 " --> pdb=" O GLN I 443 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 471 Processing helix chain 'I' and resid 479 through 482 Processing helix chain 'I' and resid 494 through 500 removed outlier: 3.868A pdb=" N LEU I 500 " --> pdb=" O GLU I 496 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS J 67 " --> pdb=" O TYR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA J 253 " --> pdb=" O GLY J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR J 269 " --> pdb=" O LEU J 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA J 278 " --> pdb=" O ILE J 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL J 279 " --> pdb=" O ASP J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 315 Processing helix chain 'J' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA J 353 " --> pdb=" O SER J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 393 Processing helix chain 'J' and resid 419 through 423 removed outlier: 3.946A pdb=" N ARG J 423 " --> pdb=" O PRO J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 424 through 441 removed outlier: 3.826A pdb=" N ARG J 428 " --> pdb=" O TYR J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL J 446 " --> pdb=" O GLN J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 471 Processing helix chain 'J' and resid 479 through 482 Processing helix chain 'J' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU J 500 " --> pdb=" O GLU J 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 63 through 75 removed outlier: 4.404A pdb=" N HIS K 67 " --> pdb=" O TYR K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA K 253 " --> pdb=" O GLY K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR K 269 " --> pdb=" O LEU K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA K 278 " --> pdb=" O ILE K 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 315 Processing helix chain 'K' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA K 353 " --> pdb=" O SER K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 393 Processing helix chain 'K' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG K 423 " --> pdb=" O PRO K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG K 428 " --> pdb=" O TYR K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL K 446 " --> pdb=" O GLN K 443 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 471 Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 494 through 500 removed outlier: 3.868A pdb=" N LEU K 500 " --> pdb=" O GLU K 496 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 63 through 75 removed outlier: 4.406A pdb=" N HIS L 67 " --> pdb=" O TYR L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA L 253 " --> pdb=" O GLY L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR L 269 " --> pdb=" O LEU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA L 278 " --> pdb=" O ILE L 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL L 279 " --> pdb=" O ASP L 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 315 Processing helix chain 'L' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA L 353 " --> pdb=" O SER L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 393 Processing helix chain 'L' and resid 419 through 423 removed outlier: 3.946A pdb=" N ARG L 423 " --> pdb=" O PRO L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 424 through 441 removed outlier: 3.826A pdb=" N ARG L 428 " --> pdb=" O TYR L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL L 446 " --> pdb=" O GLN L 443 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 471 Processing helix chain 'L' and resid 479 through 482 Processing helix chain 'L' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU L 500 " --> pdb=" O GLU L 496 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 57 Processing helix chain 'M' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS M 67 " --> pdb=" O TYR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA M 253 " --> pdb=" O GLY M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR M 269 " --> pdb=" O LEU M 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA M 278 " --> pdb=" O ILE M 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL M 279 " --> pdb=" O ASP M 275 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 315 Processing helix chain 'M' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA M 353 " --> pdb=" O SER M 349 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 393 Processing helix chain 'M' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG M 423 " --> pdb=" O PRO M 420 " (cutoff:3.500A) Processing helix chain 'M' and resid 424 through 441 removed outlier: 3.824A pdb=" N ARG M 428 " --> pdb=" O TYR M 424 " (cutoff:3.500A) Processing helix chain 'M' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL M 446 " --> pdb=" O GLN M 443 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 471 Processing helix chain 'M' and resid 479 through 482 Processing helix chain 'M' and resid 494 through 500 removed outlier: 3.868A pdb=" N LEU M 500 " --> pdb=" O GLU M 496 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 57 Processing helix chain 'N' and resid 63 through 75 removed outlier: 4.403A pdb=" N HIS N 67 " --> pdb=" O TYR N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA N 253 " --> pdb=" O GLY N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR N 269 " --> pdb=" O LEU N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA N 278 " --> pdb=" O ILE N 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL N 279 " --> pdb=" O ASP N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 315 Processing helix chain 'N' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA N 353 " --> pdb=" O SER N 349 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 393 Processing helix chain 'N' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG N 423 " --> pdb=" O PRO N 420 " (cutoff:3.500A) Processing helix chain 'N' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG N 428 " --> pdb=" O TYR N 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL N 446 " --> pdb=" O GLN N 443 " (cutoff:3.500A) Processing helix chain 'N' and resid 451 through 471 Processing helix chain 'N' and resid 479 through 482 Processing helix chain 'N' and resid 494 through 500 removed outlier: 3.868A pdb=" N LEU N 500 " --> pdb=" O GLU N 496 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 57 Processing helix chain 'O' and resid 63 through 75 removed outlier: 4.404A pdb=" N HIS O 67 " --> pdb=" O TYR O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA O 253 " --> pdb=" O GLY O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR O 269 " --> pdb=" O LEU O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 274 through 294 removed outlier: 4.143A pdb=" N ALA O 278 " --> pdb=" O ILE O 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL O 279 " --> pdb=" O ASP O 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 315 Processing helix chain 'O' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA O 353 " --> pdb=" O SER O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 393 Processing helix chain 'O' and resid 419 through 423 removed outlier: 3.946A pdb=" N ARG O 423 " --> pdb=" O PRO O 420 " (cutoff:3.500A) Processing helix chain 'O' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG O 428 " --> pdb=" O TYR O 424 " (cutoff:3.500A) Processing helix chain 'O' and resid 442 through 446 removed outlier: 3.644A pdb=" N VAL O 446 " --> pdb=" O GLN O 443 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 471 Processing helix chain 'O' and resid 479 through 482 Processing helix chain 'O' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU O 500 " --> pdb=" O GLU O 496 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 57 Processing helix chain 'P' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS P 67 " --> pdb=" O TYR P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA P 253 " --> pdb=" O GLY P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 294 removed outlier: 4.143A pdb=" N ALA P 278 " --> pdb=" O ILE P 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL P 279 " --> pdb=" O ASP P 275 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 315 Processing helix chain 'P' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA P 353 " --> pdb=" O SER P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 385 through 393 Processing helix chain 'P' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG P 423 " --> pdb=" O PRO P 420 " (cutoff:3.500A) Processing helix chain 'P' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG P 428 " --> pdb=" O TYR P 424 " (cutoff:3.500A) Processing helix chain 'P' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL P 446 " --> pdb=" O GLN P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 451 through 471 Processing helix chain 'P' and resid 479 through 482 Processing helix chain 'P' and resid 494 through 500 removed outlier: 3.868A pdb=" N LEU P 500 " --> pdb=" O GLU P 496 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 57 Processing helix chain 'Q' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS Q 67 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA Q 253 " --> pdb=" O GLY Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA Q 278 " --> pdb=" O ILE Q 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL Q 279 " --> pdb=" O ASP Q 275 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 315 Processing helix chain 'Q' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA Q 353 " --> pdb=" O SER Q 349 " (cutoff:3.500A) Processing helix chain 'Q' and resid 385 through 393 Processing helix chain 'Q' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG Q 423 " --> pdb=" O PRO Q 420 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG Q 428 " --> pdb=" O TYR Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 442 through 446 removed outlier: 3.644A pdb=" N VAL Q 446 " --> pdb=" O GLN Q 443 " (cutoff:3.500A) Processing helix chain 'Q' and resid 451 through 471 Processing helix chain 'Q' and resid 479 through 482 Processing helix chain 'Q' and resid 494 through 500 removed outlier: 3.868A pdb=" N LEU Q 500 " --> pdb=" O GLU Q 496 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 57 Processing helix chain 'R' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS R 67 " --> pdb=" O TYR R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA R 253 " --> pdb=" O GLY R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA R 278 " --> pdb=" O ILE R 274 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL R 279 " --> pdb=" O ASP R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 315 Processing helix chain 'R' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA R 353 " --> pdb=" O SER R 349 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 393 Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG R 423 " --> pdb=" O PRO R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG R 428 " --> pdb=" O TYR R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL R 446 " --> pdb=" O GLN R 443 " (cutoff:3.500A) Processing helix chain 'R' and resid 451 through 471 Processing helix chain 'R' and resid 479 through 482 Processing helix chain 'R' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU R 500 " --> pdb=" O GLU R 496 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 57 Processing helix chain 'S' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS S 67 " --> pdb=" O TYR S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA S 253 " --> pdb=" O GLY S 250 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR S 269 " --> pdb=" O LEU S 265 " (cutoff:3.500A) Processing helix chain 'S' and resid 274 through 294 removed outlier: 4.143A pdb=" N ALA S 278 " --> pdb=" O ILE S 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL S 279 " --> pdb=" O ASP S 275 " (cutoff:3.500A) Processing helix chain 'S' and resid 310 through 315 Processing helix chain 'S' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA S 353 " --> pdb=" O SER S 349 " (cutoff:3.500A) Processing helix chain 'S' and resid 385 through 393 Processing helix chain 'S' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG S 423 " --> pdb=" O PRO S 420 " (cutoff:3.500A) Processing helix chain 'S' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG S 428 " --> pdb=" O TYR S 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL S 446 " --> pdb=" O GLN S 443 " (cutoff:3.500A) Processing helix chain 'S' and resid 451 through 471 Processing helix chain 'S' and resid 479 through 482 Processing helix chain 'S' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU S 500 " --> pdb=" O GLU S 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 57 Processing helix chain 'T' and resid 63 through 75 removed outlier: 4.404A pdb=" N HIS T 67 " --> pdb=" O TYR T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA T 253 " --> pdb=" O GLY T 250 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR T 269 " --> pdb=" O LEU T 265 " (cutoff:3.500A) Processing helix chain 'T' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA T 278 " --> pdb=" O ILE T 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL T 279 " --> pdb=" O ASP T 275 " (cutoff:3.500A) Processing helix chain 'T' and resid 310 through 315 Processing helix chain 'T' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA T 353 " --> pdb=" O SER T 349 " (cutoff:3.500A) Processing helix chain 'T' and resid 385 through 393 Processing helix chain 'T' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG T 423 " --> pdb=" O PRO T 420 " (cutoff:3.500A) Processing helix chain 'T' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG T 428 " --> pdb=" O TYR T 424 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL T 446 " --> pdb=" O GLN T 443 " (cutoff:3.500A) Processing helix chain 'T' and resid 451 through 471 Processing helix chain 'T' and resid 479 through 482 Processing helix chain 'T' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU T 500 " --> pdb=" O GLU T 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 57 Processing helix chain 'U' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS U 67 " --> pdb=" O TYR U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA U 253 " --> pdb=" O GLY U 250 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR U 269 " --> pdb=" O LEU U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 274 through 294 removed outlier: 4.143A pdb=" N ALA U 278 " --> pdb=" O ILE U 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL U 279 " --> pdb=" O ASP U 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 310 through 315 Processing helix chain 'U' and resid 349 through 363 removed outlier: 3.739A pdb=" N ALA U 353 " --> pdb=" O SER U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 385 through 393 Processing helix chain 'U' and resid 419 through 423 removed outlier: 3.946A pdb=" N ARG U 423 " --> pdb=" O PRO U 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG U 428 " --> pdb=" O TYR U 424 " (cutoff:3.500A) Processing helix chain 'U' and resid 442 through 446 removed outlier: 3.644A pdb=" N VAL U 446 " --> pdb=" O GLN U 443 " (cutoff:3.500A) Processing helix chain 'U' and resid 451 through 471 Processing helix chain 'U' and resid 479 through 482 Processing helix chain 'U' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU U 500 " --> pdb=" O GLU U 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 57 Processing helix chain 'V' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS V 67 " --> pdb=" O TYR V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA V 253 " --> pdb=" O GLY V 250 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR V 269 " --> pdb=" O LEU V 265 " (cutoff:3.500A) Processing helix chain 'V' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA V 278 " --> pdb=" O ILE V 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL V 279 " --> pdb=" O ASP V 275 " (cutoff:3.500A) Processing helix chain 'V' and resid 310 through 315 Processing helix chain 'V' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA V 353 " --> pdb=" O SER V 349 " (cutoff:3.500A) Processing helix chain 'V' and resid 385 through 393 Processing helix chain 'V' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG V 423 " --> pdb=" O PRO V 420 " (cutoff:3.500A) Processing helix chain 'V' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG V 428 " --> pdb=" O TYR V 424 " (cutoff:3.500A) Processing helix chain 'V' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL V 446 " --> pdb=" O GLN V 443 " (cutoff:3.500A) Processing helix chain 'V' and resid 451 through 471 Processing helix chain 'V' and resid 479 through 482 Processing helix chain 'V' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU V 500 " --> pdb=" O GLU V 496 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 57 Processing helix chain 'W' and resid 63 through 75 removed outlier: 4.404A pdb=" N HIS W 67 " --> pdb=" O TYR W 63 " (cutoff:3.500A) Processing helix chain 'W' and resid 250 through 254 removed outlier: 3.802A pdb=" N ALA W 253 " --> pdb=" O GLY W 250 " (cutoff:3.500A) Processing helix chain 'W' and resid 265 through 272 removed outlier: 3.662A pdb=" N TYR W 269 " --> pdb=" O LEU W 265 " (cutoff:3.500A) Processing helix chain 'W' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA W 278 " --> pdb=" O ILE W 274 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL W 279 " --> pdb=" O ASP W 275 " (cutoff:3.500A) Processing helix chain 'W' and resid 310 through 315 Processing helix chain 'W' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA W 353 " --> pdb=" O SER W 349 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 393 Processing helix chain 'W' and resid 419 through 423 removed outlier: 3.947A pdb=" N ARG W 423 " --> pdb=" O PRO W 420 " (cutoff:3.500A) Processing helix chain 'W' and resid 424 through 441 removed outlier: 3.824A pdb=" N ARG W 428 " --> pdb=" O TYR W 424 " (cutoff:3.500A) Processing helix chain 'W' and resid 442 through 446 removed outlier: 3.645A pdb=" N VAL W 446 " --> pdb=" O GLN W 443 " (cutoff:3.500A) Processing helix chain 'W' and resid 451 through 471 Processing helix chain 'W' and resid 479 through 482 Processing helix chain 'W' and resid 494 through 500 removed outlier: 3.868A pdb=" N LEU W 500 " --> pdb=" O GLU W 496 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 57 Processing helix chain 'X' and resid 63 through 75 removed outlier: 4.405A pdb=" N HIS X 67 " --> pdb=" O TYR X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 250 through 254 removed outlier: 3.803A pdb=" N ALA X 253 " --> pdb=" O GLY X 250 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 272 removed outlier: 3.661A pdb=" N TYR X 269 " --> pdb=" O LEU X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 274 through 294 removed outlier: 4.144A pdb=" N ALA X 278 " --> pdb=" O ILE X 274 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL X 279 " --> pdb=" O ASP X 275 " (cutoff:3.500A) Processing helix chain 'X' and resid 310 through 315 Processing helix chain 'X' and resid 349 through 363 removed outlier: 3.738A pdb=" N ALA X 353 " --> pdb=" O SER X 349 " (cutoff:3.500A) Processing helix chain 'X' and resid 385 through 393 Processing helix chain 'X' and resid 419 through 423 removed outlier: 3.946A pdb=" N ARG X 423 " --> pdb=" O PRO X 420 " (cutoff:3.500A) Processing helix chain 'X' and resid 424 through 441 removed outlier: 3.825A pdb=" N ARG X 428 " --> pdb=" O TYR X 424 " (cutoff:3.500A) Processing helix chain 'X' and resid 442 through 446 removed outlier: 3.644A pdb=" N VAL X 446 " --> pdb=" O GLN X 443 " (cutoff:3.500A) Processing helix chain 'X' and resid 451 through 471 Processing helix chain 'X' and resid 479 through 482 Processing helix chain 'X' and resid 494 through 500 removed outlier: 3.867A pdb=" N LEU X 500 " --> pdb=" O GLU X 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA A 29 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 28 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA A 261 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA A 30 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 260 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 299 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN A 398 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU A 328 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE A 400 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 337 Processing sheet with id=AA4, first strand: chain 'A' and resid 484 through 487 removed outlier: 6.601A pdb=" N ILE A 507 " --> pdb=" O ALA H 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 502 through 503 removed outlier: 5.859A pdb=" N VAL A 503 " --> pdb=" O ILE H 519 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 517 through 520 removed outlier: 6.462A pdb=" N VAL A 518 " --> pdb=" O TYR F 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 11 Processing sheet with id=AA8, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA B 29 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 28 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA B 261 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA B 30 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 260 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 299 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN B 398 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU B 328 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE B 400 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 333 through 337 Processing sheet with id=AB1, first strand: chain 'B' and resid 484 through 487 removed outlier: 6.602A pdb=" N ILE B 507 " --> pdb=" O ALA I 523 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 502 through 503 removed outlier: 5.861A pdb=" N VAL B 503 " --> pdb=" O ILE I 519 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 8 through 11 Processing sheet with id=AB4, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.750A pdb=" N ALA C 29 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 28 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA C 261 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA C 30 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 260 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE C 299 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN C 398 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU C 328 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE C 400 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 333 through 337 Processing sheet with id=AB6, first strand: chain 'C' and resid 484 through 487 removed outlier: 6.606A pdb=" N ILE C 507 " --> pdb=" O ALA J 523 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 502 through 503 removed outlier: 5.864A pdb=" N VAL C 503 " --> pdb=" O ILE J 519 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 8 through 11 Processing sheet with id=AB9, first strand: chain 'D' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA D 29 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 28 " --> pdb=" O MET D 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA D 261 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA D 30 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 260 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 299 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN D 398 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU D 328 " --> pdb=" O ASN D 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE D 400 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 333 through 337 Processing sheet with id=AC2, first strand: chain 'D' and resid 484 through 487 removed outlier: 6.608A pdb=" N ILE D 507 " --> pdb=" O ALA K 523 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 502 through 503 removed outlier: 5.866A pdb=" N VAL D 503 " --> pdb=" O ILE K 519 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 8 through 11 Processing sheet with id=AC5, first strand: chain 'E' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA E 29 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL E 28 " --> pdb=" O MET E 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA E 261 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA E 30 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL E 260 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE E 299 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN E 398 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU E 328 " --> pdb=" O ASN E 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE E 400 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 333 through 337 Processing sheet with id=AC7, first strand: chain 'E' and resid 484 through 487 removed outlier: 6.607A pdb=" N ILE E 507 " --> pdb=" O ALA L 523 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 502 through 503 removed outlier: 5.865A pdb=" N VAL E 503 " --> pdb=" O ILE L 519 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 44 through 46 removed outlier: 3.750A pdb=" N ALA F 29 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL F 28 " --> pdb=" O MET F 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA F 261 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA F 30 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL F 260 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE F 299 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN F 398 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU F 328 " --> pdb=" O ASN F 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE F 400 " --> pdb=" O LEU F 328 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 333 through 337 Processing sheet with id=AD2, first strand: chain 'F' and resid 484 through 487 removed outlier: 6.604A pdb=" N ILE F 507 " --> pdb=" O ALA G 523 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 502 through 503 removed outlier: 5.862A pdb=" N VAL F 503 " --> pdb=" O ILE G 519 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL G 518 " --> pdb=" O TYR L 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA G 29 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL G 28 " --> pdb=" O MET G 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA G 261 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA G 30 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL G 260 " --> pdb=" O VAL G 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE G 299 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN G 398 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU G 328 " --> pdb=" O ASN G 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE G 400 " --> pdb=" O LEU G 328 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 333 through 337 Processing sheet with id=AD6, first strand: chain 'G' and resid 484 through 487 removed outlier: 6.618A pdb=" N ILE G 507 " --> pdb=" O ALA M 523 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 502 through 503 removed outlier: 5.877A pdb=" N VAL G 503 " --> pdb=" O ILE M 519 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL M 518 " --> pdb=" O TYR R 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA H 29 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL H 28 " --> pdb=" O MET H 259 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ALA H 261 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA H 30 " --> pdb=" O ALA H 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 260 " --> pdb=" O VAL H 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE H 299 " --> pdb=" O VAL H 260 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ASN H 398 " --> pdb=" O ALA H 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU H 328 " --> pdb=" O ASN H 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE H 400 " --> pdb=" O LEU H 328 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 333 through 337 Processing sheet with id=AE1, first strand: chain 'H' and resid 484 through 487 removed outlier: 6.609A pdb=" N ILE H 507 " --> pdb=" O ALA N 523 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 502 through 503 removed outlier: 5.869A pdb=" N VAL H 503 " --> pdb=" O ILE N 519 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 44 through 46 removed outlier: 3.750A pdb=" N ALA I 29 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL I 28 " --> pdb=" O MET I 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA I 261 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA I 30 " --> pdb=" O ALA I 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL I 260 " --> pdb=" O VAL I 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE I 299 " --> pdb=" O VAL I 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN I 398 " --> pdb=" O ALA I 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU I 328 " --> pdb=" O ASN I 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE I 400 " --> pdb=" O LEU I 328 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 333 through 337 Processing sheet with id=AE5, first strand: chain 'I' and resid 484 through 487 removed outlier: 6.608A pdb=" N ILE I 507 " --> pdb=" O ALA O 523 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 502 through 503 removed outlier: 5.866A pdb=" N VAL I 503 " --> pdb=" O ILE O 519 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA J 29 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL J 28 " --> pdb=" O MET J 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA J 261 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA J 30 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL J 260 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE J 299 " --> pdb=" O VAL J 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN J 398 " --> pdb=" O ALA J 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU J 328 " --> pdb=" O ASN J 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE J 400 " --> pdb=" O LEU J 328 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 333 through 337 Processing sheet with id=AE9, first strand: chain 'J' and resid 484 through 487 removed outlier: 6.613A pdb=" N ILE J 507 " --> pdb=" O ALA P 523 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 502 through 503 removed outlier: 5.871A pdb=" N VAL J 503 " --> pdb=" O ILE P 519 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA K 29 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL K 28 " --> pdb=" O MET K 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA K 261 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA K 30 " --> pdb=" O ALA K 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL K 260 " --> pdb=" O VAL K 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE K 299 " --> pdb=" O VAL K 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN K 398 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU K 328 " --> pdb=" O ASN K 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE K 400 " --> pdb=" O LEU K 328 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 333 through 337 Processing sheet with id=AF4, first strand: chain 'K' and resid 484 through 487 removed outlier: 6.622A pdb=" N ILE K 507 " --> pdb=" O ALA Q 523 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 502 through 503 removed outlier: 5.879A pdb=" N VAL K 503 " --> pdb=" O ILE Q 519 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 44 through 46 removed outlier: 3.750A pdb=" N ALA L 29 " --> pdb=" O ALA L 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL L 28 " --> pdb=" O MET L 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA L 261 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA L 30 " --> pdb=" O ALA L 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL L 260 " --> pdb=" O VAL L 297 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE L 299 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN L 398 " --> pdb=" O ALA L 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU L 328 " --> pdb=" O ASN L 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE L 400 " --> pdb=" O LEU L 328 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 333 through 337 Processing sheet with id=AF8, first strand: chain 'L' and resid 484 through 487 removed outlier: 6.624A pdb=" N ILE L 507 " --> pdb=" O ALA R 523 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 502 through 503 removed outlier: 5.882A pdb=" N VAL L 503 " --> pdb=" O ILE R 519 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA M 29 " --> pdb=" O ALA M 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL M 28 " --> pdb=" O MET M 259 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ALA M 261 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA M 30 " --> pdb=" O ALA M 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL M 260 " --> pdb=" O VAL M 297 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE M 299 " --> pdb=" O VAL M 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN M 398 " --> pdb=" O ALA M 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU M 328 " --> pdb=" O ASN M 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE M 400 " --> pdb=" O LEU M 328 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 333 through 337 Processing sheet with id=AG3, first strand: chain 'M' and resid 484 through 487 removed outlier: 6.598A pdb=" N ILE M 507 " --> pdb=" O ALA T 523 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 502 through 503 removed outlier: 5.852A pdb=" N VAL M 503 " --> pdb=" O ILE T 519 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA N 29 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL N 28 " --> pdb=" O MET N 259 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ALA N 261 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA N 30 " --> pdb=" O ALA N 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL N 260 " --> pdb=" O VAL N 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE N 299 " --> pdb=" O VAL N 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN N 398 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU N 328 " --> pdb=" O ASN N 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE N 400 " --> pdb=" O LEU N 328 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 333 through 337 Processing sheet with id=AG7, first strand: chain 'N' and resid 484 through 487 removed outlier: 6.608A pdb=" N ILE N 507 " --> pdb=" O ALA U 523 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 502 through 503 removed outlier: 5.862A pdb=" N VAL N 503 " --> pdb=" O ILE U 519 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 44 through 46 removed outlier: 3.750A pdb=" N ALA O 29 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL O 28 " --> pdb=" O MET O 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA O 261 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA O 30 " --> pdb=" O ALA O 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL O 260 " --> pdb=" O VAL O 297 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE O 299 " --> pdb=" O VAL O 260 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ASN O 398 " --> pdb=" O ALA O 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU O 328 " --> pdb=" O ASN O 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE O 400 " --> pdb=" O LEU O 328 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 333 through 337 Processing sheet with id=AH2, first strand: chain 'O' and resid 484 through 487 removed outlier: 6.607A pdb=" N ILE O 507 " --> pdb=" O ALA V 523 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 502 through 503 removed outlier: 5.860A pdb=" N VAL O 503 " --> pdb=" O ILE V 519 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA P 29 " --> pdb=" O ALA P 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL P 28 " --> pdb=" O MET P 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA P 261 " --> pdb=" O VAL P 28 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA P 30 " --> pdb=" O ALA P 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL P 260 " --> pdb=" O VAL P 297 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE P 299 " --> pdb=" O VAL P 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN P 398 " --> pdb=" O ALA P 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU P 328 " --> pdb=" O ASN P 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE P 400 " --> pdb=" O LEU P 328 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 333 through 337 Processing sheet with id=AH6, first strand: chain 'P' and resid 484 through 487 removed outlier: 6.592A pdb=" N ILE P 507 " --> pdb=" O ALA W 523 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 502 through 503 removed outlier: 5.847A pdb=" N VAL P 503 " --> pdb=" O ILE W 519 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA Q 29 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL Q 28 " --> pdb=" O MET Q 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA Q 261 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA Q 30 " --> pdb=" O ALA Q 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL Q 260 " --> pdb=" O VAL Q 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE Q 299 " --> pdb=" O VAL Q 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN Q 398 " --> pdb=" O ALA Q 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU Q 328 " --> pdb=" O ASN Q 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE Q 400 " --> pdb=" O LEU Q 328 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 333 through 337 Processing sheet with id=AI1, first strand: chain 'Q' and resid 484 through 487 removed outlier: 6.582A pdb=" N ILE Q 507 " --> pdb=" O ALA X 523 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 502 through 503 removed outlier: 5.839A pdb=" N VAL Q 503 " --> pdb=" O ILE X 519 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA R 29 " --> pdb=" O ALA R 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL R 28 " --> pdb=" O MET R 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA R 261 " --> pdb=" O VAL R 28 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA R 30 " --> pdb=" O ALA R 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL R 260 " --> pdb=" O VAL R 297 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE R 299 " --> pdb=" O VAL R 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN R 398 " --> pdb=" O ALA R 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU R 328 " --> pdb=" O ASN R 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE R 400 " --> pdb=" O LEU R 328 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 333 through 337 Processing sheet with id=AI5, first strand: chain 'R' and resid 484 through 487 removed outlier: 6.585A pdb=" N ILE R 507 " --> pdb=" O ALA S 523 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 502 through 503 removed outlier: 5.841A pdb=" N VAL R 503 " --> pdb=" O ILE S 519 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL S 518 " --> pdb=" O TYR X 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'S' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA S 29 " --> pdb=" O ALA S 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL S 28 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA S 261 " --> pdb=" O VAL S 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA S 30 " --> pdb=" O ALA S 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL S 260 " --> pdb=" O VAL S 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE S 299 " --> pdb=" O VAL S 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN S 398 " --> pdb=" O ALA S 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU S 328 " --> pdb=" O ASN S 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE S 400 " --> pdb=" O LEU S 328 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'S' and resid 333 through 337 Processing sheet with id=AI9, first strand: chain 'S' and resid 484 through 487 Processing sheet with id=AJ1, first strand: chain 'T' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA T 29 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL T 28 " --> pdb=" O MET T 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA T 261 " --> pdb=" O VAL T 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA T 30 " --> pdb=" O ALA T 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL T 260 " --> pdb=" O VAL T 297 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE T 299 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ASN T 398 " --> pdb=" O ALA T 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU T 328 " --> pdb=" O ASN T 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE T 400 " --> pdb=" O LEU T 328 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'T' and resid 333 through 337 Processing sheet with id=AJ3, first strand: chain 'T' and resid 484 through 487 Processing sheet with id=AJ4, first strand: chain 'U' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA U 29 " --> pdb=" O ALA U 79 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL U 28 " --> pdb=" O MET U 259 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ALA U 261 " --> pdb=" O VAL U 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA U 30 " --> pdb=" O ALA U 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL U 260 " --> pdb=" O VAL U 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE U 299 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N ASN U 398 " --> pdb=" O ALA U 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU U 328 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE U 400 " --> pdb=" O LEU U 328 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'U' and resid 333 through 337 Processing sheet with id=AJ6, first strand: chain 'U' and resid 484 through 487 Processing sheet with id=AJ7, first strand: chain 'V' and resid 44 through 46 removed outlier: 3.751A pdb=" N ALA V 29 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL V 28 " --> pdb=" O MET V 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA V 261 " --> pdb=" O VAL V 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA V 30 " --> pdb=" O ALA V 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL V 260 " --> pdb=" O VAL V 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE V 299 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ASN V 398 " --> pdb=" O ALA V 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU V 328 " --> pdb=" O ASN V 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE V 400 " --> pdb=" O LEU V 328 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'V' and resid 333 through 337 Processing sheet with id=AJ9, first strand: chain 'V' and resid 484 through 487 Processing sheet with id=AK1, first strand: chain 'W' and resid 44 through 46 removed outlier: 3.750A pdb=" N ALA W 29 " --> pdb=" O ALA W 79 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL W 28 " --> pdb=" O MET W 259 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ALA W 261 " --> pdb=" O VAL W 28 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA W 30 " --> pdb=" O ALA W 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL W 260 " --> pdb=" O VAL W 297 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE W 299 " --> pdb=" O VAL W 260 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ASN W 398 " --> pdb=" O ALA W 326 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU W 328 " --> pdb=" O ASN W 398 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE W 400 " --> pdb=" O LEU W 328 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'W' and resid 333 through 337 Processing sheet with id=AK3, first strand: chain 'W' and resid 484 through 487 Processing sheet with id=AK4, first strand: chain 'X' and resid 44 through 46 removed outlier: 3.750A pdb=" N ALA X 29 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL X 28 " --> pdb=" O MET X 259 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA X 261 " --> pdb=" O VAL X 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA X 30 " --> pdb=" O ALA X 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL X 260 " --> pdb=" O VAL X 297 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE X 299 " --> pdb=" O VAL X 260 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N ASN X 398 " --> pdb=" O ALA X 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU X 328 " --> pdb=" O ASN X 398 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE X 400 " --> pdb=" O LEU X 328 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'X' and resid 333 through 337 Processing sheet with id=AK6, first strand: chain 'X' and resid 484 through 487 2748 hydrogen bonds defined for protein. 7596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.50 Time building geometry restraints manager: 22.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 22920 1.35 - 1.47: 16906 1.47 - 1.58: 30038 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 70104 Sorted by residual: bond pdb=" N VAL I 378 " pdb=" CA VAL I 378 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.06e-02 8.90e+03 1.09e+01 bond pdb=" N VAL L 378 " pdb=" CA VAL L 378 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.06e-02 8.90e+03 1.07e+01 bond pdb=" N VAL R 374 " pdb=" CA VAL R 374 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.30e+00 bond pdb=" N VAL U 378 " pdb=" CA VAL U 378 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.13e+00 bond pdb=" N VAL X 378 " pdb=" CA VAL X 378 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.12e+00 ... (remaining 70099 not shown) Histogram of bond angle deviations from ideal: 100.87 - 107.56: 3408 107.56 - 114.25: 38125 114.25 - 120.94: 31456 120.94 - 127.63: 21891 127.63 - 134.32: 760 Bond angle restraints: 95640 Sorted by residual: angle pdb=" CA VAL O 374 " pdb=" C VAL O 374 " pdb=" O VAL O 374 " ideal model delta sigma weight residual 122.63 118.19 4.44 8.70e-01 1.32e+00 2.60e+01 angle pdb=" CA VAL T 374 " pdb=" C VAL T 374 " pdb=" O VAL T 374 " ideal model delta sigma weight residual 122.63 118.29 4.34 8.70e-01 1.32e+00 2.49e+01 angle pdb=" CA VAL U 378 " pdb=" C VAL U 378 " pdb=" O VAL U 378 " ideal model delta sigma weight residual 120.30 116.53 3.77 9.40e-01 1.13e+00 1.61e+01 angle pdb=" CA VAL X 378 " pdb=" C VAL X 378 " pdb=" O VAL X 378 " ideal model delta sigma weight residual 120.30 116.57 3.73 9.40e-01 1.13e+00 1.57e+01 angle pdb=" CB ARG K 375 " pdb=" CG ARG K 375 " pdb=" CD ARG K 375 " ideal model delta sigma weight residual 111.30 102.99 8.31 2.30e+00 1.89e-01 1.31e+01 ... (remaining 95635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 35670 17.98 - 35.95: 3909 35.95 - 53.93: 969 53.93 - 71.90: 276 71.90 - 89.88: 120 Dihedral angle restraints: 40944 sinusoidal: 15888 harmonic: 25056 Sorted by residual: dihedral pdb=" CB GLU G 277 " pdb=" CG GLU G 277 " pdb=" CD GLU G 277 " pdb=" OE1 GLU G 277 " ideal model delta sinusoidal sigma weight residual 0.00 -89.88 89.88 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU P 277 " pdb=" CG GLU P 277 " pdb=" CD GLU P 277 " pdb=" OE1 GLU P 277 " ideal model delta sinusoidal sigma weight residual 0.00 -89.87 89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU W 277 " pdb=" CG GLU W 277 " pdb=" CD GLU W 277 " pdb=" OE1 GLU W 277 " ideal model delta sinusoidal sigma weight residual 0.00 -89.85 89.85 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 40941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 7551 0.046 - 0.092: 1691 0.092 - 0.138: 936 0.138 - 0.183: 35 0.183 - 0.229: 11 Chirality restraints: 10224 Sorted by residual: chirality pdb=" CA ARG H 375 " pdb=" N ARG H 375 " pdb=" C ARG H 375 " pdb=" CB ARG H 375 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ARG K 375 " pdb=" N ARG K 375 " pdb=" C ARG K 375 " pdb=" CB ARG K 375 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ARG O 375 " pdb=" N ARG O 375 " pdb=" C ARG O 375 " pdb=" CB ARG O 375 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 10221 not shown) Planarity restraints: 12648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL W 378 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C VAL W 378 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL W 378 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP W 379 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL T 378 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C VAL T 378 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL T 378 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP T 379 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO O 302 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO O 303 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO O 303 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO O 303 " 0.021 5.00e-02 4.00e+02 ... (remaining 12645 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 169 2.35 - 2.98: 34246 2.98 - 3.62: 91124 3.62 - 4.26: 136316 4.26 - 4.90: 243602 Nonbonded interactions: 505457 Sorted by model distance: nonbonded pdb=" O GLU V 12 " pdb=" O ARG W 521 " model vdw 1.708 3.040 nonbonded pdb=" O GLU Q 12 " pdb=" O ARG R 521 " model vdw 1.708 3.040 nonbonded pdb=" O GLU M 12 " pdb=" O ARG N 521 " model vdw 1.709 3.040 nonbonded pdb=" O GLU O 12 " pdb=" O ARG P 521 " model vdw 1.709 3.040 nonbonded pdb=" O GLU D 12 " pdb=" O ARG E 521 " model vdw 1.709 3.040 ... (remaining 505452 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 '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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 9.630 Check model and map are aligned: 0.800 Set scattering table: 0.510 Process input model: 141.840 Find NCS groups from input model: 3.730 Set up NCS constraints: 0.500 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: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.003 0.040 70104 Z= 0.185 Angle : 0.594 10.066 95640 Z= 0.343 Chirality : 0.048 0.229 10224 Planarity : 0.004 0.038 12648 Dihedral : 16.817 89.876 25056 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.03 % Allowed : 21.97 % Favored : 78.00 % 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: -0.58 (0.09), residues: 8712 helix: 1.75 (0.11), residues: 3000 sheet: 0.10 (0.16), residues: 1152 loop : -2.13 (0.09), residues: 4560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 411 HIS 0.001 0.000 HIS T 366 PHE 0.004 0.001 PHE U 336 TYR 0.009 0.001 TYR S 433 ARG 0.005 0.000 ARG T 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 942 time to evaluate : 6.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8967 (t) cc_final: 0.8681 (m) REVERT: A 295 ASP cc_start: 0.7617 (t0) cc_final: 0.7051 (t0) REVERT: B 506 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6622 (mt-10) REVERT: C 4 TYR cc_start: 0.8638 (m-80) cc_final: 0.8386 (m-80) REVERT: C 46 VAL cc_start: 0.8887 (t) cc_final: 0.8642 (m) REVERT: C 271 ARG cc_start: 0.6888 (ptm160) cc_final: 0.6459 (mtm110) REVERT: C 293 MET cc_start: 0.8339 (mmt) cc_final: 0.7980 (tpp) REVERT: C 295 ASP cc_start: 0.7480 (t0) cc_final: 0.7043 (t0) REVERT: D 46 VAL cc_start: 0.8976 (t) cc_final: 0.8691 (m) REVERT: D 295 ASP cc_start: 0.7587 (t0) cc_final: 0.7048 (t0) REVERT: E 506 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6619 (mt-10) REVERT: F 4 TYR cc_start: 0.8637 (m-80) cc_final: 0.8389 (m-80) REVERT: F 46 VAL cc_start: 0.8893 (t) cc_final: 0.8653 (m) REVERT: F 271 ARG cc_start: 0.6878 (ptm160) cc_final: 0.6443 (mtm110) REVERT: F 291 GLU cc_start: 0.6730 (tt0) cc_final: 0.6090 (tt0) REVERT: F 293 MET cc_start: 0.8307 (mmt) cc_final: 0.7978 (tpp) REVERT: F 295 ASP cc_start: 0.7490 (t0) cc_final: 0.7046 (t0) REVERT: G 291 GLU cc_start: 0.7647 (tp30) cc_final: 0.7288 (mm-30) REVERT: H 52 TYR cc_start: 0.8928 (t80) cc_final: 0.8699 (t80) REVERT: H 266 MET cc_start: 0.8633 (mmp) cc_final: 0.8229 (mmm) REVERT: H 291 GLU cc_start: 0.7587 (tp30) cc_final: 0.7115 (mm-30) REVERT: H 293 MET cc_start: 0.7991 (mmt) cc_final: 0.7787 (mmm) REVERT: I 52 TYR cc_start: 0.8732 (t80) cc_final: 0.8515 (t80) REVERT: I 254 ILE cc_start: 0.8394 (mm) cc_final: 0.8152 (mm) REVERT: I 291 GLU cc_start: 0.7616 (tp30) cc_final: 0.7262 (mm-30) REVERT: K 266 MET cc_start: 0.8632 (mmp) cc_final: 0.8236 (mmm) REVERT: L 52 TYR cc_start: 0.8726 (t80) cc_final: 0.8510 (t80) REVERT: L 254 ILE cc_start: 0.8395 (mm) cc_final: 0.8126 (mm) REVERT: L 291 GLU cc_start: 0.7615 (tp30) cc_final: 0.7187 (mm-30) REVERT: L 322 ASP cc_start: 0.8890 (p0) cc_final: 0.8591 (p0) REVERT: M 293 MET cc_start: 0.8209 (mmt) cc_final: 0.8006 (mmm) REVERT: M 442 THR cc_start: 0.7626 (m) cc_final: 0.7381 (m) REVERT: N 385 THR cc_start: 0.8178 (p) cc_final: 0.7903 (m) REVERT: N 499 ASP cc_start: 0.8383 (t0) cc_final: 0.8178 (t0) REVERT: O 4 TYR cc_start: 0.8637 (m-80) cc_final: 0.8403 (m-80) REVERT: O 58 ASP cc_start: 0.7372 (p0) cc_final: 0.7038 (p0) REVERT: O 259 MET cc_start: 0.8065 (ptt) cc_final: 0.7787 (ptp) REVERT: P 293 MET cc_start: 0.8194 (mmt) cc_final: 0.7978 (mmm) REVERT: Q 385 THR cc_start: 0.8174 (p) cc_final: 0.7914 (m) REVERT: Q 499 ASP cc_start: 0.8376 (t0) cc_final: 0.8167 (t0) REVERT: R 4 TYR cc_start: 0.8656 (m-80) cc_final: 0.8403 (m-80) REVERT: R 58 ASP cc_start: 0.7389 (p0) cc_final: 0.7045 (p0) REVERT: R 259 MET cc_start: 0.8039 (ptt) cc_final: 0.7738 (ptp) REVERT: R 374 VAL cc_start: 0.9297 (t) cc_final: 0.9024 (t) REVERT: S 256 GLU cc_start: 0.7766 (pm20) cc_final: 0.7539 (pm20) REVERT: S 259 MET cc_start: 0.7512 (ptt) cc_final: 0.7226 (mtm) REVERT: T 259 MET cc_start: 0.7441 (ptt) cc_final: 0.7220 (mtm) REVERT: T 295 ASP cc_start: 0.7687 (t0) cc_final: 0.7307 (t0) REVERT: T 322 ASP cc_start: 0.8549 (p0) cc_final: 0.6199 (t0) REVERT: U 256 GLU cc_start: 0.7607 (pm20) cc_final: 0.7406 (pm20) REVERT: U 322 ASP cc_start: 0.8547 (p0) cc_final: 0.6438 (t0) REVERT: V 256 GLU cc_start: 0.7782 (pm20) cc_final: 0.7575 (pm20) REVERT: W 259 MET cc_start: 0.7365 (ptt) cc_final: 0.7142 (mtm) REVERT: W 291 GLU cc_start: 0.5143 (tt0) cc_final: 0.4929 (tt0) REVERT: W 295 ASP cc_start: 0.7710 (t0) cc_final: 0.7332 (t0) REVERT: W 322 ASP cc_start: 0.8561 (p0) cc_final: 0.6203 (t0) REVERT: X 322 ASP cc_start: 0.8560 (p0) cc_final: 0.6449 (t0) outliers start: 2 outliers final: 1 residues processed: 944 average time/residue: 0.6278 time to fit residues: 1011.1224 Evaluate side-chains 544 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 543 time to evaluate : 6.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 375 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 729 optimal weight: 0.0370 chunk 654 optimal weight: 10.0000 chunk 363 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 441 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 677 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 chunk 411 optimal weight: 10.0000 chunk 504 optimal weight: 10.0000 chunk 784 optimal weight: 6.9990 overall best weight: 6.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 HIS E 289 HIS E 306 GLN I 289 HIS N 482 GLN O 289 HIS Q 482 GLN R 289 HIS T 289 HIS T 359 ASN U 289 HIS U 359 ASN W 289 HIS W 359 ASN X 289 HIS X 359 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 70104 Z= 0.353 Angle : 0.620 6.260 95640 Z= 0.326 Chirality : 0.050 0.157 10224 Planarity : 0.006 0.043 12648 Dihedral : 4.406 50.097 9772 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.16 % Allowed : 20.41 % Favored : 76.44 % 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: -0.70 (0.09), residues: 8712 helix: 1.57 (0.10), residues: 3072 sheet: 0.18 (0.15), residues: 1296 loop : -2.33 (0.09), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 411 HIS 0.008 0.001 HIS S 289 PHE 0.020 0.002 PHE N 447 TYR 0.025 0.002 TYR V 433 ARG 0.008 0.001 ARG P 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 569 time to evaluate : 6.089 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: A 51 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.6754 (mp10) REVERT: A 295 ASP cc_start: 0.7781 (t0) cc_final: 0.7143 (t0) REVERT: A 522 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8275 (mm) REVERT: B 51 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: C 4 TYR cc_start: 0.8891 (m-80) cc_final: 0.8648 (m-80) REVERT: C 51 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: C 271 ARG cc_start: 0.6869 (ptm160) cc_final: 0.6503 (mtm110) REVERT: C 295 ASP cc_start: 0.7658 (t0) cc_final: 0.7269 (t0) REVERT: D 51 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.6751 (mp10) REVERT: D 295 ASP cc_start: 0.7795 (t0) cc_final: 0.7173 (t0) REVERT: D 522 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8253 (mm) REVERT: E 51 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: F 4 TYR cc_start: 0.8897 (m-80) cc_final: 0.8664 (m-80) REVERT: F 51 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: F 271 ARG cc_start: 0.6859 (ptm160) cc_final: 0.6501 (mtm110) REVERT: F 295 ASP cc_start: 0.7674 (t0) cc_final: 0.7220 (t0) REVERT: F 487 LYS cc_start: 0.8229 (tptt) cc_final: 0.7773 (mtmm) REVERT: F 491 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6351 (mt-10) REVERT: G 34 LEU cc_start: 0.8926 (mp) cc_final: 0.8712 (mt) REVERT: G 51 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: G 291 GLU cc_start: 0.7789 (tp30) cc_final: 0.7386 (mm-30) REVERT: H 51 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: H 266 MET cc_start: 0.8712 (mmp) cc_final: 0.8437 (mmm) REVERT: H 291 GLU cc_start: 0.7573 (tp30) cc_final: 0.6992 (mm-30) REVERT: I 51 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: I 266 MET cc_start: 0.8769 (mmm) cc_final: 0.8566 (mmt) REVERT: I 270 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: I 291 GLU cc_start: 0.7706 (tp30) cc_final: 0.7246 (mm-30) REVERT: I 499 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7794 (t0) REVERT: I 521 ARG cc_start: 0.7904 (mmt180) cc_final: 0.7616 (mmm-85) REVERT: J 51 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: K 51 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: K 266 MET cc_start: 0.8775 (mmp) cc_final: 0.8552 (mmm) REVERT: L 51 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: L 270 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: L 291 GLU cc_start: 0.7732 (tp30) cc_final: 0.7283 (mm-30) REVERT: L 499 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7786 (t0) REVERT: L 521 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7615 (mmm-85) REVERT: M 506 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6992 (mt-10) REVERT: N 12 GLU cc_start: 0.6060 (mt-10) cc_final: 0.5735 (mm-30) REVERT: N 280 LYS cc_start: 0.8666 (tttp) cc_final: 0.8432 (tttt) REVERT: N 333 ILE cc_start: 0.9235 (mm) cc_final: 0.8939 (tt) REVERT: N 362 GLU cc_start: 0.7225 (mm-30) cc_final: 0.7016 (mm-30) REVERT: N 385 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7719 (m) REVERT: N 410 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9104 (t) REVERT: N 435 GLU cc_start: 0.7558 (tt0) cc_final: 0.7251 (tt0) REVERT: O 4 TYR cc_start: 0.8758 (m-80) cc_final: 0.8492 (m-80) REVERT: O 12 GLU cc_start: 0.6002 (mt-10) cc_final: 0.5788 (mm-30) REVERT: O 51 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8219 (mt0) REVERT: O 522 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8489 (mm) REVERT: P 506 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7000 (mt-10) REVERT: Q 12 GLU cc_start: 0.6080 (mt-10) cc_final: 0.5763 (mm-30) REVERT: Q 280 LYS cc_start: 0.8689 (tttp) cc_final: 0.8460 (tttt) REVERT: Q 333 ILE cc_start: 0.9231 (mm) cc_final: 0.8925 (tt) REVERT: Q 362 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6993 (mm-30) REVERT: Q 385 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7667 (m) REVERT: Q 410 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.9102 (t) REVERT: Q 435 GLU cc_start: 0.7542 (tt0) cc_final: 0.7239 (tt0) REVERT: R 4 TYR cc_start: 0.8767 (m-80) cc_final: 0.8519 (m-80) REVERT: R 12 GLU cc_start: 0.6003 (mt-10) cc_final: 0.5789 (mm-30) REVERT: R 522 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8511 (mm) REVERT: S 51 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: S 290 CYS cc_start: 0.7692 (m) cc_final: 0.7385 (m) REVERT: S 390 ASP cc_start: 0.7337 (m-30) cc_final: 0.6646 (m-30) REVERT: T 51 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: T 290 CYS cc_start: 0.7878 (m) cc_final: 0.7661 (m) REVERT: T 390 ASP cc_start: 0.7218 (m-30) cc_final: 0.6594 (m-30) REVERT: V 51 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: V 290 CYS cc_start: 0.7693 (m) cc_final: 0.7383 (m) REVERT: V 390 ASP cc_start: 0.7307 (m-30) cc_final: 0.6798 (m-30) REVERT: W 51 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: W 290 CYS cc_start: 0.7901 (m) cc_final: 0.7671 (m) REVERT: W 390 ASP cc_start: 0.7214 (m-30) cc_final: 0.6584 (m-30) outliers start: 222 outliers final: 111 residues processed: 763 average time/residue: 0.6213 time to fit residues: 813.0999 Evaluate side-chains 622 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 481 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 498 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 481 ASP Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 270 GLN Chi-restraints excluded: chain I residue 365 VAL Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 481 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 499 ASP Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 481 ASP Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 51 GLN Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain K residue 481 ASP Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 270 GLN Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 439 LEU Chi-restraints excluded: chain L residue 481 ASP Chi-restraints excluded: chain L residue 498 VAL Chi-restraints excluded: chain L residue 499 ASP Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 333 ILE Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 262 VAL Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 442 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 522 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 51 GLN Chi-restraints excluded: chain S residue 260 VAL Chi-restraints excluded: chain S residue 296 ARG Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 385 THR Chi-restraints excluded: chain S residue 439 LEU Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 522 LEU Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 301 ASP Chi-restraints excluded: chain V residue 375 ARG Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 260 VAL Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 410 VAL Chi-restraints excluded: chain X residue 260 VAL Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 522 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 436 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 653 optimal weight: 9.9990 chunk 534 optimal weight: 4.9990 chunk 216 optimal weight: 0.0670 chunk 786 optimal weight: 6.9990 chunk 849 optimal weight: 8.9990 chunk 700 optimal weight: 10.0000 chunk 779 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 630 optimal weight: 0.0370 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 482 GLN F 482 GLN L 289 HIS N 51 GLN Q 51 GLN R 51 GLN S 289 HIS V 289 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 70104 Z= 0.184 Angle : 0.519 6.489 95640 Z= 0.272 Chirality : 0.047 0.148 10224 Planarity : 0.004 0.040 12648 Dihedral : 4.201 44.485 9772 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.89 % Allowed : 20.15 % Favored : 76.96 % 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: -0.59 (0.09), residues: 8712 helix: 1.70 (0.10), residues: 3096 sheet: 0.17 (0.15), residues: 1296 loop : -2.29 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 49 HIS 0.003 0.001 HIS B 452 PHE 0.007 0.001 PHE P 447 TYR 0.018 0.001 TYR V 433 ARG 0.003 0.000 ARG P 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 544 time to evaluate : 6.044 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: A 51 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: A 295 ASP cc_start: 0.7824 (t0) cc_final: 0.7180 (t0) REVERT: A 306 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: B 51 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7708 (mt0) REVERT: B 295 ASP cc_start: 0.7707 (t0) cc_final: 0.7180 (t0) REVERT: C 51 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: C 295 ASP cc_start: 0.7533 (t0) cc_final: 0.7052 (t0) REVERT: C 306 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: D 51 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: D 295 ASP cc_start: 0.7852 (t0) cc_final: 0.7222 (t0) REVERT: D 306 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: E 51 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: E 292 LEU cc_start: 0.8391 (mt) cc_final: 0.7918 (mt) REVERT: E 295 ASP cc_start: 0.7768 (t0) cc_final: 0.7247 (t0) REVERT: F 4 TYR cc_start: 0.8875 (m-80) cc_final: 0.8674 (m-80) REVERT: F 51 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: F 295 ASP cc_start: 0.7498 (t0) cc_final: 0.7039 (t0) REVERT: F 306 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: G 48 ASN cc_start: 0.7561 (t0) cc_final: 0.7216 (t0) REVERT: G 51 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: G 291 GLU cc_start: 0.7692 (tp30) cc_final: 0.7283 (mm-30) REVERT: G 306 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: G 521 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7702 (mmt180) REVERT: H 48 ASN cc_start: 0.7541 (t0) cc_final: 0.7247 (t0) REVERT: H 51 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: H 306 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7647 (mt0) REVERT: I 51 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: I 266 MET cc_start: 0.8827 (mmm) cc_final: 0.8577 (mmt) REVERT: I 270 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: I 291 GLU cc_start: 0.7685 (tp30) cc_final: 0.7194 (mm-30) REVERT: I 306 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: I 471 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7214 (mtt90) REVERT: J 48 ASN cc_start: 0.7568 (t0) cc_final: 0.7192 (t0) REVERT: J 51 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: J 306 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: K 48 ASN cc_start: 0.7529 (t0) cc_final: 0.7266 (t0) REVERT: K 51 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: K 306 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: L 51 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: L 291 GLU cc_start: 0.7701 (tp30) cc_final: 0.7207 (mm-30) REVERT: L 306 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: L 471 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7225 (mtt90) REVERT: M 270 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: M 306 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: M 498 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8845 (p) REVERT: M 506 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6961 (mt-10) REVERT: N 12 GLU cc_start: 0.6241 (mt-10) cc_final: 0.5797 (mm-30) REVERT: N 333 ILE cc_start: 0.9201 (mm) cc_final: 0.8905 (tt) REVERT: O 4 TYR cc_start: 0.8714 (m-80) cc_final: 0.8473 (m-80) REVERT: O 12 GLU cc_start: 0.6097 (mt-10) cc_final: 0.5823 (mm-30) REVERT: O 306 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: O 385 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8002 (m) REVERT: P 498 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8844 (p) REVERT: P 506 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6964 (mt-10) REVERT: Q 12 GLU cc_start: 0.6222 (mt-10) cc_final: 0.5801 (mm-30) REVERT: Q 333 ILE cc_start: 0.9209 (mm) cc_final: 0.8903 (tt) REVERT: R 12 GLU cc_start: 0.5942 (mt-10) cc_final: 0.5716 (mm-30) REVERT: R 306 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: S 51 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: S 290 CYS cc_start: 0.7612 (m) cc_final: 0.7212 (m) REVERT: S 306 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7321 (mt0) REVERT: S 390 ASP cc_start: 0.7320 (m-30) cc_final: 0.6773 (m-30) REVERT: T 51 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: T 290 CYS cc_start: 0.7767 (m) cc_final: 0.7507 (m) REVERT: T 306 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7863 (mm-40) REVERT: T 390 ASP cc_start: 0.7219 (m-30) cc_final: 0.6556 (m-30) REVERT: V 51 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: V 290 CYS cc_start: 0.7580 (m) cc_final: 0.7175 (m) REVERT: V 306 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: V 390 ASP cc_start: 0.7341 (m-30) cc_final: 0.6764 (m-30) REVERT: W 51 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: W 290 CYS cc_start: 0.7787 (m) cc_final: 0.7524 (m) REVERT: W 306 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7864 (mm-40) REVERT: W 390 ASP cc_start: 0.7246 (m-30) cc_final: 0.6698 (m-30) outliers start: 203 outliers final: 105 residues processed: 729 average time/residue: 0.6209 time to fit residues: 781.5743 Evaluate side-chains 652 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 509 time to evaluate : 5.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 306 GLN Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 481 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 306 GLN Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 498 VAL Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 467 VAL Chi-restraints excluded: chain H residue 471 ARG Chi-restraints excluded: chain H residue 481 ASP Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 270 GLN Chi-restraints excluded: chain I residue 306 GLN Chi-restraints excluded: chain I residue 365 VAL Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 481 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 306 GLN Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain J residue 481 ASP Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain K residue 51 GLN Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain K residue 467 VAL Chi-restraints excluded: chain K residue 471 ARG Chi-restraints excluded: chain K residue 481 ASP Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 306 GLN Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 439 LEU Chi-restraints excluded: chain L residue 481 ASP Chi-restraints excluded: chain L residue 498 VAL Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 270 GLN Chi-restraints excluded: chain M residue 306 GLN Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 498 VAL Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 313 VAL Chi-restraints excluded: chain N residue 467 VAL Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 313 VAL Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 262 VAL Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 442 THR Chi-restraints excluded: chain P residue 498 VAL Chi-restraints excluded: chain Q residue 260 VAL Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 467 VAL Chi-restraints excluded: chain R residue 306 GLN Chi-restraints excluded: chain S residue 51 GLN Chi-restraints excluded: chain S residue 260 VAL Chi-restraints excluded: chain S residue 296 ARG Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 385 THR Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 306 GLN Chi-restraints excluded: chain T residue 385 THR Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 296 ARG Chi-restraints excluded: chain U residue 311 ILE Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 301 ASP Chi-restraints excluded: chain V residue 306 GLN Chi-restraints excluded: chain V residue 375 ARG Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 301 ASP Chi-restraints excluded: chain W residue 306 GLN Chi-restraints excluded: chain W residue 385 THR Chi-restraints excluded: chain X residue 260 VAL Chi-restraints excluded: chain X residue 296 ARG Chi-restraints excluded: chain X residue 311 ILE Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 776 optimal weight: 7.9990 chunk 590 optimal weight: 4.9990 chunk 407 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 375 optimal weight: 4.9990 chunk 527 optimal weight: 10.0000 chunk 788 optimal weight: 5.9990 chunk 835 optimal weight: 9.9990 chunk 412 optimal weight: 9.9990 chunk 747 optimal weight: 10.0000 chunk 225 optimal weight: 0.2980 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 70104 Z= 0.235 Angle : 0.534 6.890 95640 Z= 0.281 Chirality : 0.048 0.188 10224 Planarity : 0.004 0.041 12648 Dihedral : 4.236 43.377 9772 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.40 % Allowed : 19.85 % Favored : 76.75 % 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: -0.65 (0.09), residues: 8712 helix: 1.67 (0.10), residues: 3096 sheet: 0.12 (0.15), residues: 1296 loop : -2.34 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 49 HIS 0.003 0.001 HIS E 452 PHE 0.009 0.001 PHE V 56 TYR 0.020 0.001 TYR S 433 ARG 0.011 0.000 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 551 time to evaluate : 6.044 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: A 51 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: A 295 ASP cc_start: 0.7864 (t0) cc_final: 0.7211 (t0) REVERT: A 306 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: B 51 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: B 291 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 295 ASP cc_start: 0.7765 (t0) cc_final: 0.7240 (t0) REVERT: C 51 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: C 295 ASP cc_start: 0.7654 (t0) cc_final: 0.6936 (t0) REVERT: C 306 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: D 51 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: D 295 ASP cc_start: 0.7886 (t0) cc_final: 0.7255 (t0) REVERT: D 306 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: E 51 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: E 292 LEU cc_start: 0.8518 (mt) cc_final: 0.8060 (mt) REVERT: E 295 ASP cc_start: 0.7843 (t0) cc_final: 0.7295 (t0) REVERT: F 4 TYR cc_start: 0.8885 (m-80) cc_final: 0.8668 (m-80) REVERT: F 51 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: F 295 ASP cc_start: 0.7633 (t0) cc_final: 0.6912 (t0) REVERT: F 306 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: G 48 ASN cc_start: 0.7614 (t0) cc_final: 0.7257 (t0) REVERT: G 51 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: G 291 GLU cc_start: 0.7756 (tp30) cc_final: 0.7377 (mm-30) REVERT: G 306 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: H 48 ASN cc_start: 0.7654 (t0) cc_final: 0.7347 (t0) REVERT: H 51 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: H 291 GLU cc_start: 0.7510 (tp30) cc_final: 0.6972 (mm-30) REVERT: H 306 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: H 439 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8157 (tt) REVERT: H 490 GLU cc_start: 0.6734 (tp30) cc_final: 0.6527 (tp30) REVERT: H 522 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8769 (mm) REVERT: I 51 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: I 266 MET cc_start: 0.8807 (mmm) cc_final: 0.8562 (mmt) REVERT: I 270 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: I 291 GLU cc_start: 0.7698 (tp30) cc_final: 0.7213 (mm-30) REVERT: I 306 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: I 471 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7139 (mtt90) REVERT: I 522 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8631 (mm) REVERT: J 48 ASN cc_start: 0.7641 (t0) cc_final: 0.7235 (t0) REVERT: J 51 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: J 306 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: K 51 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: K 306 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: K 490 GLU cc_start: 0.6739 (tp30) cc_final: 0.6527 (tp30) REVERT: K 522 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8774 (mm) REVERT: L 51 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7575 (mp10) REVERT: L 270 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: L 291 GLU cc_start: 0.7710 (tp30) cc_final: 0.7227 (mm-30) REVERT: L 306 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: L 471 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7133 (mtt90) REVERT: L 522 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8619 (mm) REVERT: M 270 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: M 293 MET cc_start: 0.8194 (mmm) cc_final: 0.7683 (tpp) REVERT: M 306 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: M 506 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7048 (mt-10) REVERT: N 12 GLU cc_start: 0.6279 (mt-10) cc_final: 0.5895 (mm-30) REVERT: N 270 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: N 333 ILE cc_start: 0.9199 (mm) cc_final: 0.8876 (tt) REVERT: N 410 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9017 (t) REVERT: O 4 TYR cc_start: 0.8744 (m-80) cc_final: 0.8533 (m-80) REVERT: O 306 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: P 270 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: P 293 MET cc_start: 0.8155 (mmm) cc_final: 0.7657 (tpp) REVERT: P 506 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7049 (mt-10) REVERT: Q 12 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5769 (mm-30) REVERT: Q 270 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: Q 333 ILE cc_start: 0.9203 (mm) cc_final: 0.8871 (tt) REVERT: Q 410 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9002 (t) REVERT: R 306 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: S 51 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: S 290 CYS cc_start: 0.7575 (m) cc_final: 0.7190 (m) REVERT: S 306 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: S 390 ASP cc_start: 0.7312 (m-30) cc_final: 0.6937 (m-30) REVERT: S 490 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: T 51 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: T 290 CYS cc_start: 0.7794 (m) cc_final: 0.7526 (m) REVERT: T 306 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7834 (mm-40) REVERT: T 390 ASP cc_start: 0.7234 (m-30) cc_final: 0.6401 (m-30) REVERT: V 51 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: V 290 CYS cc_start: 0.7582 (m) cc_final: 0.7189 (m) REVERT: V 306 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: V 390 ASP cc_start: 0.7322 (m-30) cc_final: 0.6931 (m-30) REVERT: V 490 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: W 51 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: W 290 CYS cc_start: 0.7819 (m) cc_final: 0.7551 (m) REVERT: W 306 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7825 (mm-40) REVERT: W 390 ASP cc_start: 0.7276 (m-30) cc_final: 0.6624 (m-30) outliers start: 239 outliers final: 154 residues processed: 765 average time/residue: 0.6248 time to fit residues: 821.2190 Evaluate side-chains 693 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 491 time to evaluate : 5.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 306 GLN Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 306 GLN Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 498 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 481 ASP Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 270 GLN Chi-restraints excluded: chain I residue 301 ASP Chi-restraints excluded: chain I residue 306 GLN Chi-restraints excluded: chain I residue 365 VAL Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 481 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 306 GLN Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 481 ASP Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 51 GLN Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain K residue 481 ASP Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 270 GLN Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 306 GLN Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 439 LEU Chi-restraints excluded: chain L residue 481 ASP Chi-restraints excluded: chain L residue 498 VAL Chi-restraints excluded: chain L residue 522 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 270 GLN Chi-restraints excluded: chain M residue 306 GLN Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 333 ILE Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 270 GLN Chi-restraints excluded: chain N residue 313 VAL Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 467 VAL Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 313 VAL Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain O residue 481 ASP Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 262 VAL Chi-restraints excluded: chain P residue 270 GLN Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 442 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 260 VAL Chi-restraints excluded: chain Q residue 270 GLN Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 467 VAL Chi-restraints excluded: chain Q residue 522 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 306 GLN Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 51 GLN Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 260 VAL Chi-restraints excluded: chain S residue 296 ARG Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 385 THR Chi-restraints excluded: chain S residue 490 GLU Chi-restraints excluded: chain S residue 504 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 306 GLN Chi-restraints excluded: chain T residue 385 THR Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 522 LEU Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 301 ASP Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 522 LEU Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 301 ASP Chi-restraints excluded: chain V residue 306 GLN Chi-restraints excluded: chain V residue 375 ARG Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain V residue 490 GLU Chi-restraints excluded: chain V residue 504 VAL Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 260 VAL Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 301 ASP Chi-restraints excluded: chain W residue 306 GLN Chi-restraints excluded: chain W residue 385 THR Chi-restraints excluded: chain W residue 410 VAL Chi-restraints excluded: chain W residue 522 LEU Chi-restraints excluded: chain X residue 260 VAL Chi-restraints excluded: chain X residue 296 ARG Chi-restraints excluded: chain X residue 301 ASP Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain X residue 522 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 695 optimal weight: 20.0000 chunk 474 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 621 optimal weight: 7.9990 chunk 344 optimal weight: 5.9990 chunk 712 optimal weight: 9.9990 chunk 577 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 chunk 749 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 HIS O 48 ASN P 67 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 70104 Z= 0.272 Angle : 0.557 7.145 95640 Z= 0.294 Chirality : 0.048 0.170 10224 Planarity : 0.004 0.043 12648 Dihedral : 4.350 43.930 9772 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.70 % Allowed : 20.18 % Favored : 76.12 % 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: -0.74 (0.09), residues: 8712 helix: 1.60 (0.10), residues: 3096 sheet: 0.01 (0.15), residues: 1296 loop : -2.37 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 49 HIS 0.003 0.001 HIS F 452 PHE 0.011 0.001 PHE V 56 TYR 0.019 0.002 TYR S 433 ARG 0.009 0.000 ARG F 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 537 time to evaluate : 5.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7675 (mt0) REVERT: A 295 ASP cc_start: 0.7855 (t0) cc_final: 0.7216 (t0) REVERT: A 306 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: A 522 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8298 (mm) REVERT: B 51 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: B 291 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7098 (tm-30) REVERT: B 295 ASP cc_start: 0.7743 (t0) cc_final: 0.7264 (t0) REVERT: C 51 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: C 271 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7383 (ptp-170) REVERT: C 295 ASP cc_start: 0.7712 (t0) cc_final: 0.6980 (t0) REVERT: C 306 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8175 (mp10) REVERT: D 51 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: D 295 ASP cc_start: 0.7907 (t0) cc_final: 0.7413 (t0) REVERT: D 306 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: D 522 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8274 (mm) REVERT: E 51 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: E 295 ASP cc_start: 0.7864 (t0) cc_final: 0.7201 (t0) REVERT: F 4 TYR cc_start: 0.8873 (m-80) cc_final: 0.8668 (m-80) REVERT: F 51 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: F 271 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7386 (ptp-170) REVERT: F 293 MET cc_start: 0.8538 (tpp) cc_final: 0.8025 (tpp) REVERT: F 295 ASP cc_start: 0.7675 (t0) cc_final: 0.6966 (t0) REVERT: F 306 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: G 48 ASN cc_start: 0.7683 (t0) cc_final: 0.7319 (t0) REVERT: G 51 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: G 291 GLU cc_start: 0.7801 (tp30) cc_final: 0.7352 (mm-30) REVERT: G 306 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: H 48 ASN cc_start: 0.7650 (t0) cc_final: 0.7365 (t0) REVERT: H 51 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: H 306 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: H 522 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8760 (mm) REVERT: I 51 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: I 266 MET cc_start: 0.8790 (mmm) cc_final: 0.8530 (mmt) REVERT: I 270 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: I 291 GLU cc_start: 0.7695 (tp30) cc_final: 0.7209 (mm-30) REVERT: I 306 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: I 471 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7193 (mtt90) REVERT: I 522 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8690 (mm) REVERT: J 48 ASN cc_start: 0.7684 (t0) cc_final: 0.7284 (t0) REVERT: J 51 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: J 306 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: K 48 ASN cc_start: 0.7644 (t0) cc_final: 0.7392 (t0) REVERT: K 51 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: K 306 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: K 522 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8767 (mm) REVERT: L 51 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: L 270 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: L 291 GLU cc_start: 0.7711 (tp30) cc_final: 0.7231 (mm-30) REVERT: L 306 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: L 471 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7187 (mtt90) REVERT: L 522 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8682 (mm) REVERT: M 40 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6816 (mp) REVERT: M 270 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: M 293 MET cc_start: 0.8278 (mmm) cc_final: 0.7842 (tpp) REVERT: M 306 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: M 506 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7095 (mt-10) REVERT: N 40 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7248 (mp) REVERT: N 333 ILE cc_start: 0.9191 (mm) cc_final: 0.8866 (tt) REVERT: N 410 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9019 (t) REVERT: O 4 TYR cc_start: 0.8717 (m-80) cc_final: 0.8510 (m-80) REVERT: O 264 ASP cc_start: 0.7646 (t0) cc_final: 0.7443 (t0) REVERT: O 306 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: P 40 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6821 (mp) REVERT: P 270 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: P 293 MET cc_start: 0.8244 (mmm) cc_final: 0.7685 (tpp) REVERT: P 506 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7098 (mt-10) REVERT: Q 40 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7258 (mp) REVERT: Q 333 ILE cc_start: 0.9195 (mm) cc_final: 0.8864 (tt) REVERT: Q 410 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.9006 (t) REVERT: R 306 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: S 51 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: S 290 CYS cc_start: 0.7583 (m) cc_final: 0.7191 (m) REVERT: S 306 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: S 390 ASP cc_start: 0.7335 (m-30) cc_final: 0.6960 (m-30) REVERT: S 490 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: T 51 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: T 290 CYS cc_start: 0.7772 (m) cc_final: 0.7520 (m) REVERT: T 306 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7949 (mm-40) REVERT: T 390 ASP cc_start: 0.7242 (m-30) cc_final: 0.6431 (m-30) REVERT: V 51 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: V 290 CYS cc_start: 0.7593 (m) cc_final: 0.7193 (m) REVERT: V 306 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7227 (mt0) REVERT: V 390 ASP cc_start: 0.7358 (m-30) cc_final: 0.6974 (m-30) REVERT: V 490 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: W 51 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: W 290 CYS cc_start: 0.7796 (m) cc_final: 0.7536 (m) REVERT: W 306 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7955 (mm-40) REVERT: W 390 ASP cc_start: 0.7404 (m-30) cc_final: 0.6755 (m-30) outliers start: 260 outliers final: 172 residues processed: 772 average time/residue: 0.6156 time to fit residues: 815.0848 Evaluate side-chains 718 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 495 time to evaluate : 5.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 306 GLN Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 481 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 306 GLN Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 498 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 467 VAL Chi-restraints excluded: chain H residue 481 ASP Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 270 GLN Chi-restraints excluded: chain I residue 301 ASP Chi-restraints excluded: chain I residue 306 GLN Chi-restraints excluded: chain I residue 365 VAL Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 481 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 306 GLN Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 481 ASP Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 51 GLN Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain K residue 467 VAL Chi-restraints excluded: chain K residue 481 ASP Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 270 GLN Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 306 GLN Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 439 LEU Chi-restraints excluded: chain L residue 481 ASP Chi-restraints excluded: chain L residue 498 VAL Chi-restraints excluded: chain L residue 522 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 270 GLN Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 306 GLN Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 333 ILE Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 313 VAL Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 467 VAL Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 313 VAL Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 262 VAL Chi-restraints excluded: chain P residue 270 GLN Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain P residue 442 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 260 VAL Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 467 VAL Chi-restraints excluded: chain Q residue 522 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 306 GLN Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 481 ASP Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 51 GLN Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 260 VAL Chi-restraints excluded: chain S residue 296 ARG Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 385 THR Chi-restraints excluded: chain S residue 490 GLU Chi-restraints excluded: chain S residue 504 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 306 GLN Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 522 LEU Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 287 ILE Chi-restraints excluded: chain U residue 296 ARG Chi-restraints excluded: chain U residue 301 ASP Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 503 VAL Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 301 ASP Chi-restraints excluded: chain V residue 306 GLN Chi-restraints excluded: chain V residue 375 ARG Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain V residue 490 GLU Chi-restraints excluded: chain V residue 504 VAL Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 260 VAL Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 301 ASP Chi-restraints excluded: chain W residue 306 GLN Chi-restraints excluded: chain W residue 385 THR Chi-restraints excluded: chain W residue 410 VAL Chi-restraints excluded: chain W residue 522 LEU Chi-restraints excluded: chain X residue 260 VAL Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 296 ARG Chi-restraints excluded: chain X residue 301 ASP Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain X residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 280 optimal weight: 0.7980 chunk 752 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 490 optimal weight: 5.9990 chunk 206 optimal weight: 0.0030 chunk 835 optimal weight: 9.9990 chunk 693 optimal weight: 0.8980 chunk 387 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 438 optimal weight: 10.0000 overall best weight: 2.1394 ------------------------------------------------------------------------------- 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: 0.8365 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 70104 Z= 0.157 Angle : 0.500 7.339 95640 Z= 0.261 Chirality : 0.046 0.172 10224 Planarity : 0.004 0.038 12648 Dihedral : 4.143 44.207 9772 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.94 % Allowed : 21.10 % Favored : 75.95 % 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: -0.56 (0.09), residues: 8712 helix: 1.79 (0.10), residues: 3096 sheet: 0.06 (0.15), residues: 1296 loop : -2.28 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 49 HIS 0.002 0.001 HIS B 452 PHE 0.009 0.001 PHE V 56 TYR 0.017 0.001 TYR S 433 ARG 0.007 0.000 ARG F 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 542 time to evaluate : 6.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7794 (t0) cc_final: 0.7282 (t0) REVERT: A 306 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: A 522 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 51 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: B 291 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7064 (tm-30) REVERT: B 295 ASP cc_start: 0.7756 (t0) cc_final: 0.7222 (t0) REVERT: C 51 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: C 295 ASP cc_start: 0.7660 (t0) cc_final: 0.6943 (t0) REVERT: C 306 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: C 440 ILE cc_start: 0.8106 (mt) cc_final: 0.7786 (mm) REVERT: D 295 ASP cc_start: 0.7918 (t0) cc_final: 0.7386 (t0) REVERT: D 306 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: D 522 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8225 (mm) REVERT: E 51 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: E 291 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7403 (mm-30) REVERT: E 295 ASP cc_start: 0.7836 (t0) cc_final: 0.7300 (t0) REVERT: F 4 TYR cc_start: 0.8866 (m-80) cc_final: 0.8646 (m-80) REVERT: F 51 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: F 293 MET cc_start: 0.8589 (tpp) cc_final: 0.8200 (tpp) REVERT: F 295 ASP cc_start: 0.7631 (t0) cc_final: 0.6924 (t0) REVERT: F 306 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: F 440 ILE cc_start: 0.8071 (mt) cc_final: 0.7762 (mm) REVERT: G 51 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: G 291 GLU cc_start: 0.7727 (tp30) cc_final: 0.7347 (mm-30) REVERT: G 306 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: H 51 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: H 306 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: H 522 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8720 (mm) REVERT: I 51 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: I 291 GLU cc_start: 0.7665 (tp30) cc_final: 0.7184 (mm-30) REVERT: I 306 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: I 471 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7057 (mtt90) REVERT: I 522 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8618 (mm) REVERT: J 51 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7908 (mt0) REVERT: J 306 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: K 51 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: K 306 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: K 522 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8725 (mm) REVERT: L 51 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: L 270 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: L 291 GLU cc_start: 0.7684 (tp30) cc_final: 0.7198 (mm-30) REVERT: L 306 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: L 471 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7038 (mtt90) REVERT: L 522 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8626 (mm) REVERT: M 306 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: M 442 THR cc_start: 0.8782 (m) cc_final: 0.8411 (m) REVERT: M 506 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7128 (mt-10) REVERT: N 40 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7246 (mp) REVERT: N 333 ILE cc_start: 0.9176 (mm) cc_final: 0.8847 (tt) REVERT: N 410 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8984 (t) REVERT: O 4 TYR cc_start: 0.8690 (m-80) cc_final: 0.8477 (m-80) REVERT: O 306 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: O 522 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8550 (mm) REVERT: P 270 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8232 (mt0) REVERT: P 506 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7131 (mt-10) REVERT: Q 40 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7261 (mp) REVERT: Q 410 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8973 (t) REVERT: R 306 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: R 522 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8562 (mm) REVERT: S 51 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: S 290 CYS cc_start: 0.7470 (m) cc_final: 0.7083 (m) REVERT: S 306 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7178 (mt0) REVERT: S 390 ASP cc_start: 0.7209 (m-30) cc_final: 0.6822 (m-30) REVERT: S 490 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: T 51 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: T 290 CYS cc_start: 0.7728 (m) cc_final: 0.7497 (m) REVERT: T 306 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7882 (mm-40) REVERT: T 390 ASP cc_start: 0.7385 (m-30) cc_final: 0.6667 (m-30) REVERT: V 51 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7951 (mt0) REVERT: V 290 CYS cc_start: 0.7485 (m) cc_final: 0.7087 (m) REVERT: V 306 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: V 390 ASP cc_start: 0.7262 (m-30) cc_final: 0.6868 (m-30) REVERT: V 490 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: W 51 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: W 290 CYS cc_start: 0.7753 (m) cc_final: 0.7513 (m) REVERT: W 306 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7888 (mm-40) REVERT: W 390 ASP cc_start: 0.7348 (m-30) cc_final: 0.6736 (m-30) outliers start: 207 outliers final: 136 residues processed: 714 average time/residue: 0.6266 time to fit residues: 765.8390 Evaluate side-chains 686 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 503 time to evaluate : 5.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 306 GLN Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 481 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 306 GLN Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 498 VAL Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 467 VAL Chi-restraints excluded: chain H residue 481 ASP Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 301 ASP Chi-restraints excluded: chain I residue 306 GLN Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 481 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 306 GLN Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 481 ASP Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 51 GLN Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 467 VAL Chi-restraints excluded: chain K residue 481 ASP Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 270 GLN Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 306 GLN Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 439 LEU Chi-restraints excluded: chain L residue 481 ASP Chi-restraints excluded: chain L residue 498 VAL Chi-restraints excluded: chain L residue 522 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 306 GLN Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 467 VAL Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain O residue 481 ASP Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 262 VAL Chi-restraints excluded: chain P residue 270 GLN Chi-restraints excluded: chain P residue 442 THR Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 467 VAL Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 306 GLN Chi-restraints excluded: chain R residue 481 ASP Chi-restraints excluded: chain R residue 522 LEU Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 51 GLN Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 260 VAL Chi-restraints excluded: chain S residue 296 ARG Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 385 THR Chi-restraints excluded: chain S residue 490 GLU Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 306 GLN Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 522 LEU Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 296 ARG Chi-restraints excluded: chain U residue 301 ASP Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 522 LEU Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 301 ASP Chi-restraints excluded: chain V residue 306 GLN Chi-restraints excluded: chain V residue 375 ARG Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain V residue 490 GLU Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 260 VAL Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 301 ASP Chi-restraints excluded: chain W residue 306 GLN Chi-restraints excluded: chain W residue 410 VAL Chi-restraints excluded: chain W residue 522 LEU Chi-restraints excluded: chain X residue 260 VAL Chi-restraints excluded: chain X residue 301 ASP Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain X residue 522 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 805 optimal weight: 9.9990 chunk 94 optimal weight: 0.0370 chunk 476 optimal weight: 20.0000 chunk 610 optimal weight: 0.6980 chunk 472 optimal weight: 2.9990 chunk 703 optimal weight: 10.0000 chunk 466 optimal weight: 6.9990 chunk 832 optimal weight: 10.0000 chunk 521 optimal weight: 6.9990 chunk 507 optimal weight: 9.9990 chunk 384 optimal weight: 1.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- 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: 0.8370 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 70104 Z= 0.174 Angle : 0.506 8.486 95640 Z= 0.263 Chirality : 0.047 0.147 10224 Planarity : 0.004 0.051 12648 Dihedral : 4.101 45.869 9772 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.43 % Allowed : 20.63 % Favored : 75.94 % 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: -0.51 (0.09), residues: 8712 helix: 1.84 (0.10), residues: 3096 sheet: 0.10 (0.15), residues: 1296 loop : -2.26 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 49 HIS 0.003 0.001 HIS B 452 PHE 0.010 0.001 PHE V 56 TYR 0.017 0.001 TYR V 433 ARG 0.012 0.000 ARG F 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 521 time to evaluate : 6.294 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: A 295 ASP cc_start: 0.7834 (t0) cc_final: 0.7295 (t0) REVERT: A 306 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: A 522 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8230 (mm) REVERT: B 51 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: B 291 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7066 (tm-30) REVERT: B 295 ASP cc_start: 0.7766 (t0) cc_final: 0.7236 (t0) REVERT: C 51 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: C 295 ASP cc_start: 0.7715 (t0) cc_final: 0.6957 (t0) REVERT: C 306 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: C 440 ILE cc_start: 0.8092 (mt) cc_final: 0.7776 (mm) REVERT: D 295 ASP cc_start: 0.7908 (t0) cc_final: 0.7392 (t0) REVERT: D 306 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: D 522 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8190 (mm) REVERT: E 51 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: E 292 LEU cc_start: 0.8620 (mt) cc_final: 0.8163 (mt) REVERT: E 295 ASP cc_start: 0.7850 (t0) cc_final: 0.7311 (t0) REVERT: F 4 TYR cc_start: 0.8862 (m-80) cc_final: 0.8643 (m-80) REVERT: F 51 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: F 271 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7450 (ptp-170) REVERT: F 293 MET cc_start: 0.8631 (tpp) cc_final: 0.8299 (tpp) REVERT: F 295 ASP cc_start: 0.7645 (t0) cc_final: 0.6890 (t0) REVERT: F 306 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: F 440 ILE cc_start: 0.8012 (mt) cc_final: 0.7719 (mm) REVERT: G 51 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: G 291 GLU cc_start: 0.7747 (tp30) cc_final: 0.7346 (mm-30) REVERT: H 51 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: H 306 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: H 522 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8738 (mm) REVERT: I 51 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: I 270 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: I 291 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: I 306 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: I 471 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7093 (mtt90) REVERT: I 522 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8642 (mm) REVERT: J 51 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: J 436 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6780 (tp30) REVERT: K 51 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7767 (mp10) REVERT: K 306 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: K 522 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8757 (mm) REVERT: L 51 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: L 270 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: L 291 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: L 306 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: L 471 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7077 (mtt90) REVERT: L 522 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8638 (mm) REVERT: M 270 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: M 306 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: M 442 THR cc_start: 0.8736 (m) cc_final: 0.8350 (m) REVERT: M 506 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7141 (mt-10) REVERT: N 40 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7298 (mp) REVERT: N 333 ILE cc_start: 0.9157 (mm) cc_final: 0.8822 (tt) REVERT: N 410 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8994 (t) REVERT: O 4 TYR cc_start: 0.8687 (m-80) cc_final: 0.8465 (m-80) REVERT: O 40 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7693 (mp) REVERT: O 306 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: O 522 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8533 (mm) REVERT: P 270 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: P 506 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7184 (mt-10) REVERT: Q 333 ILE cc_start: 0.9140 (mm) cc_final: 0.8866 (tt) REVERT: Q 410 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8972 (t) REVERT: R 306 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: R 522 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8536 (mm) REVERT: S 51 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: S 290 CYS cc_start: 0.7474 (m) cc_final: 0.7107 (m) REVERT: S 306 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: S 390 ASP cc_start: 0.7264 (m-30) cc_final: 0.6860 (m-30) REVERT: T 51 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: T 306 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7873 (mm-40) REVERT: T 390 ASP cc_start: 0.7387 (m-30) cc_final: 0.6692 (m-30) REVERT: V 51 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: V 290 CYS cc_start: 0.7484 (m) cc_final: 0.7100 (m) REVERT: V 306 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: V 390 ASP cc_start: 0.7328 (m-30) cc_final: 0.6929 (m-30) REVERT: V 490 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: W 51 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: W 290 CYS cc_start: 0.7763 (m) cc_final: 0.7524 (m) REVERT: W 306 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7881 (mm-40) REVERT: W 390 ASP cc_start: 0.7352 (m-30) cc_final: 0.6735 (m-30) outliers start: 241 outliers final: 161 residues processed: 725 average time/residue: 0.6182 time to fit residues: 771.3717 Evaluate side-chains 713 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 503 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 306 GLN Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 481 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 306 GLN Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 498 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 467 VAL Chi-restraints excluded: chain H residue 481 ASP Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 270 GLN Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 301 ASP Chi-restraints excluded: chain I residue 306 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 365 VAL Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 481 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 306 GLN Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 436 GLU Chi-restraints excluded: chain J residue 481 ASP Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 51 GLN Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain K residue 467 VAL Chi-restraints excluded: chain K residue 481 ASP Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 270 GLN Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 306 GLN Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 439 LEU Chi-restraints excluded: chain L residue 481 ASP Chi-restraints excluded: chain L residue 498 VAL Chi-restraints excluded: chain L residue 522 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 270 GLN Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 306 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 313 VAL Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 467 VAL Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 276 LEU Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 313 VAL Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain O residue 481 ASP Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 262 VAL Chi-restraints excluded: chain P residue 270 GLN Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 442 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 467 VAL Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 306 GLN Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 481 ASP Chi-restraints excluded: chain R residue 522 LEU Chi-restraints excluded: chain S residue 51 GLN Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 260 VAL Chi-restraints excluded: chain S residue 296 ARG Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 385 THR Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 306 GLN Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 522 LEU Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 296 ARG Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 522 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 301 ASP Chi-restraints excluded: chain V residue 306 GLN Chi-restraints excluded: chain V residue 375 ARG Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain V residue 490 GLU Chi-restraints excluded: chain V residue 503 VAL Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 260 VAL Chi-restraints excluded: chain W residue 287 ILE Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 301 ASP Chi-restraints excluded: chain W residue 306 GLN Chi-restraints excluded: chain W residue 410 VAL Chi-restraints excluded: chain W residue 522 LEU Chi-restraints excluded: chain X residue 260 VAL Chi-restraints excluded: chain X residue 296 ARG Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain X residue 522 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 515 optimal weight: 5.9990 chunk 332 optimal weight: 20.0000 chunk 497 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 529 optimal weight: 6.9990 chunk 567 optimal weight: 2.9990 chunk 411 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 654 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8384 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 70104 Z= 0.202 Angle : 0.520 9.263 95640 Z= 0.272 Chirality : 0.047 0.140 10224 Planarity : 0.004 0.043 12648 Dihedral : 4.131 45.602 9772 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.53 % Allowed : 20.52 % Favored : 75.95 % 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: -0.52 (0.09), residues: 8712 helix: 1.82 (0.10), residues: 3096 sheet: 0.09 (0.15), residues: 1296 loop : -2.26 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 49 HIS 0.003 0.001 HIS E 452 PHE 0.010 0.001 PHE S 56 TYR 0.018 0.001 TYR S 433 ARG 0.010 0.000 ARG F 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 530 time to evaluate : 5.999 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: A 295 ASP cc_start: 0.7858 (t0) cc_final: 0.7313 (t0) REVERT: A 306 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: A 522 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8325 (mm) REVERT: B 51 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: B 291 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7074 (tm-30) REVERT: B 295 ASP cc_start: 0.7787 (t0) cc_final: 0.7253 (t0) REVERT: C 51 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: C 295 ASP cc_start: 0.7741 (t0) cc_final: 0.6964 (t0) REVERT: C 306 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: C 440 ILE cc_start: 0.8124 (mt) cc_final: 0.7799 (mm) REVERT: D 295 ASP cc_start: 0.7927 (t0) cc_final: 0.7388 (t0) REVERT: D 306 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: D 522 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8241 (mm) REVERT: E 51 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: E 291 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7426 (mm-30) REVERT: E 292 LEU cc_start: 0.8662 (mt) cc_final: 0.8143 (mt) REVERT: E 295 ASP cc_start: 0.7878 (t0) cc_final: 0.7358 (t0) REVERT: F 4 TYR cc_start: 0.8861 (m-80) cc_final: 0.8640 (m-80) REVERT: F 51 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7564 (mt0) REVERT: F 271 ARG cc_start: 0.7953 (mtm110) cc_final: 0.7454 (ptp-170) REVERT: F 291 GLU cc_start: 0.7753 (tt0) cc_final: 0.6820 (tt0) REVERT: F 293 MET cc_start: 0.8554 (tpp) cc_final: 0.8122 (tpp) REVERT: F 295 ASP cc_start: 0.7617 (t0) cc_final: 0.6868 (t0) REVERT: F 306 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: G 51 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: G 291 GLU cc_start: 0.7798 (tp30) cc_final: 0.7404 (mm-30) REVERT: H 51 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: H 306 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7749 (mt0) REVERT: H 522 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8761 (mm) REVERT: I 51 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: I 270 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: I 291 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: I 306 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: I 471 ARG cc_start: 0.7693 (ttm-80) cc_final: 0.7074 (mtt90) REVERT: I 522 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8644 (mm) REVERT: J 51 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: J 436 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: K 51 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: K 306 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7714 (mt0) REVERT: K 522 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8765 (mm) REVERT: L 51 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: L 270 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: L 291 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: L 306 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: L 471 ARG cc_start: 0.7762 (ttm-80) cc_final: 0.7100 (mtt90) REVERT: L 522 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8625 (mm) REVERT: M 270 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8238 (mt0) REVERT: M 306 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: M 442 THR cc_start: 0.8706 (m) cc_final: 0.8321 (m) REVERT: M 506 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7167 (mt-10) REVERT: N 333 ILE cc_start: 0.9167 (mm) cc_final: 0.8829 (tt) REVERT: N 410 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.9005 (t) REVERT: N 469 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7553 (mm-30) REVERT: O 4 TYR cc_start: 0.8688 (m-80) cc_final: 0.8488 (m-80) REVERT: O 40 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7621 (mp) REVERT: O 306 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: O 522 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8539 (mm) REVERT: P 270 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: P 506 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7027 (mt-10) REVERT: Q 333 ILE cc_start: 0.9159 (mm) cc_final: 0.8862 (tt) REVERT: Q 410 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8995 (t) REVERT: Q 469 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7564 (mm-30) REVERT: R 306 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: R 522 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8551 (mm) REVERT: S 51 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: S 290 CYS cc_start: 0.7497 (m) cc_final: 0.7112 (m) REVERT: S 306 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7157 (mt0) REVERT: S 390 ASP cc_start: 0.7278 (m-30) cc_final: 0.6878 (m-30) REVERT: S 490 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: T 51 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: T 290 CYS cc_start: 0.7874 (m) cc_final: 0.7629 (m) REVERT: T 390 ASP cc_start: 0.7399 (m-30) cc_final: 0.6708 (m-30) REVERT: V 51 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: V 290 CYS cc_start: 0.7506 (m) cc_final: 0.7116 (m) REVERT: V 306 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: V 390 ASP cc_start: 0.7338 (m-30) cc_final: 0.6943 (m-30) REVERT: V 490 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: W 51 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: W 290 CYS cc_start: 0.7792 (m) cc_final: 0.7533 (m) REVERT: W 390 ASP cc_start: 0.7373 (m-30) cc_final: 0.6763 (m-30) REVERT: W 436 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7051 (tt0) outliers start: 248 outliers final: 177 residues processed: 744 average time/residue: 0.6398 time to fit residues: 821.4320 Evaluate side-chains 739 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 514 time to evaluate : 6.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 306 GLN Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 481 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 306 GLN Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 498 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 467 VAL Chi-restraints excluded: chain H residue 481 ASP Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 270 GLN Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 301 ASP Chi-restraints excluded: chain I residue 306 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 365 VAL Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 481 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 306 GLN Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 436 GLU Chi-restraints excluded: chain J residue 481 ASP Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 51 GLN Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 467 VAL Chi-restraints excluded: chain K residue 481 ASP Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 270 GLN Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 306 GLN Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 439 LEU Chi-restraints excluded: chain L residue 481 ASP Chi-restraints excluded: chain L residue 498 VAL Chi-restraints excluded: chain L residue 522 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 270 GLN Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 306 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 313 VAL Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 467 VAL Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 276 LEU Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain O residue 481 ASP Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 262 VAL Chi-restraints excluded: chain P residue 270 GLN Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 442 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 467 VAL Chi-restraints excluded: chain Q residue 522 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 306 GLN Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 481 ASP Chi-restraints excluded: chain R residue 522 LEU Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 51 GLN Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 260 VAL Chi-restraints excluded: chain S residue 296 ARG Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 385 THR Chi-restraints excluded: chain S residue 490 GLU Chi-restraints excluded: chain S residue 498 VAL Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 522 LEU Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 296 ARG Chi-restraints excluded: chain U residue 301 ASP Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 522 LEU Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 301 ASP Chi-restraints excluded: chain V residue 306 GLN Chi-restraints excluded: chain V residue 375 ARG Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain V residue 490 GLU Chi-restraints excluded: chain V residue 498 VAL Chi-restraints excluded: chain V residue 503 VAL Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 260 VAL Chi-restraints excluded: chain W residue 287 ILE Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 301 ASP Chi-restraints excluded: chain W residue 410 VAL Chi-restraints excluded: chain W residue 436 GLU Chi-restraints excluded: chain W residue 522 LEU Chi-restraints excluded: chain X residue 260 VAL Chi-restraints excluded: chain X residue 296 ARG Chi-restraints excluded: chain X residue 301 ASP Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain X residue 522 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 757 optimal weight: 20.0000 chunk 797 optimal weight: 0.0670 chunk 727 optimal weight: 4.9990 chunk 776 optimal weight: 6.9990 chunk 467 optimal weight: 6.9990 chunk 338 optimal weight: 10.0000 chunk 609 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 701 optimal weight: 0.5980 chunk 733 optimal weight: 6.9990 chunk 773 optimal weight: 10.0000 overall best weight: 2.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 67 HIS S 383 GLN T 306 GLN T 383 GLN W 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 70104 Z= 0.156 Angle : 0.499 9.591 95640 Z= 0.260 Chirality : 0.046 0.142 10224 Planarity : 0.004 0.038 12648 Dihedral : 4.055 47.583 9772 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.31 % Allowed : 20.88 % Favored : 75.81 % 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: -0.42 (0.09), residues: 8712 helix: 1.91 (0.10), residues: 3096 sheet: 0.13 (0.15), residues: 1296 loop : -2.20 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 411 HIS 0.002 0.001 HIS E 452 PHE 0.009 0.001 PHE S 56 TYR 0.017 0.001 TYR S 433 ARG 0.009 0.000 ARG F 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 528 time to evaluate : 5.980 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: A 295 ASP cc_start: 0.7815 (t0) cc_final: 0.7287 (t0) REVERT: A 306 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: A 522 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8282 (mm) REVERT: B 51 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: B 291 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7066 (tm-30) REVERT: B 295 ASP cc_start: 0.7755 (t0) cc_final: 0.7225 (t0) REVERT: B 459 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7681 (ttp80) REVERT: C 295 ASP cc_start: 0.7724 (t0) cc_final: 0.6983 (t0) REVERT: C 306 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: D 295 ASP cc_start: 0.7898 (t0) cc_final: 0.7375 (t0) REVERT: D 306 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: D 522 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8249 (mm) REVERT: E 51 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: E 291 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7536 (mm-30) REVERT: E 292 LEU cc_start: 0.8622 (mt) cc_final: 0.8139 (mt) REVERT: E 295 ASP cc_start: 0.7859 (t0) cc_final: 0.7344 (t0) REVERT: F 4 TYR cc_start: 0.8854 (m-80) cc_final: 0.8626 (m-80) REVERT: F 51 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: F 271 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7504 (ptp-170) REVERT: F 293 MET cc_start: 0.8490 (tpp) cc_final: 0.8179 (tpp) REVERT: F 295 ASP cc_start: 0.7553 (t0) cc_final: 0.6790 (t0) REVERT: F 306 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: G 51 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: G 291 GLU cc_start: 0.7725 (tp30) cc_final: 0.7330 (mm-30) REVERT: H 51 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: H 306 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7698 (mt0) REVERT: H 522 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8836 (mm) REVERT: I 51 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: I 270 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: I 291 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: I 306 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: I 471 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7342 (ttp-170) REVERT: I 522 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8624 (mm) REVERT: J 51 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: J 436 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6767 (tp30) REVERT: K 51 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: K 306 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: K 522 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8752 (mm) REVERT: L 51 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: L 270 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: L 291 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: L 306 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: L 471 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7339 (ttp-170) REVERT: L 522 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8624 (mm) REVERT: M 306 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: M 442 THR cc_start: 0.8670 (m) cc_final: 0.8309 (m) REVERT: M 506 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7135 (mt-10) REVERT: N 333 ILE cc_start: 0.9153 (mm) cc_final: 0.8810 (tt) REVERT: N 410 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8983 (t) REVERT: O 4 TYR cc_start: 0.8676 (m-80) cc_final: 0.8458 (m-80) REVERT: O 306 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: O 522 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8505 (mm) REVERT: P 270 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: P 506 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7137 (mt-10) REVERT: Q 333 ILE cc_start: 0.9153 (mm) cc_final: 0.8862 (tt) REVERT: Q 410 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8985 (t) REVERT: R 264 ASP cc_start: 0.7602 (t0) cc_final: 0.7378 (t0) REVERT: R 306 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: R 522 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8517 (mm) REVERT: S 290 CYS cc_start: 0.7454 (m) cc_final: 0.7084 (m) REVERT: S 306 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7114 (mt0) REVERT: S 390 ASP cc_start: 0.7236 (m-30) cc_final: 0.6721 (m-30) REVERT: S 490 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: T 51 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: T 390 ASP cc_start: 0.7377 (m-30) cc_final: 0.6685 (m-30) REVERT: T 436 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: V 290 CYS cc_start: 0.7461 (m) cc_final: 0.7081 (m) REVERT: V 306 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7116 (mt0) REVERT: V 390 ASP cc_start: 0.7315 (m-30) cc_final: 0.6929 (m-30) REVERT: V 490 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: W 51 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: W 390 ASP cc_start: 0.7351 (m-30) cc_final: 0.6737 (m-30) REVERT: W 436 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: X 291 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.4907 (tt0) outliers start: 233 outliers final: 164 residues processed: 726 average time/residue: 0.6213 time to fit residues: 774.5360 Evaluate side-chains 723 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 514 time to evaluate : 5.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 306 GLN Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 481 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 306 GLN Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 498 VAL Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 467 VAL Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 270 GLN Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 301 ASP Chi-restraints excluded: chain I residue 306 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 365 VAL Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 481 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 306 GLN Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 436 GLU Chi-restraints excluded: chain J residue 481 ASP Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 51 GLN Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 467 VAL Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 270 GLN Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 306 GLN Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 439 LEU Chi-restraints excluded: chain L residue 498 VAL Chi-restraints excluded: chain L residue 522 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 306 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 313 VAL Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 467 VAL Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 276 LEU Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain O residue 481 ASP Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 262 VAL Chi-restraints excluded: chain P residue 270 GLN Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 442 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 467 VAL Chi-restraints excluded: chain Q residue 522 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 306 GLN Chi-restraints excluded: chain R residue 481 ASP Chi-restraints excluded: chain R residue 522 LEU Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 260 VAL Chi-restraints excluded: chain S residue 296 ARG Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 385 THR Chi-restraints excluded: chain S residue 490 GLU Chi-restraints excluded: chain S residue 498 VAL Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 276 LEU Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 436 GLU Chi-restraints excluded: chain T residue 522 LEU Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 296 ARG Chi-restraints excluded: chain U residue 301 ASP Chi-restraints excluded: chain U residue 311 ILE Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 522 LEU Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 301 ASP Chi-restraints excluded: chain V residue 306 GLN Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain V residue 490 GLU Chi-restraints excluded: chain V residue 498 VAL Chi-restraints excluded: chain V residue 503 VAL Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 260 VAL Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 301 ASP Chi-restraints excluded: chain W residue 410 VAL Chi-restraints excluded: chain W residue 436 GLU Chi-restraints excluded: chain W residue 522 LEU Chi-restraints excluded: chain X residue 260 VAL Chi-restraints excluded: chain X residue 291 GLU Chi-restraints excluded: chain X residue 296 ARG Chi-restraints excluded: chain X residue 301 ASP Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain X residue 522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 509 optimal weight: 10.0000 chunk 820 optimal weight: 6.9990 chunk 500 optimal weight: 8.9990 chunk 389 optimal weight: 2.9990 chunk 570 optimal weight: 4.9990 chunk 860 optimal weight: 2.9990 chunk 792 optimal weight: 4.9990 chunk 685 optimal weight: 0.2980 chunk 71 optimal weight: 7.9990 chunk 529 optimal weight: 4.9990 chunk 420 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 70104 Z= 0.179 Angle : 0.510 10.029 95640 Z= 0.266 Chirality : 0.046 0.138 10224 Planarity : 0.004 0.039 12648 Dihedral : 4.001 17.558 9768 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.23 % Allowed : 21.02 % Favored : 75.75 % 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: -0.42 (0.09), residues: 8712 helix: 1.91 (0.10), residues: 3096 sheet: 0.13 (0.15), residues: 1296 loop : -2.20 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 49 HIS 0.003 0.001 HIS E 452 PHE 0.010 0.001 PHE S 56 TYR 0.017 0.001 TYR S 433 ARG 0.009 0.000 ARG F 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17424 Ramachandran restraints generated. 8712 Oldfield, 0 Emsley, 8712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 522 time to evaluate : 6.051 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: A 295 ASP cc_start: 0.7836 (t0) cc_final: 0.7296 (t0) REVERT: A 306 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: A 522 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8318 (mm) REVERT: B 51 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7710 (mt0) REVERT: B 291 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7068 (tm-30) REVERT: B 295 ASP cc_start: 0.7773 (t0) cc_final: 0.7241 (t0) REVERT: B 459 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7702 (ttp80) REVERT: C 46 VAL cc_start: 0.8838 (t) cc_final: 0.8596 (m) REVERT: C 295 ASP cc_start: 0.7758 (t0) cc_final: 0.6998 (t0) REVERT: C 306 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: D 295 ASP cc_start: 0.7924 (t0) cc_final: 0.7389 (t0) REVERT: D 306 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: D 522 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8199 (mm) REVERT: E 51 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: E 291 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7414 (mm-30) REVERT: E 292 LEU cc_start: 0.8629 (mt) cc_final: 0.8129 (mt) REVERT: E 295 ASP cc_start: 0.7912 (t0) cc_final: 0.7386 (t0) REVERT: E 459 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7706 (ttp80) REVERT: F 4 TYR cc_start: 0.8852 (m-80) cc_final: 0.8629 (m-80) REVERT: F 51 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: F 293 MET cc_start: 0.8405 (tpp) cc_final: 0.7969 (tpp) REVERT: F 295 ASP cc_start: 0.7545 (t0) cc_final: 0.6771 (t0) REVERT: F 306 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: G 51 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: G 291 GLU cc_start: 0.7729 (tp30) cc_final: 0.7337 (mm-30) REVERT: H 51 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: H 306 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: H 522 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8847 (mm) REVERT: I 51 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: I 270 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: I 291 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: I 306 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: I 471 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7056 (mtt90) REVERT: I 522 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8635 (mm) REVERT: J 51 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7908 (mt0) REVERT: J 291 GLU cc_start: 0.7842 (tt0) cc_final: 0.7382 (tt0) REVERT: J 436 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6764 (tp30) REVERT: K 51 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: K 306 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7727 (mt0) REVERT: K 522 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8848 (mm) REVERT: L 51 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: L 270 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: L 291 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7216 (mm-30) REVERT: L 306 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: L 471 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7340 (ttp-170) REVERT: L 522 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8613 (mm) REVERT: M 270 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: M 306 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: M 442 THR cc_start: 0.8696 (m) cc_final: 0.8340 (m) REVERT: M 506 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7153 (mt-10) REVERT: N 333 ILE cc_start: 0.9157 (mm) cc_final: 0.8814 (tt) REVERT: N 410 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8994 (t) REVERT: O 4 TYR cc_start: 0.8683 (m-80) cc_final: 0.8465 (m-80) REVERT: O 306 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: O 522 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8509 (mm) REVERT: P 270 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: P 506 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7021 (mt-10) REVERT: Q 333 ILE cc_start: 0.9159 (mm) cc_final: 0.8867 (tt) REVERT: Q 410 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8991 (t) REVERT: R 306 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: R 522 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8498 (mm) REVERT: S 290 CYS cc_start: 0.7476 (m) cc_final: 0.7105 (m) REVERT: S 306 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7115 (mt0) REVERT: S 390 ASP cc_start: 0.7252 (m-30) cc_final: 0.6731 (m-30) REVERT: S 490 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: T 51 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: T 390 ASP cc_start: 0.7391 (m-30) cc_final: 0.6721 (m-30) REVERT: T 436 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7029 (tt0) REVERT: U 291 GLU cc_start: 0.5652 (OUTLIER) cc_final: 0.4917 (tt0) REVERT: V 290 CYS cc_start: 0.7482 (m) cc_final: 0.7101 (m) REVERT: V 306 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7119 (mt0) REVERT: V 390 ASP cc_start: 0.7337 (m-30) cc_final: 0.6943 (m-30) REVERT: V 490 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: W 51 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: W 390 ASP cc_start: 0.7365 (m-30) cc_final: 0.6751 (m-30) REVERT: W 436 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: X 291 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.4927 (tt0) outliers start: 227 outliers final: 173 residues processed: 711 average time/residue: 0.6434 time to fit residues: 784.6964 Evaluate side-chains 724 residues out of total 7056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 504 time to evaluate : 5.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 306 GLN Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 481 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 306 GLN Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 498 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 467 VAL Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 270 GLN Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 301 ASP Chi-restraints excluded: chain I residue 306 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 365 VAL Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 481 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain J residue 306 GLN Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 436 GLU Chi-restraints excluded: chain J residue 481 ASP Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 51 GLN Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 467 VAL Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 270 GLN Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 306 GLN Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 439 LEU Chi-restraints excluded: chain L residue 481 ASP Chi-restraints excluded: chain L residue 498 VAL Chi-restraints excluded: chain L residue 522 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 270 GLN Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 306 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 313 VAL Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 467 VAL Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain O residue 481 ASP Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 262 VAL Chi-restraints excluded: chain P residue 270 GLN Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 442 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 260 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 467 VAL Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 306 GLN Chi-restraints excluded: chain R residue 481 ASP Chi-restraints excluded: chain R residue 522 LEU Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 260 VAL Chi-restraints excluded: chain S residue 296 ARG Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 306 GLN Chi-restraints excluded: chain S residue 385 THR Chi-restraints excluded: chain S residue 490 GLU Chi-restraints excluded: chain S residue 498 VAL Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 276 LEU Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 301 ASP Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 436 GLU Chi-restraints excluded: chain T residue 522 LEU Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 291 GLU Chi-restraints excluded: chain U residue 296 ARG Chi-restraints excluded: chain U residue 301 ASP Chi-restraints excluded: chain U residue 311 ILE Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 522 LEU Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 301 ASP Chi-restraints excluded: chain V residue 306 GLN Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain V residue 490 GLU Chi-restraints excluded: chain V residue 498 VAL Chi-restraints excluded: chain V residue 503 VAL Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 260 VAL Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 301 ASP Chi-restraints excluded: chain W residue 410 VAL Chi-restraints excluded: chain W residue 436 GLU Chi-restraints excluded: chain W residue 522 LEU Chi-restraints excluded: chain X residue 260 VAL Chi-restraints excluded: chain X residue 291 GLU Chi-restraints excluded: chain X residue 301 ASP Chi-restraints excluded: chain X residue 311 ILE Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain X residue 522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 544 optimal weight: 10.0000 chunk 730 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 632 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 686 optimal weight: 0.1980 chunk 287 optimal weight: 5.9990 chunk 704 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 67 HIS ** T 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.103377 restraints weight = 106549.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106010 restraints weight = 65557.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107825 restraints weight = 45806.638| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 70104 Z= 0.133 Angle : 0.482 10.046 95640 Z= 0.249 Chirality : 0.046 0.132 10224 Planarity : 0.004 0.039 12648 Dihedral : 3.861 15.925 9768 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.52 % Allowed : 21.73 % Favored : 75.75 % 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: -0.29 (0.09), residues: 8712 helix: 2.03 (0.10), residues: 3096 sheet: 0.18 (0.15), residues: 1296 loop : -2.12 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 411 HIS 0.002 0.000 HIS X 289 PHE 0.011 0.001 PHE V 56 TYR 0.016 0.001 TYR V 433 ARG 0.009 0.000 ARG F 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12610.38 seconds wall clock time: 222 minutes 21.12 seconds (13341.12 seconds total)