Starting phenix.real_space_refine on Sun Mar 24 21:25:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uix_20790/03_2024/6uix_20790.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uix_20790/03_2024/6uix_20790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uix_20790/03_2024/6uix_20790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uix_20790/03_2024/6uix_20790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uix_20790/03_2024/6uix_20790.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uix_20790/03_2024/6uix_20790.pdb" } resolution = 3.5 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= 0.000 sd= 0.002 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 154 5.16 5 C 28776 2.51 5 N 8030 2.21 5 O 7238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "H PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 159": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 275": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Residue "J ARG 159": "NH1" <-> "NH2" Residue "J ARG 178": "NH1" <-> "NH2" Residue "J ARG 224": "NH1" <-> "NH2" Residue "J PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 275": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 159": "NH1" <-> "NH2" Residue "K ARG 178": "NH1" <-> "NH2" Residue "K ARG 224": "NH1" <-> "NH2" Residue "K PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 275": "NH1" <-> "NH2" Residue "L ARG 109": "NH1" <-> "NH2" Residue "L ARG 159": "NH1" <-> "NH2" Residue "L ARG 178": "NH1" <-> "NH2" Residue "L ARG 224": "NH1" <-> "NH2" Residue "L PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 275": "NH1" <-> "NH2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M ARG 159": "NH1" <-> "NH2" Residue "M ARG 178": "NH1" <-> "NH2" Residue "M ARG 224": "NH1" <-> "NH2" Residue "M PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "N ARG 109": "NH1" <-> "NH2" Residue "N ARG 159": "NH1" <-> "NH2" Residue "N ARG 178": "NH1" <-> "NH2" Residue "N ARG 224": "NH1" <-> "NH2" Residue "N ARG 275": "NH1" <-> "NH2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "O ARG 178": "NH1" <-> "NH2" Residue "O ARG 224": "NH1" <-> "NH2" Residue "O ARG 275": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "P ARG 159": "NH1" <-> "NH2" Residue "P ARG 178": "NH1" <-> "NH2" Residue "P ARG 224": "NH1" <-> "NH2" Residue "P ARG 275": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "Q ARG 159": "NH1" <-> "NH2" Residue "Q ARG 178": "NH1" <-> "NH2" Residue "Q ARG 224": "NH1" <-> "NH2" Residue "Q ARG 275": "NH1" <-> "NH2" Residue "R ARG 109": "NH1" <-> "NH2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R ARG 178": "NH1" <-> "NH2" Residue "R ARG 224": "NH1" <-> "NH2" Residue "R PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 275": "NH1" <-> "NH2" Residue "S ARG 109": "NH1" <-> "NH2" Residue "S ARG 159": "NH1" <-> "NH2" Residue "S ARG 178": "NH1" <-> "NH2" Residue "S ARG 224": "NH1" <-> "NH2" Residue "S PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 275": "NH1" <-> "NH2" Residue "T ARG 109": "NH1" <-> "NH2" Residue "T ARG 159": "NH1" <-> "NH2" Residue "T ARG 178": "NH1" <-> "NH2" Residue "T ARG 224": "NH1" <-> "NH2" Residue "T ARG 275": "NH1" <-> "NH2" Residue "U ARG 109": "NH1" <-> "NH2" Residue "U ARG 159": "NH1" <-> "NH2" Residue "U ARG 178": "NH1" <-> "NH2" Residue "U ARG 224": "NH1" <-> "NH2" Residue "U PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 275": "NH1" <-> "NH2" Residue "V ARG 109": "NH1" <-> "NH2" Residue "V ARG 159": "NH1" <-> "NH2" Residue "V ARG 178": "NH1" <-> "NH2" Residue "V ARG 224": "NH1" <-> "NH2" Residue "V ARG 275": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44198 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "C" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "E" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "F" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "I" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "J" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "K" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "L" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "M" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "N" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "O" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "P" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "Q" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "R" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "S" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "T" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "U" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "V" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Time building chain proxies: 22.17, per 1000 atoms: 0.50 Number of scatterers: 44198 At special positions: 0 Unit cell: (148.77, 146.718, 189.81, 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 154 16.00 O 7238 8.00 N 8030 7.00 C 28776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.02 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.02 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.02 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.02 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.02 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.02 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.02 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.02 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.02 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.02 Simple disulfide: pdb=" SG CYS L 46 " - pdb=" SG CYS L 130 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 162 " distance=2.02 Simple disulfide: pdb=" SG CYS M 46 " - pdb=" SG CYS M 130 " distance=2.03 Simple disulfide: pdb=" SG CYS M 48 " - pdb=" SG CYS M 162 " distance=2.02 Simple disulfide: pdb=" SG CYS N 46 " - pdb=" SG CYS N 130 " distance=2.03 Simple disulfide: pdb=" SG CYS N 48 " - pdb=" SG CYS N 162 " distance=2.02 Simple disulfide: pdb=" SG CYS O 46 " - pdb=" SG CYS O 130 " distance=2.03 Simple disulfide: pdb=" SG CYS O 48 " - pdb=" SG CYS O 162 " distance=2.02 Simple disulfide: pdb=" SG CYS P 46 " - pdb=" SG CYS P 130 " distance=2.03 Simple disulfide: pdb=" SG CYS P 48 " - pdb=" SG CYS P 162 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 46 " - pdb=" SG CYS Q 130 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 48 " - pdb=" SG CYS Q 162 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 130 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 162 " distance=2.02 Simple disulfide: pdb=" SG CYS S 46 " - pdb=" SG CYS S 130 " distance=2.03 Simple disulfide: pdb=" SG CYS S 48 " - pdb=" SG CYS S 162 " distance=2.02 Simple disulfide: pdb=" SG CYS T 46 " - pdb=" SG CYS T 130 " distance=2.03 Simple disulfide: pdb=" SG CYS T 48 " - pdb=" SG CYS T 162 " distance=2.02 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 130 " distance=2.03 Simple disulfide: pdb=" SG CYS U 48 " - pdb=" SG CYS U 162 " distance=2.02 Simple disulfide: pdb=" SG CYS V 46 " - pdb=" SG CYS V 130 " distance=2.03 Simple disulfide: pdb=" SG CYS V 48 " - pdb=" SG CYS V 162 " distance=2.02 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: 17.61 Conformation dependent library (CDL) restraints added in 8.1 seconds 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11528 Finding SS restraints... Secondary structure from input PDB file: 330 helices and 22 sheets defined 79.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 32 through 40 Processing helix chain 'A' and resid 52 through 76 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 169 through 209 Processing helix chain 'A' and resid 214 through 251 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 52 through 76 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 120 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 169 through 209 Processing helix chain 'B' and resid 214 through 251 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 52 through 76 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.507A pdb=" N VAL C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 169 through 209 Processing helix chain 'C' and resid 214 through 251 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 52 through 76 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 169 through 209 Processing helix chain 'D' and resid 214 through 251 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 52 through 76 Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU E 155 " --> pdb=" O ALA E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 169 through 209 Processing helix chain 'E' and resid 214 through 251 Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 306 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 52 through 76 Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 111 Processing helix chain 'F' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 169 through 209 Processing helix chain 'F' and resid 214 through 251 Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 306 Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 52 through 76 Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 111 Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 133 Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 163 Processing helix chain 'G' and resid 169 through 209 Processing helix chain 'G' and resid 214 through 251 Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 306 Processing helix chain 'H' and resid 33 through 40 Processing helix chain 'H' and resid 52 through 76 Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 111 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG H 124 " --> pdb=" O ILE H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 133 Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 138 through 145 Processing helix chain 'H' and resid 149 through 159 removed outlier: 3.964A pdb=" N GLU H 155 " --> pdb=" O ALA H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 169 through 209 Processing helix chain 'H' and resid 214 through 251 Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 306 Processing helix chain 'I' and resid 33 through 40 Processing helix chain 'I' and resid 52 through 76 Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 77 through 88 removed outlier: 4.327A pdb=" N HIS I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 111 Processing helix chain 'I' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 120 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG I 124 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 133 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 138 through 145 Processing helix chain 'I' and resid 149 through 159 removed outlier: 3.964A pdb=" N GLU I 155 " --> pdb=" O ALA I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 169 through 209 Processing helix chain 'I' and resid 214 through 251 Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 306 Processing helix chain 'J' and resid 33 through 40 Processing helix chain 'J' and resid 52 through 76 Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 111 Processing helix chain 'J' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 120 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 133 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 138 through 145 Processing helix chain 'J' and resid 149 through 159 removed outlier: 3.966A pdb=" N GLU J 155 " --> pdb=" O ALA J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 163 Processing helix chain 'J' and resid 169 through 209 Processing helix chain 'J' and resid 214 through 251 Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 280 Processing helix chain 'J' and resid 297 through 306 Processing helix chain 'K' and resid 33 through 40 Processing helix chain 'K' and resid 52 through 76 Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS K 88 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 111 Processing helix chain 'K' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL K 115 " --> pdb=" O ALA K 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 120 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG K 124 " --> pdb=" O ILE K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 133 Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 138 through 145 Processing helix chain 'K' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU K 155 " --> pdb=" O ALA K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 163 Processing helix chain 'K' and resid 169 through 209 Processing helix chain 'K' and resid 214 through 251 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 280 Processing helix chain 'K' and resid 297 through 306 Processing helix chain 'L' and resid 33 through 40 Processing helix chain 'L' and resid 52 through 76 Proline residue: L 64 - end of helix Processing helix chain 'L' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS L 88 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 111 Processing helix chain 'L' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE L 120 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG L 124 " --> pdb=" O ILE L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 133 Processing helix chain 'L' and resid 134 through 136 No H-bonds generated for 'chain 'L' and resid 134 through 136' Processing helix chain 'L' and resid 138 through 145 Processing helix chain 'L' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU L 155 " --> pdb=" O ALA L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 163 Processing helix chain 'L' and resid 169 through 209 Processing helix chain 'L' and resid 214 through 251 Processing helix chain 'L' and resid 257 through 267 Processing helix chain 'L' and resid 274 through 280 Processing helix chain 'L' and resid 297 through 306 Processing helix chain 'M' and resid 33 through 40 Processing helix chain 'M' and resid 52 through 76 Proline residue: M 64 - end of helix Processing helix chain 'M' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS M 88 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 111 Processing helix chain 'M' and resid 111 through 125 removed outlier: 3.507A pdb=" N VAL M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG M 124 " --> pdb=" O ILE M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 133 Processing helix chain 'M' and resid 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU M 155 " --> pdb=" O ALA M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 163 Processing helix chain 'M' and resid 169 through 209 Processing helix chain 'M' and resid 214 through 251 Processing helix chain 'M' and resid 257 through 267 Processing helix chain 'M' and resid 274 through 280 Processing helix chain 'M' and resid 297 through 306 Processing helix chain 'N' and resid 33 through 40 Processing helix chain 'N' and resid 52 through 76 Proline residue: N 64 - end of helix Processing helix chain 'N' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS N 88 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 111 Processing helix chain 'N' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL N 115 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE N 120 " --> pdb=" O THR N 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG N 124 " --> pdb=" O ILE N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 133 Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 138 through 145 Processing helix chain 'N' and resid 149 through 159 removed outlier: 3.964A pdb=" N GLU N 155 " --> pdb=" O ALA N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 163 Processing helix chain 'N' and resid 169 through 209 Processing helix chain 'N' and resid 214 through 251 Processing helix chain 'N' and resid 257 through 267 Processing helix chain 'N' and resid 274 through 280 Processing helix chain 'N' and resid 297 through 306 Processing helix chain 'O' and resid 33 through 40 Processing helix chain 'O' and resid 52 through 76 Proline residue: O 64 - end of helix Processing helix chain 'O' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 111 Processing helix chain 'O' and resid 111 through 125 removed outlier: 3.507A pdb=" N VAL O 115 " --> pdb=" O ALA O 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE O 120 " --> pdb=" O THR O 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG O 124 " --> pdb=" O ILE O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 133 Processing helix chain 'O' and resid 134 through 136 No H-bonds generated for 'chain 'O' and resid 134 through 136' Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU O 155 " --> pdb=" O ALA O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 163 Processing helix chain 'O' and resid 169 through 209 Processing helix chain 'O' and resid 214 through 251 Processing helix chain 'O' and resid 257 through 267 Processing helix chain 'O' and resid 274 through 280 Processing helix chain 'O' and resid 297 through 306 Processing helix chain 'P' and resid 33 through 40 Processing helix chain 'P' and resid 52 through 76 Proline residue: P 64 - end of helix Processing helix chain 'P' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS P 88 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 111 Processing helix chain 'P' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE P 120 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG P 124 " --> pdb=" O ILE P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 133 Processing helix chain 'P' and resid 134 through 136 No H-bonds generated for 'chain 'P' and resid 134 through 136' Processing helix chain 'P' and resid 138 through 145 Processing helix chain 'P' and resid 149 through 159 removed outlier: 3.966A pdb=" N GLU P 155 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 163 Processing helix chain 'P' and resid 169 through 209 Processing helix chain 'P' and resid 214 through 251 Processing helix chain 'P' and resid 257 through 267 Processing helix chain 'P' and resid 274 through 280 Processing helix chain 'P' and resid 297 through 306 Processing helix chain 'Q' and resid 33 through 40 Processing helix chain 'Q' and resid 52 through 76 Proline residue: Q 64 - end of helix Processing helix chain 'Q' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS Q 88 " --> pdb=" O ALA Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 111 Processing helix chain 'Q' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL Q 115 " --> pdb=" O ALA Q 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE Q 120 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG Q 124 " --> pdb=" O ILE Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 133 Processing helix chain 'Q' and resid 134 through 136 No H-bonds generated for 'chain 'Q' and resid 134 through 136' Processing helix chain 'Q' and resid 138 through 145 Processing helix chain 'Q' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU Q 155 " --> pdb=" O ALA Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 163 Processing helix chain 'Q' and resid 169 through 209 Processing helix chain 'Q' and resid 214 through 251 Processing helix chain 'Q' and resid 257 through 267 Processing helix chain 'Q' and resid 274 through 280 Processing helix chain 'Q' and resid 297 through 306 Processing helix chain 'R' and resid 33 through 40 Processing helix chain 'R' and resid 52 through 76 Proline residue: R 64 - end of helix Processing helix chain 'R' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 111 Processing helix chain 'R' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL R 115 " --> pdb=" O ALA R 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 120 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG R 124 " --> pdb=" O ILE R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 133 Processing helix chain 'R' and resid 134 through 136 No H-bonds generated for 'chain 'R' and resid 134 through 136' Processing helix chain 'R' and resid 138 through 145 Processing helix chain 'R' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 163 Processing helix chain 'R' and resid 169 through 209 Processing helix chain 'R' and resid 214 through 251 Processing helix chain 'R' and resid 257 through 267 Processing helix chain 'R' and resid 274 through 280 Processing helix chain 'R' and resid 297 through 306 Processing helix chain 'S' and resid 33 through 40 Processing helix chain 'S' and resid 52 through 76 Proline residue: S 64 - end of helix Processing helix chain 'S' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS S 88 " --> pdb=" O ALA S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL S 115 " --> pdb=" O ALA S 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE S 120 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG S 124 " --> pdb=" O ILE S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 133 Processing helix chain 'S' and resid 134 through 136 No H-bonds generated for 'chain 'S' and resid 134 through 136' Processing helix chain 'S' and resid 138 through 145 Processing helix chain 'S' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU S 155 " --> pdb=" O ALA S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 163 Processing helix chain 'S' and resid 169 through 209 Processing helix chain 'S' and resid 214 through 251 Processing helix chain 'S' and resid 257 through 267 Processing helix chain 'S' and resid 274 through 280 Processing helix chain 'S' and resid 297 through 306 Processing helix chain 'T' and resid 33 through 40 Processing helix chain 'T' and resid 52 through 76 Proline residue: T 64 - end of helix Processing helix chain 'T' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS T 88 " --> pdb=" O ALA T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 111 Processing helix chain 'T' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL T 115 " --> pdb=" O ALA T 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE T 120 " --> pdb=" O THR T 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG T 124 " --> pdb=" O ILE T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 133 Processing helix chain 'T' and resid 134 through 136 No H-bonds generated for 'chain 'T' and resid 134 through 136' Processing helix chain 'T' and resid 138 through 145 Processing helix chain 'T' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU T 155 " --> pdb=" O ALA T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 163 Processing helix chain 'T' and resid 169 through 209 Processing helix chain 'T' and resid 214 through 251 Processing helix chain 'T' and resid 257 through 267 Processing helix chain 'T' and resid 274 through 280 Processing helix chain 'T' and resid 297 through 306 Processing helix chain 'U' and resid 33 through 40 Processing helix chain 'U' and resid 52 through 76 Proline residue: U 64 - end of helix Processing helix chain 'U' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS U 88 " --> pdb=" O ALA U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 111 Processing helix chain 'U' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL U 115 " --> pdb=" O ALA U 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE U 120 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG U 124 " --> pdb=" O ILE U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 133 Processing helix chain 'U' and resid 134 through 136 No H-bonds generated for 'chain 'U' and resid 134 through 136' Processing helix chain 'U' and resid 138 through 145 Processing helix chain 'U' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU U 155 " --> pdb=" O ALA U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 160 through 163 Processing helix chain 'U' and resid 169 through 209 Processing helix chain 'U' and resid 214 through 251 Processing helix chain 'U' and resid 257 through 267 Processing helix chain 'U' and resid 274 through 280 Processing helix chain 'U' and resid 297 through 306 Processing helix chain 'V' and resid 33 through 40 Processing helix chain 'V' and resid 52 through 76 Proline residue: V 64 - end of helix Processing helix chain 'V' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS V 88 " --> pdb=" O ALA V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 111 Processing helix chain 'V' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL V 115 " --> pdb=" O ALA V 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE V 120 " --> pdb=" O THR V 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG V 124 " --> pdb=" O ILE V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 133 Processing helix chain 'V' and resid 134 through 136 No H-bonds generated for 'chain 'V' and resid 134 through 136' Processing helix chain 'V' and resid 138 through 145 Processing helix chain 'V' and resid 149 through 159 removed outlier: 3.966A pdb=" N GLU V 155 " --> pdb=" O ALA V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 163 Processing helix chain 'V' and resid 169 through 209 Processing helix chain 'V' and resid 214 through 251 Processing helix chain 'V' and resid 257 through 267 Processing helix chain 'V' and resid 274 through 280 Processing helix chain 'V' and resid 297 through 306 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AA2, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AA3, first strand: chain 'C' and resid 289 through 290 Processing sheet with id=AA4, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AA5, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AA6, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AA7, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AA8, first strand: chain 'H' and resid 289 through 290 Processing sheet with id=AA9, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AB1, first strand: chain 'J' and resid 289 through 290 Processing sheet with id=AB2, first strand: chain 'K' and resid 289 through 290 Processing sheet with id=AB3, first strand: chain 'L' and resid 289 through 290 Processing sheet with id=AB4, first strand: chain 'M' and resid 289 through 290 Processing sheet with id=AB5, first strand: chain 'N' and resid 289 through 290 Processing sheet with id=AB6, first strand: chain 'O' and resid 289 through 290 Processing sheet with id=AB7, first strand: chain 'P' and resid 289 through 290 Processing sheet with id=AB8, first strand: chain 'Q' and resid 289 through 290 Processing sheet with id=AB9, first strand: chain 'R' and resid 289 through 290 Processing sheet with id=AC1, first strand: chain 'S' and resid 289 through 290 Processing sheet with id=AC2, first strand: chain 'T' and resid 289 through 290 Processing sheet with id=AC3, first strand: chain 'U' and resid 289 through 290 Processing sheet with id=AC4, first strand: chain 'V' and resid 289 through 290 3389 hydrogen bonds defined for protein. 10035 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: 15.67 Time building geometry restraints manager: 19.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14263 1.34 - 1.46: 10720 1.46 - 1.58: 20249 1.58 - 1.70: 0 1.70 - 1.81: 154 Bond restraints: 45386 Sorted by residual: bond pdb=" CB VAL E 247 " pdb=" CG1 VAL E 247 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.89e+00 bond pdb=" CB VAL Q 247 " pdb=" CG1 VAL Q 247 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.86e+00 bond pdb=" CB VAL N 247 " pdb=" CG1 VAL N 247 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.86e+00 bond pdb=" CB VAL P 247 " pdb=" CG1 VAL P 247 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.85e+00 bond pdb=" CB VAL F 247 " pdb=" CG1 VAL F 247 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.82e+00 ... (remaining 45381 not shown) Histogram of bond angle deviations from ideal: 102.23 - 108.63: 2761 108.63 - 115.03: 25442 115.03 - 121.43: 24399 121.43 - 127.83: 9128 127.83 - 134.23: 574 Bond angle restraints: 62304 Sorted by residual: angle pdb=" N GLY V 62 " pdb=" CA GLY V 62 " pdb=" C GLY V 62 " ideal model delta sigma weight residual 112.49 116.69 -4.20 1.21e+00 6.83e-01 1.20e+01 angle pdb=" N GLY D 62 " pdb=" CA GLY D 62 " pdb=" C GLY D 62 " ideal model delta sigma weight residual 112.49 116.68 -4.19 1.21e+00 6.83e-01 1.20e+01 angle pdb=" N GLY K 62 " pdb=" CA GLY K 62 " pdb=" C GLY K 62 " ideal model delta sigma weight residual 112.49 116.68 -4.19 1.21e+00 6.83e-01 1.20e+01 angle pdb=" N GLY G 62 " pdb=" CA GLY G 62 " pdb=" C GLY G 62 " ideal model delta sigma weight residual 112.49 116.66 -4.17 1.21e+00 6.83e-01 1.19e+01 angle pdb=" N GLY R 62 " pdb=" CA GLY R 62 " pdb=" C GLY R 62 " ideal model delta sigma weight residual 112.49 116.66 -4.17 1.21e+00 6.83e-01 1.19e+01 ... (remaining 62299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 23438 15.00 - 30.01: 2301 30.01 - 45.01: 661 45.01 - 60.01: 88 60.01 - 75.01: 44 Dihedral angle restraints: 26532 sinusoidal: 8734 harmonic: 17798 Sorted by residual: dihedral pdb=" CA LEU H 256 " pdb=" C LEU H 256 " pdb=" N ASN H 257 " pdb=" CA ASN H 257 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU S 256 " pdb=" C LEU S 256 " pdb=" N ASN S 257 " pdb=" CA ASN S 257 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU L 256 " pdb=" C LEU L 256 " pdb=" N ASN L 257 " pdb=" CA ASN L 257 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 26529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3791 0.034 - 0.068: 1931 0.068 - 0.102: 1087 0.102 - 0.136: 287 0.136 - 0.169: 142 Chirality restraints: 7238 Sorted by residual: chirality pdb=" CA THR I 234 " pdb=" N THR I 234 " pdb=" C THR I 234 " pdb=" CB THR I 234 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA THR B 234 " pdb=" N THR B 234 " pdb=" C THR B 234 " pdb=" CB THR B 234 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA THR U 234 " pdb=" N THR U 234 " pdb=" C THR U 234 " pdb=" CB THR U 234 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 7235 not shown) Planarity restraints: 7986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 113 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO L 114 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 114 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 114 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 113 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO J 114 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO J 114 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 114 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Q 113 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO Q 114 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO Q 114 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO Q 114 " -0.030 5.00e-02 4.00e+02 ... (remaining 7983 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 6203 2.74 - 3.28: 45562 3.28 - 3.82: 79557 3.82 - 4.36: 84921 4.36 - 4.90: 147452 Nonbonded interactions: 363695 Sorted by model distance: nonbonded pdb=" OD1 ASN L 226 " pdb=" OG SER M 239 " model vdw 2.204 2.440 nonbonded pdb=" OD1 ASN A 226 " pdb=" OG SER B 239 " model vdw 2.204 2.440 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASN K 226 " model vdw 2.207 2.440 nonbonded pdb=" OD1 ASN F 226 " pdb=" OG SER G 239 " model vdw 2.208 2.440 nonbonded pdb=" OG SER L 239 " pdb=" OD1 ASN V 226 " model vdw 2.208 2.440 ... (remaining 363690 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' } 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.510 Check model and map are aligned: 0.630 Set scattering table: 0.370 Process input model: 108.710 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.009 0.073 45386 Z= 0.579 Angle : 0.958 7.888 62304 Z= 0.540 Chirality : 0.054 0.169 7238 Planarity : 0.008 0.053 7986 Dihedral : 13.688 75.013 14872 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % 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: -3.80 (0.08), residues: 6006 helix: -2.20 (0.06), residues: 4444 sheet: None (None), residues: 0 loop : -2.89 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 80 HIS 0.004 0.001 HIS E 78 PHE 0.012 0.002 PHE J 253 TYR 0.020 0.003 TYR U 214 ARG 0.005 0.001 ARG L 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 4.391 Fit side-chains revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8726 (t0) cc_final: 0.8514 (t0) REVERT: A 233 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7907 (mtp180) REVERT: D 233 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7872 (mtp180) REVERT: F 228 ASP cc_start: 0.8702 (t0) cc_final: 0.8484 (t0) REVERT: F 233 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7883 (mtp180) REVERT: G 228 ASP cc_start: 0.8602 (t0) cc_final: 0.8347 (t0) REVERT: J 228 ASP cc_start: 0.8735 (t0) cc_final: 0.8443 (t0) REVERT: K 228 ASP cc_start: 0.8596 (t0) cc_final: 0.8344 (t0) REVERT: L 126 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8740 (pm20) REVERT: L 228 ASP cc_start: 0.8643 (t0) cc_final: 0.8393 (t0) REVERT: M 126 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8514 (mp0) REVERT: M 228 ASP cc_start: 0.8757 (t0) cc_final: 0.8463 (t0) REVERT: N 126 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8560 (mp0) REVERT: N 228 ASP cc_start: 0.8620 (t0) cc_final: 0.8407 (t0) REVERT: O 126 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8737 (pm20) REVERT: O 228 ASP cc_start: 0.8561 (t0) cc_final: 0.8265 (t0) REVERT: P 126 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8779 (pm20) REVERT: P 228 ASP cc_start: 0.8616 (t0) cc_final: 0.8379 (t0) REVERT: Q 126 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8547 (mp0) REVERT: Q 228 ASP cc_start: 0.8608 (t0) cc_final: 0.8364 (t0) REVERT: R 126 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8548 (pm20) REVERT: R 228 ASP cc_start: 0.8618 (t0) cc_final: 0.8278 (t0) REVERT: R 232 GLN cc_start: 0.9131 (mm110) cc_final: 0.8923 (mm110) REVERT: S 126 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8580 (mp0) REVERT: S 228 ASP cc_start: 0.8605 (t0) cc_final: 0.8379 (t0) REVERT: T 126 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8603 (mp0) REVERT: T 228 ASP cc_start: 0.8705 (t0) cc_final: 0.8472 (t0) REVERT: U 126 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8555 (mp0) REVERT: U 228 ASP cc_start: 0.8613 (t0) cc_final: 0.8392 (t0) REVERT: V 126 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8454 (mp0) REVERT: V 228 ASP cc_start: 0.8564 (t0) cc_final: 0.8337 (t0) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.5046 time to fit residues: 241.1858 Evaluate side-chains 184 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 4.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 501 optimal weight: 9.9990 chunk 450 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 465 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 346 optimal weight: 1.9990 chunk 539 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 246 ASN A 273 GLN A 279 ASN B 226 ASN B 246 ASN B 273 GLN B 279 ASN C 226 ASN C 246 ASN C 273 GLN C 279 ASN D 226 ASN D 246 ASN D 273 GLN D 279 ASN E 226 ASN E 246 ASN E 273 GLN E 279 ASN F 226 ASN F 246 ASN F 273 GLN F 279 ASN G 226 ASN G 246 ASN G 273 GLN G 279 ASN H 226 ASN H 246 ASN H 273 GLN H 279 ASN I 226 ASN I 246 ASN I 273 GLN I 279 ASN J 226 ASN J 246 ASN J 273 GLN J 279 ASN K 226 ASN K 246 ASN K 273 GLN K 279 ASN L 226 ASN L 246 ASN L 273 GLN L 279 ASN M 226 ASN M 246 ASN M 273 GLN M 279 ASN N 226 ASN N 246 ASN N 273 GLN N 279 ASN O 226 ASN O 246 ASN O 273 GLN O 279 ASN P 226 ASN P 246 ASN P 273 GLN P 279 ASN Q 226 ASN Q 246 ASN Q 273 GLN Q 279 ASN R 226 ASN R 246 ASN R 273 GLN R 279 ASN S 226 ASN S 246 ASN S 273 GLN S 279 ASN T 226 ASN T 246 ASN T 273 GLN T 279 ASN U 226 ASN U 246 ASN U 273 GLN U 279 ASN V 226 ASN V 246 ASN V 273 GLN V 279 ASN Total number of N/Q/H flips: 88 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 45386 Z= 0.178 Angle : 0.579 6.396 62304 Z= 0.297 Chirality : 0.034 0.139 7238 Planarity : 0.004 0.029 7986 Dihedral : 4.680 18.441 6644 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.29 % Allowed : 15.38 % Favored : 84.34 % 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: -0.76 (0.10), residues: 6006 helix: 0.16 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.49 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 80 HIS 0.003 0.001 HIS L 78 PHE 0.011 0.001 PHE L 69 TYR 0.009 0.001 TYR P 223 ARG 0.003 0.000 ARG E 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 230 time to evaluate : 6.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8634 (t0) cc_final: 0.8417 (t0) REVERT: F 228 ASP cc_start: 0.8567 (t0) cc_final: 0.8360 (t0) REVERT: G 228 ASP cc_start: 0.8522 (t0) cc_final: 0.8241 (t0) REVERT: J 228 ASP cc_start: 0.8697 (t0) cc_final: 0.8418 (t0) REVERT: L 126 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8835 (pm20) REVERT: M 126 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8665 (pm20) REVERT: M 228 ASP cc_start: 0.8660 (t0) cc_final: 0.8354 (t0) REVERT: N 126 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8693 (pm20) REVERT: N 228 ASP cc_start: 0.8538 (t0) cc_final: 0.8291 (t0) REVERT: O 126 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8790 (pm20) REVERT: O 228 ASP cc_start: 0.8463 (t0) cc_final: 0.8199 (t0) REVERT: P 126 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8855 (pm20) REVERT: P 228 ASP cc_start: 0.8556 (t0) cc_final: 0.8337 (t0) REVERT: Q 126 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8745 (pm20) REVERT: Q 228 ASP cc_start: 0.8485 (t0) cc_final: 0.8262 (t0) REVERT: R 126 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8667 (pm20) REVERT: R 228 ASP cc_start: 0.8560 (t0) cc_final: 0.8171 (t0) REVERT: R 232 GLN cc_start: 0.9024 (mm110) cc_final: 0.8751 (mm110) REVERT: S 126 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8729 (pm20) REVERT: T 126 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8846 (pm20) REVERT: T 228 ASP cc_start: 0.8589 (t0) cc_final: 0.8314 (t0) REVERT: U 126 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8792 (pm20) REVERT: U 228 ASP cc_start: 0.8541 (t0) cc_final: 0.8328 (t0) REVERT: V 126 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8700 (pm20) REVERT: V 228 ASP cc_start: 0.8564 (t0) cc_final: 0.8292 (t0) outliers start: 11 outliers final: 11 residues processed: 230 average time/residue: 0.5174 time to fit residues: 207.8128 Evaluate side-chains 205 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 5.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 299 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 448 optimal weight: 6.9990 chunk 367 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 540 optimal weight: 80.0000 chunk 583 optimal weight: 7.9990 chunk 481 optimal weight: 0.7980 chunk 535 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 433 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN D 81 ASN E 81 ASN G 81 ASN H 81 ASN J 81 ASN R 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 45386 Z= 0.152 Angle : 0.530 7.188 62304 Z= 0.271 Chirality : 0.034 0.107 7238 Planarity : 0.003 0.025 7986 Dihedral : 4.187 16.052 6644 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.08 % Allowed : 18.62 % Favored : 81.30 % 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 (0.11), residues: 6006 helix: 1.26 (0.08), residues: 4554 sheet: None (None), residues: 0 loop : -2.09 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 302 HIS 0.003 0.001 HIS V 78 PHE 0.012 0.001 PHE N 69 TYR 0.006 0.001 TYR G 287 ARG 0.005 0.000 ARG V 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 4.245 Fit side-chains revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8634 (t0) cc_final: 0.8383 (t0) REVERT: A 229 GLN cc_start: 0.8347 (tm-30) cc_final: 0.8080 (tm-30) REVERT: B 227 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: D 227 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: F 228 ASP cc_start: 0.8560 (t0) cc_final: 0.8354 (t0) REVERT: G 228 ASP cc_start: 0.8529 (t0) cc_final: 0.8235 (t0) REVERT: J 228 ASP cc_start: 0.8732 (t0) cc_final: 0.8411 (t0) REVERT: K 227 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: L 126 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8875 (pm20) REVERT: M 126 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8684 (pm20) REVERT: M 228 ASP cc_start: 0.8649 (t0) cc_final: 0.8362 (t0) REVERT: N 126 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8726 (pm20) REVERT: N 228 ASP cc_start: 0.8539 (t0) cc_final: 0.8270 (t0) REVERT: O 126 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8820 (pm20) REVERT: O 228 ASP cc_start: 0.8503 (t0) cc_final: 0.8282 (t0) REVERT: P 126 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8876 (pm20) REVERT: P 228 ASP cc_start: 0.8569 (t0) cc_final: 0.8322 (t0) REVERT: Q 126 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8748 (pm20) REVERT: Q 228 ASP cc_start: 0.8508 (t0) cc_final: 0.8276 (t0) REVERT: R 126 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8800 (pm20) REVERT: R 228 ASP cc_start: 0.8581 (t0) cc_final: 0.8343 (t0) REVERT: S 126 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8766 (pm20) REVERT: T 126 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8867 (pm20) REVERT: T 228 ASP cc_start: 0.8605 (t0) cc_final: 0.8317 (t0) REVERT: U 126 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8823 (pm20) REVERT: U 228 ASP cc_start: 0.8570 (t0) cc_final: 0.8326 (t0) REVERT: V 126 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8814 (pm20) REVERT: V 228 ASP cc_start: 0.8636 (t0) cc_final: 0.8313 (t0) outliers start: 3 outliers final: 0 residues processed: 236 average time/residue: 0.4910 time to fit residues: 202.2253 Evaluate side-chains 194 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 4.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain K residue 227 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 533 optimal weight: 0.9980 chunk 406 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 257 optimal weight: 20.0000 chunk 362 optimal weight: 20.0000 chunk 542 optimal weight: 7.9990 chunk 574 optimal weight: 20.0000 chunk 283 optimal weight: 0.0060 chunk 513 optimal weight: 90.0000 chunk 154 optimal weight: 9.9990 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN B 246 ASN C 246 ASN D 246 ASN E 246 ASN F 246 ASN G 246 ASN H 246 ASN I 246 ASN J 246 ASN K 246 ASN L 246 ASN M 246 ASN N 246 ASN O 246 ASN P 246 ASN Q 246 ASN R 246 ASN S 246 ASN T 246 ASN U 246 ASN V 246 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 45386 Z= 0.308 Angle : 0.585 6.728 62304 Z= 0.305 Chirality : 0.036 0.141 7238 Planarity : 0.004 0.025 7986 Dihedral : 4.134 14.610 6644 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.35 % Allowed : 19.27 % Favored : 79.38 % 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: 1.42 (0.11), residues: 6006 helix: 1.80 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -2.10 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 80 HIS 0.003 0.001 HIS S 78 PHE 0.037 0.001 PHE U 69 TYR 0.012 0.001 TYR B 223 ARG 0.003 0.000 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 4.669 Fit side-chains revert: symmetry clash REVERT: A 227 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: A 228 ASP cc_start: 0.8759 (t0) cc_final: 0.8513 (t0) REVERT: B 227 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: C 227 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: D 222 GLN cc_start: 0.8966 (mt0) cc_final: 0.8672 (tt0) REVERT: D 227 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: E 227 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: G 227 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: G 228 ASP cc_start: 0.8671 (t0) cc_final: 0.8405 (t0) REVERT: H 227 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: H 229 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8311 (tm-30) REVERT: I 227 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: J 222 GLN cc_start: 0.8993 (mt0) cc_final: 0.8594 (tt0) REVERT: J 227 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: J 228 ASP cc_start: 0.8777 (t0) cc_final: 0.8503 (t0) REVERT: K 227 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: L 126 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8864 (pm20) REVERT: L 228 ASP cc_start: 0.8830 (t0) cc_final: 0.8456 (t0) REVERT: M 126 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8696 (pm20) REVERT: M 222 GLN cc_start: 0.9057 (mt0) cc_final: 0.8827 (tt0) REVERT: M 228 ASP cc_start: 0.8802 (t0) cc_final: 0.8487 (t0) REVERT: N 126 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8788 (pm20) REVERT: N 228 ASP cc_start: 0.8672 (t0) cc_final: 0.8430 (t0) REVERT: O 126 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8841 (pm20) REVERT: O 228 ASP cc_start: 0.8676 (t0) cc_final: 0.8436 (t0) REVERT: P 126 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8890 (pm20) REVERT: P 228 ASP cc_start: 0.8689 (t0) cc_final: 0.8436 (t0) REVERT: Q 126 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8781 (pm20) REVERT: Q 228 ASP cc_start: 0.8640 (t0) cc_final: 0.8403 (t0) REVERT: R 126 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8824 (pm20) REVERT: R 228 ASP cc_start: 0.8705 (t0) cc_final: 0.8491 (t0) REVERT: S 126 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8783 (pm20) REVERT: T 126 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8908 (pm20) REVERT: T 228 ASP cc_start: 0.8760 (t0) cc_final: 0.8498 (t0) REVERT: U 126 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8843 (pm20) REVERT: U 228 ASP cc_start: 0.8656 (t0) cc_final: 0.8434 (t0) REVERT: V 126 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8834 (pm20) REVERT: V 228 ASP cc_start: 0.8656 (t0) cc_final: 0.8425 (t0) outliers start: 52 outliers final: 40 residues processed: 227 average time/residue: 0.4554 time to fit residues: 187.3705 Evaluate side-chains 220 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 170 time to evaluate : 4.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 260 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 260 ASP Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 260 ASP Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 260 ASP Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 260 ASP Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 260 ASP Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 260 ASP Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 232 GLN Chi-restraints excluded: chain S residue 260 ASP Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 260 ASP Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 260 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 478 optimal weight: 1.9990 chunk 325 optimal weight: 30.0000 chunk 8 optimal weight: 0.1980 chunk 427 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 489 optimal weight: 6.9990 chunk 396 optimal weight: 4.9990 chunk 0 optimal weight: 100.0000 chunk 293 optimal weight: 7.9990 chunk 515 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN B 81 ASN B 246 ASN C 81 ASN C 246 ASN D 246 ASN E 246 ASN F 246 ASN G 246 ASN H 246 ASN I 246 ASN J 246 ASN K 246 ASN L 246 ASN M 246 ASN O 246 ASN Q 246 ASN R 246 ASN T 246 ASN U 246 ASN V 246 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 45386 Z= 0.214 Angle : 0.542 7.606 62304 Z= 0.278 Chirality : 0.035 0.105 7238 Planarity : 0.003 0.025 7986 Dihedral : 4.024 13.778 6644 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.58 % Allowed : 19.95 % Favored : 78.47 % 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: 1.80 (0.11), residues: 6006 helix: 2.08 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -2.00 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 80 HIS 0.002 0.001 HIS T 78 PHE 0.033 0.001 PHE L 69 TYR 0.005 0.001 TYR G 287 ARG 0.002 0.000 ARG T 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 188 time to evaluate : 4.764 Fit side-chains REVERT: A 227 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: A 228 ASP cc_start: 0.8731 (t0) cc_final: 0.8484 (t0) REVERT: B 222 GLN cc_start: 0.9056 (mt0) cc_final: 0.8805 (tt0) REVERT: B 227 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: D 227 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: E 227 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: G 227 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: G 228 ASP cc_start: 0.8638 (t0) cc_final: 0.8359 (t0) REVERT: H 227 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: I 227 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: J 227 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: J 228 ASP cc_start: 0.8745 (t0) cc_final: 0.8461 (t0) REVERT: K 222 GLN cc_start: 0.8941 (mt0) cc_final: 0.8645 (tt0) REVERT: L 126 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8857 (pm20) REVERT: L 228 ASP cc_start: 0.8812 (t0) cc_final: 0.8434 (t0) REVERT: M 126 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8695 (pm20) REVERT: M 228 ASP cc_start: 0.8742 (t0) cc_final: 0.8425 (t0) REVERT: N 126 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8768 (pm20) REVERT: N 228 ASP cc_start: 0.8629 (t0) cc_final: 0.8390 (t0) REVERT: O 126 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8836 (pm20) REVERT: O 228 ASP cc_start: 0.8660 (t0) cc_final: 0.8395 (t0) REVERT: P 126 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8872 (pm20) REVERT: P 228 ASP cc_start: 0.8665 (t0) cc_final: 0.8413 (t0) REVERT: Q 126 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8770 (pm20) REVERT: Q 228 ASP cc_start: 0.8592 (t0) cc_final: 0.8341 (t0) REVERT: R 126 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8824 (pm20) REVERT: R 228 ASP cc_start: 0.8683 (t0) cc_final: 0.8444 (t0) REVERT: S 126 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8767 (pm20) REVERT: T 126 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8901 (pm20) REVERT: T 228 ASP cc_start: 0.8738 (t0) cc_final: 0.8448 (t0) REVERT: U 126 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8835 (pm20) REVERT: U 228 ASP cc_start: 0.8643 (t0) cc_final: 0.8403 (t0) REVERT: V 126 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8827 (pm20) REVERT: V 228 ASP cc_start: 0.8599 (t0) cc_final: 0.8351 (t0) outliers start: 61 outliers final: 34 residues processed: 238 average time/residue: 0.4654 time to fit residues: 200.0609 Evaluate side-chains 219 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 177 time to evaluate : 5.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 260 ASP Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 260 ASP Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 193 optimal weight: 20.0000 chunk 517 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 337 optimal weight: 0.3980 chunk 141 optimal weight: 8.9990 chunk 574 optimal weight: 6.9990 chunk 477 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 301 optimal weight: 8.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN C 246 ASN E 246 ASN F 246 ASN G 246 ASN I 246 ASN K 246 ASN L 246 ASN M 246 ASN O 246 ASN Q 246 ASN R 246 ASN T 246 ASN U 246 ASN V 246 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 45386 Z= 0.271 Angle : 0.578 8.480 62304 Z= 0.294 Chirality : 0.036 0.165 7238 Planarity : 0.003 0.024 7986 Dihedral : 3.990 13.684 6644 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.44 % Allowed : 20.08 % Favored : 77.48 % 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: 2.03 (0.12), residues: 6006 helix: 2.25 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.96 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 80 HIS 0.003 0.001 HIS S 78 PHE 0.030 0.001 PHE L 69 TYR 0.009 0.001 TYR N 223 ARG 0.007 0.000 ARG H 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 183 time to evaluate : 4.578 Fit side-chains REVERT: A 227 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: A 228 ASP cc_start: 0.8692 (t0) cc_final: 0.8415 (t0) REVERT: B 227 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: D 222 GLN cc_start: 0.8950 (mt0) cc_final: 0.8718 (tt0) REVERT: D 227 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: E 222 GLN cc_start: 0.8962 (mt0) cc_final: 0.8573 (tt0) REVERT: E 227 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: G 227 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: G 228 ASP cc_start: 0.8684 (t0) cc_final: 0.8405 (t0) REVERT: H 222 GLN cc_start: 0.9026 (mt0) cc_final: 0.8756 (tt0) REVERT: I 191 LEU cc_start: 0.9761 (tt) cc_final: 0.9535 (pp) REVERT: I 227 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: I 229 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8349 (tm-30) REVERT: J 227 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: J 228 ASP cc_start: 0.8769 (t0) cc_final: 0.8511 (t0) REVERT: K 228 ASP cc_start: 0.8868 (t0) cc_final: 0.8662 (t0) REVERT: L 126 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8860 (pm20) REVERT: L 228 ASP cc_start: 0.8848 (t0) cc_final: 0.8474 (t0) REVERT: M 126 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8705 (pm20) REVERT: M 228 ASP cc_start: 0.8810 (t0) cc_final: 0.8486 (t0) REVERT: N 126 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8778 (pm20) REVERT: N 222 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (tt0) REVERT: N 228 ASP cc_start: 0.8679 (t0) cc_final: 0.8417 (t0) REVERT: O 126 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8846 (pm20) REVERT: O 228 ASP cc_start: 0.8674 (t0) cc_final: 0.8420 (t0) REVERT: P 126 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8869 (pm20) REVERT: P 228 ASP cc_start: 0.8714 (t0) cc_final: 0.8462 (t0) REVERT: Q 126 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8789 (pm20) REVERT: Q 228 ASP cc_start: 0.8648 (t0) cc_final: 0.8425 (t0) REVERT: R 126 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8823 (pm20) REVERT: R 228 ASP cc_start: 0.8734 (t0) cc_final: 0.8487 (t0) REVERT: S 126 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8766 (pm20) REVERT: T 126 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8903 (pm20) REVERT: T 228 ASP cc_start: 0.8776 (t0) cc_final: 0.8493 (t0) REVERT: U 126 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8845 (pm20) REVERT: U 228 ASP cc_start: 0.8680 (t0) cc_final: 0.8447 (t0) REVERT: V 126 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8835 (pm20) REVERT: V 228 ASP cc_start: 0.8643 (t0) cc_final: 0.8380 (t0) outliers start: 94 outliers final: 62 residues processed: 257 average time/residue: 0.4420 time to fit residues: 206.0925 Evaluate side-chains 240 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 170 time to evaluate : 4.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 260 ASP Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 260 ASP Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 260 ASP Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain N residue 260 ASP Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 260 ASP Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 260 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 232 GLN Chi-restraints excluded: chain S residue 260 ASP Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 260 ASP Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 260 ASP Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 260 ASP Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 554 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 327 optimal weight: 4.9990 chunk 419 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 483 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 572 optimal weight: 3.9990 chunk 358 optimal weight: 8.9990 chunk 349 optimal weight: 9.9990 chunk 264 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN C 246 ASN E 246 ASN F 246 ASN I 246 ASN R 45 HIS S 45 HIS V 246 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 45386 Z= 0.255 Angle : 0.576 8.265 62304 Z= 0.292 Chirality : 0.036 0.175 7238 Planarity : 0.003 0.024 7986 Dihedral : 3.961 13.722 6644 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.52 % Allowed : 20.18 % Favored : 77.30 % 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: 2.14 (0.12), residues: 6006 helix: 2.33 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.89 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 80 HIS 0.003 0.001 HIS K 238 PHE 0.029 0.001 PHE L 69 TYR 0.006 0.001 TYR S 223 ARG 0.002 0.000 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 172 time to evaluate : 5.023 Fit side-chains REVERT: A 227 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: A 228 ASP cc_start: 0.8697 (t0) cc_final: 0.8425 (t0) REVERT: B 222 GLN cc_start: 0.9064 (mt0) cc_final: 0.8836 (tt0) REVERT: B 227 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: D 222 GLN cc_start: 0.8951 (mt0) cc_final: 0.8690 (tt0) REVERT: D 227 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: E 222 GLN cc_start: 0.8956 (mt0) cc_final: 0.8702 (tt0) REVERT: E 227 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: G 227 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: G 228 ASP cc_start: 0.8684 (t0) cc_final: 0.8396 (t0) REVERT: I 191 LEU cc_start: 0.9745 (tt) cc_final: 0.9518 (pp) REVERT: I 227 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: K 222 GLN cc_start: 0.8959 (mt0) cc_final: 0.8742 (tt0) REVERT: L 126 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8903 (pm20) REVERT: L 228 ASP cc_start: 0.8851 (t0) cc_final: 0.8477 (t0) REVERT: M 126 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8706 (pm20) REVERT: M 228 ASP cc_start: 0.8804 (t0) cc_final: 0.8489 (t0) REVERT: N 126 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8790 (pm20) REVERT: N 228 ASP cc_start: 0.8689 (t0) cc_final: 0.8407 (t0) REVERT: O 126 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8852 (pm20) REVERT: O 228 ASP cc_start: 0.8679 (t0) cc_final: 0.8427 (t0) REVERT: P 126 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8867 (pm20) REVERT: P 228 ASP cc_start: 0.8714 (t0) cc_final: 0.8457 (t0) REVERT: Q 126 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8779 (pm20) REVERT: Q 228 ASP cc_start: 0.8641 (t0) cc_final: 0.8402 (t0) REVERT: R 126 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8816 (pm20) REVERT: R 222 GLN cc_start: 0.9039 (mt0) cc_final: 0.8735 (tt0) REVERT: R 228 ASP cc_start: 0.8741 (t0) cc_final: 0.8394 (t0) REVERT: S 126 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8750 (pm20) REVERT: T 126 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8902 (pm20) REVERT: T 228 ASP cc_start: 0.8758 (t0) cc_final: 0.8475 (t0) REVERT: U 126 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8838 (pm20) REVERT: U 228 ASP cc_start: 0.8677 (t0) cc_final: 0.8449 (t0) REVERT: V 126 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8829 (pm20) REVERT: V 228 ASP cc_start: 0.8647 (t0) cc_final: 0.8385 (t0) outliers start: 97 outliers final: 74 residues processed: 255 average time/residue: 0.4418 time to fit residues: 206.2193 Evaluate side-chains 243 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 163 time to evaluate : 5.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 260 ASP Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 260 ASP Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 260 ASP Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 260 ASP Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 260 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 260 ASP Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 260 ASP Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 260 ASP Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 354 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 chunk 341 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 363 optimal weight: 0.0870 chunk 390 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 450 optimal weight: 3.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN G 246 ASN K 246 ASN L 246 ASN M 246 ASN O 246 ASN P 45 HIS P 246 ASN Q 246 ASN R 246 ASN S 246 ASN T 246 ASN U 45 HIS U 246 ASN V 45 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 45386 Z= 0.172 Angle : 0.561 9.682 62304 Z= 0.277 Chirality : 0.035 0.171 7238 Planarity : 0.003 0.024 7986 Dihedral : 3.867 13.516 6644 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.74 % Allowed : 20.68 % Favored : 77.58 % 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: 2.30 (0.12), residues: 6006 helix: 2.43 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.81 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 302 HIS 0.002 0.001 HIS M 88 PHE 0.028 0.001 PHE L 69 TYR 0.007 0.001 TYR F 287 ARG 0.002 0.000 ARG K 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 195 time to evaluate : 5.566 Fit side-chains REVERT: A 227 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: A 228 ASP cc_start: 0.8721 (t0) cc_final: 0.8422 (t0) REVERT: B 222 GLN cc_start: 0.9047 (mt0) cc_final: 0.8817 (tt0) REVERT: D 222 GLN cc_start: 0.8954 (mt0) cc_final: 0.8666 (tt0) REVERT: D 227 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: E 222 GLN cc_start: 0.8934 (mt0) cc_final: 0.8677 (tt0) REVERT: E 227 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: G 227 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: G 228 ASP cc_start: 0.8606 (t0) cc_final: 0.8309 (t0) REVERT: I 191 LEU cc_start: 0.9731 (tt) cc_final: 0.9514 (pp) REVERT: I 227 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: I 229 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8393 (tm-30) REVERT: K 222 GLN cc_start: 0.8925 (mt0) cc_final: 0.8628 (tt0) REVERT: L 126 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8875 (pm20) REVERT: L 228 ASP cc_start: 0.8830 (t0) cc_final: 0.8461 (t0) REVERT: M 126 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8705 (pm20) REVERT: M 228 ASP cc_start: 0.8739 (t0) cc_final: 0.8414 (t0) REVERT: N 126 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8763 (pm20) REVERT: N 222 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: N 228 ASP cc_start: 0.8614 (t0) cc_final: 0.8337 (t0) REVERT: O 126 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8840 (pm20) REVERT: O 228 ASP cc_start: 0.8656 (t0) cc_final: 0.8382 (t0) REVERT: P 126 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8854 (pm20) REVERT: P 228 ASP cc_start: 0.8653 (t0) cc_final: 0.8384 (t0) REVERT: Q 126 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8769 (pm20) REVERT: Q 228 ASP cc_start: 0.8560 (t0) cc_final: 0.8306 (t0) REVERT: R 126 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8803 (pm20) REVERT: R 222 GLN cc_start: 0.9012 (mt0) cc_final: 0.8804 (tt0) REVERT: R 228 ASP cc_start: 0.8653 (t0) cc_final: 0.8388 (t0) REVERT: S 126 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8742 (pm20) REVERT: T 126 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8892 (pm20) REVERT: T 228 ASP cc_start: 0.8729 (t0) cc_final: 0.8458 (t0) REVERT: U 126 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8838 (pm20) REVERT: U 228 ASP cc_start: 0.8642 (t0) cc_final: 0.8396 (t0) REVERT: V 126 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8801 (pm20) REVERT: V 228 ASP cc_start: 0.8594 (t0) cc_final: 0.8319 (t0) outliers start: 67 outliers final: 55 residues processed: 257 average time/residue: 0.4530 time to fit residues: 214.2361 Evaluate side-chains 234 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 173 time to evaluate : 5.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 232 GLN Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 520 optimal weight: 9.9990 chunk 548 optimal weight: 0.7980 chunk 500 optimal weight: 5.9990 chunk 533 optimal weight: 2.9990 chunk 321 optimal weight: 0.0020 chunk 232 optimal weight: 3.9990 chunk 418 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 482 optimal weight: 0.7980 chunk 504 optimal weight: 4.9990 chunk 531 optimal weight: 5.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN F 45 HIS G 246 ASN L 45 HIS M 45 HIS N 45 HIS N 246 ASN O 45 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 45386 Z= 0.158 Angle : 0.559 9.491 62304 Z= 0.275 Chirality : 0.035 0.174 7238 Planarity : 0.003 0.023 7986 Dihedral : 3.779 14.227 6644 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.87 % Allowed : 20.91 % Favored : 77.22 % 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: 2.42 (0.12), residues: 6006 helix: 2.51 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.74 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 117 HIS 0.002 0.001 HIS I 88 PHE 0.027 0.001 PHE L 69 TYR 0.006 0.001 TYR U 287 ARG 0.005 0.000 ARG N 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 221 time to evaluate : 4.731 Fit side-chains REVERT: A 227 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: A 228 ASP cc_start: 0.8696 (t0) cc_final: 0.8411 (t0) REVERT: A 229 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8321 (tm-30) REVERT: D 222 GLN cc_start: 0.8957 (mt0) cc_final: 0.8659 (tt0) REVERT: D 227 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: E 222 GLN cc_start: 0.8936 (mt0) cc_final: 0.8736 (tt0) REVERT: E 227 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: G 227 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: G 228 ASP cc_start: 0.8577 (t0) cc_final: 0.8289 (t0) REVERT: I 191 LEU cc_start: 0.9722 (tt) cc_final: 0.9488 (pp) REVERT: I 229 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8272 (tm-30) REVERT: J 227 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8463 (tm-30) REVERT: L 126 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8827 (pm20) REVERT: L 228 ASP cc_start: 0.8798 (t0) cc_final: 0.8435 (t0) REVERT: M 126 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8725 (pm20) REVERT: M 228 ASP cc_start: 0.8726 (t0) cc_final: 0.8414 (t0) REVERT: N 126 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8745 (pm20) REVERT: N 222 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: N 228 ASP cc_start: 0.8597 (t0) cc_final: 0.8315 (t0) REVERT: O 126 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8839 (pm20) REVERT: O 228 ASP cc_start: 0.8647 (t0) cc_final: 0.8372 (t0) REVERT: P 126 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8841 (pm20) REVERT: P 228 ASP cc_start: 0.8635 (t0) cc_final: 0.8364 (t0) REVERT: Q 126 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8733 (pm20) REVERT: Q 228 ASP cc_start: 0.8532 (t0) cc_final: 0.8281 (t0) REVERT: R 126 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8803 (pm20) REVERT: R 222 GLN cc_start: 0.8993 (mt0) cc_final: 0.8791 (tt0) REVERT: R 228 ASP cc_start: 0.8648 (t0) cc_final: 0.8388 (t0) REVERT: S 126 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8736 (pm20) REVERT: T 126 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8870 (pm20) REVERT: T 222 GLN cc_start: 0.8969 (mt0) cc_final: 0.8665 (tt0) REVERT: T 228 ASP cc_start: 0.8716 (t0) cc_final: 0.8441 (t0) REVERT: U 126 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8818 (pm20) REVERT: U 228 ASP cc_start: 0.8630 (t0) cc_final: 0.8383 (t0) REVERT: V 126 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8793 (pm20) REVERT: V 228 ASP cc_start: 0.8554 (t0) cc_final: 0.8278 (t0) outliers start: 72 outliers final: 60 residues processed: 287 average time/residue: 0.4308 time to fit residues: 226.2657 Evaluate side-chains 246 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 181 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 232 GLN Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 350 optimal weight: 0.9990 chunk 564 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 392 optimal weight: 0.9990 chunk 591 optimal weight: 0.9980 chunk 544 optimal weight: 9.9990 chunk 471 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 chunk 288 optimal weight: 0.0870 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 ASN N 246 ASN Q 45 HIS T 45 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 45386 Z= 0.147 Angle : 0.564 9.957 62304 Z= 0.275 Chirality : 0.035 0.175 7238 Planarity : 0.003 0.023 7986 Dihedral : 3.717 13.356 6644 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.56 % Allowed : 21.92 % Favored : 76.52 % 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: 2.52 (0.12), residues: 6006 helix: 2.61 (0.08), residues: 4598 sheet: None (None), residues: 0 loop : -1.74 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 117 HIS 0.003 0.001 HIS C 238 PHE 0.033 0.001 PHE M 69 TYR 0.006 0.001 TYR B 219 ARG 0.003 0.000 ARG B 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 194 time to evaluate : 4.985 Fit side-chains REVERT: A 227 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: A 228 ASP cc_start: 0.8636 (t0) cc_final: 0.8348 (t0) REVERT: A 229 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8294 (tm-30) REVERT: D 222 GLN cc_start: 0.8906 (mt0) cc_final: 0.8610 (tt0) REVERT: E 222 GLN cc_start: 0.8999 (mt0) cc_final: 0.8764 (tt0) REVERT: E 227 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: G 227 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: G 228 ASP cc_start: 0.8572 (t0) cc_final: 0.8263 (t0) REVERT: I 227 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: I 229 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8265 (tm-30) REVERT: L 126 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8851 (pm20) REVERT: M 126 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8715 (pm20) REVERT: M 228 ASP cc_start: 0.8706 (t0) cc_final: 0.8388 (t0) REVERT: N 126 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8743 (pm20) REVERT: N 228 ASP cc_start: 0.8581 (t0) cc_final: 0.8306 (t0) REVERT: O 126 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8820 (pm20) REVERT: O 222 GLN cc_start: 0.8913 (mt0) cc_final: 0.8667 (tt0) REVERT: O 228 ASP cc_start: 0.8614 (t0) cc_final: 0.8334 (t0) REVERT: P 126 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8852 (pm20) REVERT: P 228 ASP cc_start: 0.8615 (t0) cc_final: 0.8339 (t0) REVERT: Q 126 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8724 (pm20) REVERT: Q 228 ASP cc_start: 0.8550 (t0) cc_final: 0.8281 (t0) REVERT: R 126 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8718 (pm20) REVERT: R 228 ASP cc_start: 0.8637 (t0) cc_final: 0.8376 (t0) REVERT: S 126 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8755 (pm20) REVERT: T 126 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8869 (pm20) REVERT: T 222 GLN cc_start: 0.8971 (mt0) cc_final: 0.8731 (tt0) REVERT: T 228 ASP cc_start: 0.8684 (t0) cc_final: 0.8406 (t0) REVERT: U 126 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8813 (pm20) REVERT: U 228 ASP cc_start: 0.8611 (t0) cc_final: 0.8370 (t0) REVERT: V 126 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8709 (pm20) REVERT: V 228 ASP cc_start: 0.8539 (t0) cc_final: 0.8259 (t0) outliers start: 60 outliers final: 54 residues processed: 252 average time/residue: 0.4373 time to fit residues: 202.4008 Evaluate side-chains 243 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 185 time to evaluate : 5.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 374 optimal weight: 1.9990 chunk 501 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 434 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 130 optimal weight: 0.0670 chunk 471 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 484 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN B 246 ASN E 246 ASN F 246 ASN G 246 ASN ** J 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 ASN L 246 ASN M 246 ASN O 246 ASN P 246 ASN S 246 ASN T 246 ASN U 246 ASN V 246 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.062576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.046875 restraints weight = 261553.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.048430 restraints weight = 119550.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.049503 restraints weight = 74994.570| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 45386 Z= 0.221 Angle : 0.578 9.044 62304 Z= 0.287 Chirality : 0.036 0.172 7238 Planarity : 0.003 0.023 7986 Dihedral : 3.720 13.160 6644 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.95 % Allowed : 21.64 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.12), residues: 6006 helix: 2.66 (0.08), residues: 4598 sheet: None (None), residues: 0 loop : -1.72 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 117 HIS 0.002 0.001 HIS T 78 PHE 0.034 0.001 PHE M 69 TYR 0.006 0.001 TYR F 128 ARG 0.003 0.000 ARG P 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6066.33 seconds wall clock time: 113 minutes 29.31 seconds (6809.31 seconds total)