Starting phenix.real_space_refine on Fri Mar 22 02:39:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/03_2024/6k43_9913_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/03_2024/6k43_9913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/03_2024/6k43_9913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/03_2024/6k43_9913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/03_2024/6k43_9913_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/03_2024/6k43_9913_trim_updated.pdb" } resolution = 3.7 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= 0.030 sd= 1.242 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: 5 Type Number sf(0) Gaussians Fe 36 7.16 5 S 96 5.16 5 C 20132 2.51 5 N 5428 2.21 5 O 6116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C ASP 139": "OD1" <-> "OD2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "F ASP 4": "OD1" <-> "OD2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H ASP 139": "OD1" <-> "OD2" Residue "I ASP 4": "OD1" <-> "OD2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 51": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K GLU 127": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "L ASP 33": "OD1" <-> "OD2" Residue "L TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "M TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "M ASP 139": "OD1" <-> "OD2" Residue "M GLU 146": "OE1" <-> "OE2" Residue "N ASP 4": "OD1" <-> "OD2" Residue "N ASP 33": "OD1" <-> "OD2" Residue "N TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "O TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 113": "OD1" <-> "OD2" Residue "O GLU 121": "OE1" <-> "OE2" Residue "O ASP 132": "OD1" <-> "OD2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "O GLU 155": "OE1" <-> "OE2" Residue "P GLU 18": "OE1" <-> "OE2" Residue "P TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P ASP 139": "OD1" <-> "OD2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "Q ASP 33": "OD1" <-> "OD2" Residue "Q ASP 50": "OD1" <-> "OD2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q ASP 139": "OD1" <-> "OD2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "R TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 50": "OD1" <-> "OD2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R ASP 139": "OD1" <-> "OD2" Residue "R GLU 146": "OE1" <-> "OE2" Residue "S ASP 33": "OD1" <-> "OD2" Residue "S TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 50": "OD1" <-> "OD2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "S ASP 160": "OD1" <-> "OD2" Residue "T TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T GLU 121": "OE1" <-> "OE2" Residue "T ASP 139": "OD1" <-> "OD2" Residue "T GLU 146": "OE1" <-> "OE2" Residue "U ASP 4": "OD1" <-> "OD2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "U ASP 132": "OD1" <-> "OD2" Residue "U GLU 146": "OE1" <-> "OE2" Residue "V ASP 33": "OD1" <-> "OD2" Residue "V TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 50": "OD1" <-> "OD2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V ASP 132": "OD1" <-> "OD2" Residue "V ASP 139": "OD1" <-> "OD2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 50": "OD1" <-> "OD2" Residue "W GLU 51": "OE1" <-> "OE2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "W ASP 139": "OD1" <-> "OD2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "X ASP 4": "OD1" <-> "OD2" Residue "X ASP 33": "OD1" <-> "OD2" Residue "X TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 50": "OD1" <-> "OD2" Residue "X GLU 127": "OE1" <-> "OE2" Residue "X ASP 139": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X ASP 160": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31808 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.50, per 1000 atoms: 0.49 Number of scatterers: 31808 At special positions: 0 Unit cell: (132.09, 132.09, 132.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 36 26.01 S 96 16.00 O 6116 8.00 N 5428 7.00 C 20132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=29, symmetry=0 Number of additional bonds: simple=29, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.99 Conformation dependent library (CDL) restraints added in 6.0 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 removed outlier: 3.695A pdb=" N LYS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 64 Processing helix chain 'A' and resid 83 through 109 Processing helix chain 'A' and resid 114 through 144 Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.695A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 removed outlier: 3.711A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 64 removed outlier: 3.810A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 111 removed outlier: 3.821A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 144 Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.832A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 35 removed outlier: 3.698A pdb=" N LYS C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 64 Processing helix chain 'C' and resid 83 through 111 removed outlier: 3.833A pdb=" N LYS C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 144 Processing helix chain 'C' and resid 146 through 152 removed outlier: 4.683A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 35 removed outlier: 3.695A pdb=" N LYS D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 64 removed outlier: 3.851A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 109 Processing helix chain 'D' and resid 115 through 144 Processing helix chain 'D' and resid 146 through 152 removed outlier: 4.618A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 35 removed outlier: 3.680A pdb=" N LYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 64 removed outlier: 3.518A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 111 removed outlier: 3.817A pdb=" N LYS F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 144 Processing helix chain 'F' and resid 146 through 152 removed outlier: 4.642A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.711A pdb=" N LYS E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 64 Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.845A pdb=" N LYS E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 144 Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.690A pdb=" N THR E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 removed outlier: 3.723A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 64 Processing helix chain 'G' and resid 83 through 111 removed outlier: 3.825A pdb=" N LYS G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 144 Processing helix chain 'G' and resid 146 through 152 removed outlier: 4.681A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 35 removed outlier: 3.715A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 64 Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.814A pdb=" N LYS H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 144 Processing helix chain 'H' and resid 146 through 152 removed outlier: 3.905A pdb=" N THR H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 removed outlier: 3.720A pdb=" N LYS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 64 Processing helix chain 'I' and resid 83 through 109 Processing helix chain 'I' and resid 114 through 144 Processing helix chain 'I' and resid 146 through 152 removed outlier: 3.896A pdb=" N THR I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 35 removed outlier: 3.707A pdb=" N LYS J 35 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 64 Processing helix chain 'J' and resid 83 through 109 Processing helix chain 'J' and resid 114 through 144 Processing helix chain 'J' and resid 146 through 152 removed outlier: 4.698A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 removed outlier: 3.743A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 64 removed outlier: 3.768A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.842A pdb=" N LYS K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 144 Processing helix chain 'K' and resid 146 through 152 removed outlier: 3.826A pdb=" N THR K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 removed outlier: 3.699A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 64 Processing helix chain 'L' and resid 83 through 111 removed outlier: 3.834A pdb=" N LYS L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 144 Processing helix chain 'L' and resid 146 through 152 removed outlier: 4.685A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 35 removed outlier: 3.745A pdb=" N LYS M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 64 removed outlier: 3.827A pdb=" N TYR M 43 " --> pdb=" O LYS M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 109 Processing helix chain 'M' and resid 115 through 144 Processing helix chain 'M' and resid 146 through 152 removed outlier: 4.599A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 35 removed outlier: 3.708A pdb=" N LYS N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 64 Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.815A pdb=" N LYS N 111 " --> pdb=" O VAL N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 144 Processing helix chain 'N' and resid 146 through 152 removed outlier: 4.680A pdb=" N THR N 152 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 35 removed outlier: 3.709A pdb=" N LYS O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 64 Processing helix chain 'O' and resid 83 through 109 Processing helix chain 'O' and resid 114 through 144 Processing helix chain 'O' and resid 146 through 152 removed outlier: 3.878A pdb=" N THR O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 35 removed outlier: 3.737A pdb=" N LYS P 35 " --> pdb=" O LEU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 64 removed outlier: 3.815A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 111 removed outlier: 3.833A pdb=" N LYS P 111 " --> pdb=" O VAL P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 144 Processing helix chain 'P' and resid 146 through 152 removed outlier: 3.805A pdb=" N THR P 152 " --> pdb=" O LEU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 35 removed outlier: 3.680A pdb=" N LYS Q 35 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 64 Processing helix chain 'Q' and resid 83 through 109 Processing helix chain 'Q' and resid 114 through 144 Processing helix chain 'Q' and resid 146 through 152 removed outlier: 4.684A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 35 removed outlier: 3.745A pdb=" N LYS R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 64 removed outlier: 3.845A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 111 removed outlier: 3.820A pdb=" N LYS R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 144 Processing helix chain 'R' and resid 146 through 152 removed outlier: 4.599A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 35 removed outlier: 3.683A pdb=" N LYS S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 64 removed outlier: 3.598A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 3.821A pdb=" N LYS S 111 " --> pdb=" O VAL S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 144 Processing helix chain 'S' and resid 146 through 152 removed outlier: 4.677A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 35 removed outlier: 3.685A pdb=" N LYS T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 64 Processing helix chain 'T' and resid 83 through 109 Processing helix chain 'T' and resid 114 through 144 Processing helix chain 'T' and resid 146 through 152 removed outlier: 3.876A pdb=" N THR T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 35 removed outlier: 3.746A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 64 removed outlier: 3.749A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.831A pdb=" N LYS U 111 " --> pdb=" O VAL U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 144 Processing helix chain 'U' and resid 146 through 152 removed outlier: 3.850A pdb=" N THR U 152 " --> pdb=" O LEU U 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 35 removed outlier: 3.682A pdb=" N LYS V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 64 Processing helix chain 'V' and resid 83 through 111 removed outlier: 3.829A pdb=" N LYS V 111 " --> pdb=" O VAL V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 144 Processing helix chain 'V' and resid 146 through 152 removed outlier: 4.684A pdb=" N THR V 152 " --> pdb=" O LEU V 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 35 removed outlier: 3.742A pdb=" N LYS W 35 " --> pdb=" O LEU W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 64 removed outlier: 3.814A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 111 removed outlier: 3.831A pdb=" N LYS W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 114 through 144 Processing helix chain 'W' and resid 146 through 152 removed outlier: 4.626A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 35 removed outlier: 3.743A pdb=" N LYS X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 64 removed outlier: 3.586A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 111 removed outlier: 3.822A pdb=" N LYS X 111 " --> pdb=" O VAL X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 144 Processing helix chain 'X' and resid 146 through 152 removed outlier: 4.671A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 2415 hydrogen bonds defined for protein. 7245 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: 9.62 Time building geometry restraints manager: 14.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 13491 1.39 - 1.56: 18653 1.56 - 1.73: 0 1.73 - 1.90: 192 1.90 - 2.07: 48 Bond restraints: 32384 Sorted by residual: bond pdb=" C ASP R 99 " pdb=" O ASP R 99 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.15e-02 7.56e+03 1.60e+00 bond pdb=" C ASP W 99 " pdb=" O ASP W 99 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.51e+00 bond pdb=" C ASP A 99 " pdb=" O ASP A 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" C ASP T 99 " pdb=" O ASP T 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" C ASP O 99 " pdb=" O ASP O 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 ... (remaining 32379 not shown) Histogram of bond angle deviations from ideal: 85.34 - 104.16: 285 104.16 - 122.98: 41844 122.98 - 141.80: 1783 141.80 - 160.62: 0 160.62 - 179.44: 24 Bond angle restraints: 43936 Sorted by residual: angle pdb=" C TYR R 25 " pdb=" N PHE R 26 " pdb=" CA PHE R 26 " ideal model delta sigma weight residual 120.29 116.11 4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" C TYR W 25 " pdb=" N PHE W 26 " pdb=" CA PHE W 26 " ideal model delta sigma weight residual 120.29 116.25 4.04 1.42e+00 4.96e-01 8.09e+00 angle pdb=" C TYR I 25 " pdb=" N PHE I 26 " pdb=" CA PHE I 26 " ideal model delta sigma weight residual 120.29 116.26 4.03 1.42e+00 4.96e-01 8.05e+00 angle pdb=" C TYR G 25 " pdb=" N PHE G 26 " pdb=" CA PHE G 26 " ideal model delta sigma weight residual 120.29 116.33 3.96 1.42e+00 4.96e-01 7.76e+00 angle pdb=" C TYR N 25 " pdb=" N PHE N 26 " pdb=" CA PHE N 26 " ideal model delta sigma weight residual 120.29 116.34 3.95 1.42e+00 4.96e-01 7.74e+00 ... (remaining 43931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.74: 16963 18.74 - 37.48: 2063 37.48 - 56.22: 259 56.22 - 74.95: 61 74.95 - 93.69: 38 Dihedral angle restraints: 19384 sinusoidal: 8064 harmonic: 11320 Sorted by residual: dihedral pdb=" C2B HEM K 301 " pdb=" C3B HEM K 301 " pdb=" CAB HEM K 301 " pdb=" CBB HEM K 301 " ideal model delta sinusoidal sigma weight residual -0.00 -39.28 39.28 2 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CA PRO T 159 " pdb=" C PRO T 159 " pdb=" N ASP T 160 " pdb=" CA ASP T 160 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" C2C HEM X 201 " pdb=" C3C HEM X 201 " pdb=" CAC HEM X 201 " pdb=" CBC HEM X 201 " ideal model delta sinusoidal sigma weight residual 0.00 37.74 -37.74 2 1.00e+01 1.00e-02 1.80e+01 ... (remaining 19381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2435 0.024 - 0.049: 1594 0.049 - 0.073: 595 0.073 - 0.097: 161 0.097 - 0.121: 91 Chirality restraints: 4876 Sorted by residual: chirality pdb=" CA PRO J 159 " pdb=" N PRO J 159 " pdb=" C PRO J 159 " pdb=" CB PRO J 159 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA PRO L 161 " pdb=" N PRO L 161 " pdb=" C PRO L 161 " pdb=" CB PRO L 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA PRO Q 161 " pdb=" N PRO Q 161 " pdb=" C PRO Q 161 " pdb=" CB PRO Q 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 4873 not shown) Planarity restraints: 5680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEM K 301 " 0.002 2.00e-02 2.50e+03 1.07e-02 2.58e+00 pdb=" C1B HEM K 301 " -0.008 2.00e-02 2.50e+03 pdb=" C2B HEM K 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3B HEM K 301 " -0.019 2.00e-02 2.50e+03 pdb=" C4B HEM K 301 " -0.008 2.00e-02 2.50e+03 pdb=" CAB HEM K 301 " 0.016 2.00e-02 2.50e+03 pdb=" CHB HEM K 301 " 0.011 2.00e-02 2.50e+03 pdb=" CHC HEM K 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMB HEM K 301 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 37 " -0.016 2.00e-02 2.50e+03 9.74e-03 2.37e+00 pdb=" CG TRP G 37 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP G 37 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP G 37 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 37 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 37 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM O 202 " -0.024 2.00e-02 2.50e+03 1.03e-02 2.37e+00 pdb=" C1B HEM O 202 " 0.005 2.00e-02 2.50e+03 pdb=" C2B HEM O 202 " 0.006 2.00e-02 2.50e+03 pdb=" C3B HEM O 202 " -0.005 2.00e-02 2.50e+03 pdb=" C4B HEM O 202 " 0.000 2.00e-02 2.50e+03 pdb=" CAB HEM O 202 " -0.001 2.00e-02 2.50e+03 pdb=" CHB HEM O 202 " 0.010 2.00e-02 2.50e+03 pdb=" CHC HEM O 202 " 0.013 2.00e-02 2.50e+03 pdb=" CMB HEM O 202 " -0.004 2.00e-02 2.50e+03 ... (remaining 5677 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 26 1.99 - 2.72: 2837 2.72 - 3.45: 46904 3.45 - 4.17: 62780 4.17 - 4.90: 122129 Nonbonded interactions: 234676 Sorted by model distance: nonbonded pdb=" OE1 GLU J 18 " pdb=" OE1 GLU J 51 " model vdw 1.266 3.040 nonbonded pdb=" OE1 GLU B 18 " pdb=" OE1 GLU B 51 " model vdw 1.287 3.040 nonbonded pdb=" OE1 GLU T 18 " pdb=" OE1 GLU T 51 " model vdw 1.303 3.040 nonbonded pdb=" OE1 GLU P 18 " pdb=" OE1 GLU P 51 " model vdw 1.308 3.040 nonbonded pdb=" OE1 GLU L 18 " pdb=" OE1 GLU L 51 " model vdw 1.319 3.040 ... (remaining 234671 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' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'B' and resid 1 through 157) selection = (chain 'C' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'D' and resid 1 through 157) selection = (chain 'E' and resid 1 through 157) selection = (chain 'F' and resid 1 through 157) selection = (chain 'G' and resid 1 through 157) selection = (chain 'H' and resid 1 through 157) selection = (chain 'I' and resid 1 through 157) selection = (chain 'J' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'K' and resid 1 through 157) selection = (chain 'L' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'M' and resid 1 through 157) selection = (chain 'N' and resid 1 through 157) selection = (chain 'O' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'P' and resid 1 through 157) selection = (chain 'Q' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'R' and resid 1 through 157) selection = (chain 'S' and resid 1 through 157) selection = (chain 'T' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'U' and resid 1 through 157) selection = (chain 'V' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'W' and resid 1 through 157) selection = (chain 'X' and resid 1 through 157) } 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: 0.680 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: 0.040 Extract box with map and model: 4.930 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 80.980 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.120 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.007 0.082 32384 Z= 0.485 Angle : 0.716 15.729 43936 Z= 0.393 Chirality : 0.037 0.121 4876 Planarity : 0.003 0.027 5680 Dihedral : 15.849 93.692 12000 Min Nonbonded Distance : 1.266 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.12 % Allowed : 7.78 % Favored : 92.11 % 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: -2.02 (0.11), residues: 3792 helix: -0.37 (0.08), residues: 2888 sheet: None (None), residues: 0 loop : -4.43 (0.15), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP G 37 HIS 0.005 0.001 HIS U 54 PHE 0.025 0.003 PHE T 120 TYR 0.008 0.001 TYR C 71 ARG 0.004 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1011 time to evaluate : 4.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.7144 (mt) cc_final: 0.6787 (mt) REVERT: B 1 MET cc_start: 0.5502 (mtm) cc_final: 0.5292 (mtm) REVERT: B 105 ILE cc_start: 0.7188 (mt) cc_final: 0.6844 (mt) REVERT: C 105 ILE cc_start: 0.7282 (mt) cc_final: 0.6922 (mt) REVERT: C 130 HIS cc_start: 0.7478 (t-170) cc_final: 0.7103 (m170) REVERT: D 105 ILE cc_start: 0.7115 (mt) cc_final: 0.6724 (mt) REVERT: D 130 HIS cc_start: 0.7503 (t-170) cc_final: 0.7251 (m170) REVERT: F 105 ILE cc_start: 0.7251 (mt) cc_final: 0.6915 (mt) REVERT: F 130 HIS cc_start: 0.7467 (t-170) cc_final: 0.7204 (m170) REVERT: E 1 MET cc_start: 0.5331 (mtm) cc_final: 0.5069 (mtm) REVERT: E 105 ILE cc_start: 0.7306 (mt) cc_final: 0.6972 (mt) REVERT: G 1 MET cc_start: 0.5342 (mtm) cc_final: 0.5094 (mtm) REVERT: G 105 ILE cc_start: 0.7284 (mt) cc_final: 0.6932 (mt) REVERT: G 130 HIS cc_start: 0.7560 (t-170) cc_final: 0.7271 (m170) REVERT: H 105 ILE cc_start: 0.7268 (mt) cc_final: 0.6914 (mt) REVERT: H 130 HIS cc_start: 0.7526 (t-170) cc_final: 0.7229 (m170) REVERT: I 105 ILE cc_start: 0.7252 (mt) cc_final: 0.6895 (mt) REVERT: J 105 ILE cc_start: 0.7276 (mt) cc_final: 0.6917 (mt) REVERT: J 130 HIS cc_start: 0.7582 (t-170) cc_final: 0.7294 (m170) REVERT: K 105 ILE cc_start: 0.7204 (mt) cc_final: 0.6871 (mt) REVERT: K 126 ASP cc_start: 0.8496 (m-30) cc_final: 0.8134 (t0) REVERT: L 105 ILE cc_start: 0.7282 (mt) cc_final: 0.6931 (mt) REVERT: L 130 HIS cc_start: 0.7611 (t-170) cc_final: 0.7216 (m170) REVERT: M 1 MET cc_start: 0.4551 (mtp) cc_final: 0.3681 (mtm) REVERT: M 105 ILE cc_start: 0.7112 (mt) cc_final: 0.6736 (mt) REVERT: M 130 HIS cc_start: 0.7472 (t-170) cc_final: 0.7238 (m170) REVERT: N 105 ILE cc_start: 0.7250 (mt) cc_final: 0.6917 (mt) REVERT: N 130 HIS cc_start: 0.7547 (t-170) cc_final: 0.7287 (m170) REVERT: O 1 MET cc_start: 0.5650 (mtm) cc_final: 0.5170 (mtm) REVERT: O 105 ILE cc_start: 0.7355 (mt) cc_final: 0.7043 (mt) REVERT: O 130 HIS cc_start: 0.7585 (t-170) cc_final: 0.7276 (m170) REVERT: P 105 ILE cc_start: 0.7147 (mt) cc_final: 0.6811 (mt) REVERT: P 130 HIS cc_start: 0.7518 (t-170) cc_final: 0.7225 (m170) REVERT: Q 105 ILE cc_start: 0.7282 (mt) cc_final: 0.6918 (mt) REVERT: R 1 MET cc_start: 0.4463 (ptm) cc_final: 0.4128 (ptt) REVERT: R 105 ILE cc_start: 0.7150 (mt) cc_final: 0.6766 (mt) REVERT: R 130 HIS cc_start: 0.7528 (t-170) cc_final: 0.7246 (m170) REVERT: S 105 ILE cc_start: 0.7276 (mt) cc_final: 0.6920 (mt) REVERT: T 1 MET cc_start: 0.5351 (mtm) cc_final: 0.5023 (mtm) REVERT: T 105 ILE cc_start: 0.7167 (mt) cc_final: 0.6805 (mt) REVERT: T 130 HIS cc_start: 0.7503 (t-170) cc_final: 0.7087 (m170) REVERT: U 105 ILE cc_start: 0.7236 (mt) cc_final: 0.6899 (mt) REVERT: U 156 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8154 (mm-40) REVERT: V 105 ILE cc_start: 0.7281 (mt) cc_final: 0.6910 (mt) REVERT: V 130 HIS cc_start: 0.7644 (t-170) cc_final: 0.7230 (m170) REVERT: W 1 MET cc_start: 0.4443 (ptm) cc_final: 0.3736 (ptt) REVERT: W 105 ILE cc_start: 0.7164 (mt) cc_final: 0.6807 (mt) REVERT: W 130 HIS cc_start: 0.7568 (t-170) cc_final: 0.7255 (m170) REVERT: X 105 ILE cc_start: 0.7261 (mt) cc_final: 0.6908 (mt) REVERT: X 130 HIS cc_start: 0.7547 (t-170) cc_final: 0.7269 (m170) outliers start: 4 outliers final: 4 residues processed: 1015 average time/residue: 0.4429 time to fit residues: 696.7023 Evaluate side-chains 674 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 670 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain V residue 160 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 179 optimal weight: 0.3980 chunk 219 optimal weight: 0.1980 chunk 341 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 130 HIS C 24 GLN C 130 HIS D 24 GLN D 130 HIS D 156 GLN F 24 GLN F 118 ASN F 130 HIS F 156 GLN E 24 GLN E 130 HIS G 24 GLN H 24 GLN H 130 HIS I 24 GLN J 24 GLN J 130 HIS K 24 GLN L 24 GLN L 130 HIS M 24 GLN M 130 HIS N 24 GLN N 118 ASN O 24 GLN O 130 HIS P 129 HIS Q 24 GLN R 24 GLN S 24 GLN S 118 ASN S 130 HIS S 156 GLN T 24 GLN T 130 HIS U 24 GLN U 156 GLN V 24 GLN V 130 HIS W 24 GLN W 130 HIS W 156 GLN X 118 ASN X 130 HIS X 156 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32384 Z= 0.210 Angle : 0.627 12.235 43936 Z= 0.299 Chirality : 0.034 0.132 4876 Planarity : 0.003 0.027 5680 Dihedral : 7.039 87.023 4280 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.18 % Allowed : 12.71 % Favored : 85.11 % 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: 2.55 (0.13), residues: 3792 helix: 3.14 (0.08), residues: 2908 sheet: None (None), residues: 0 loop : -3.80 (0.15), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 37 HIS 0.006 0.001 HIS K 54 PHE 0.027 0.001 PHE N 26 TYR 0.005 0.001 TYR W 149 ARG 0.004 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 866 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5168 (mtm) cc_final: 0.3515 (mtm) REVERT: A 137 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8091 (tp-100) REVERT: B 53 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7817 (ttp-110) REVERT: B 137 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8504 (tp40) REVERT: C 81 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7519 (mt0) REVERT: D 1 MET cc_start: 0.5993 (ptt) cc_final: 0.4771 (ptt) REVERT: F 1 MET cc_start: 0.5331 (mtm) cc_final: 0.3574 (mtm) REVERT: F 137 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8569 (tp40) REVERT: G 128 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7736 (mm-30) REVERT: H 1 MET cc_start: 0.5146 (mtm) cc_final: 0.4104 (ptm) REVERT: H 78 ARG cc_start: 0.8604 (mtp85) cc_final: 0.7963 (ttm110) REVERT: H 128 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7665 (mm-30) REVERT: H 137 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8574 (tp40) REVERT: I 1 MET cc_start: 0.5017 (mtm) cc_final: 0.3776 (mtm) REVERT: I 32 GLN cc_start: 0.8978 (mt0) cc_final: 0.8740 (mt0) REVERT: I 137 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8548 (tp40) REVERT: J 78 ARG cc_start: 0.8621 (mtp85) cc_final: 0.7988 (ttm110) REVERT: K 32 GLN cc_start: 0.9019 (mt0) cc_final: 0.8771 (mt0) REVERT: K 126 ASP cc_start: 0.8105 (m-30) cc_final: 0.7707 (t0) REVERT: L 81 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7524 (mt0) REVERT: N 53 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.7895 (ttp-110) REVERT: N 78 ARG cc_start: 0.8614 (mtp85) cc_final: 0.7914 (ttm110) REVERT: O 32 GLN cc_start: 0.8977 (mt0) cc_final: 0.8692 (mt0) REVERT: O 132 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8706 (t0) REVERT: O 137 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8562 (tp40) REVERT: P 53 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.7407 (mtm110) REVERT: P 128 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7640 (mm-30) REVERT: T 137 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8600 (tp40) REVERT: V 81 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7504 (mt0) REVERT: W 128 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7816 (tp30) outliers start: 73 outliers final: 62 residues processed: 872 average time/residue: 0.4318 time to fit residues: 625.8046 Evaluate side-chains 753 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 690 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 160 ASP Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 232 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 3.9990 chunk 369 optimal weight: 4.9990 chunk 304 optimal weight: 0.0020 chunk 339 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 274 optimal weight: 7.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 28 HIS C 28 HIS C 72 GLN D 72 GLN D 156 GLN F 72 GLN E 28 HIS G 28 HIS H 28 HIS J 137 GLN K 28 HIS K 137 GLN L 28 HIS M 72 GLN M 137 GLN N 72 GLN N 137 GLN O 28 HIS P 28 HIS Q 72 GLN R 72 GLN R 137 GLN R 156 GLN S 137 GLN U 28 HIS V 28 HIS V 72 GLN W 72 GLN X 137 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32384 Z= 0.227 Angle : 0.599 21.299 43936 Z= 0.283 Chirality : 0.033 0.131 4876 Planarity : 0.002 0.017 5680 Dihedral : 6.953 86.845 4280 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.71 % Allowed : 13.76 % Favored : 82.54 % 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: 3.65 (0.14), residues: 3792 helix: 3.93 (0.08), residues: 2896 sheet: None (None), residues: 0 loop : -3.31 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 37 HIS 0.004 0.001 HIS W 130 PHE 0.019 0.001 PHE M 26 TYR 0.007 0.001 TYR H 149 ARG 0.004 0.000 ARG U 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 653 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 130 HIS cc_start: 0.7582 (t-90) cc_final: 0.6853 (m170) REVERT: F 130 HIS cc_start: 0.7743 (t70) cc_final: 0.6881 (m170) REVERT: E 1 MET cc_start: 0.4977 (mtm) cc_final: 0.4690 (ptm) REVERT: E 78 ARG cc_start: 0.8534 (mtp85) cc_final: 0.7971 (ttm110) REVERT: E 132 ASP cc_start: 0.9003 (t70) cc_final: 0.8458 (t0) REVERT: G 53 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.7588 (mtm110) REVERT: G 128 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7887 (mm-30) REVERT: G 130 HIS cc_start: 0.7973 (t70) cc_final: 0.6839 (m170) REVERT: H 78 ARG cc_start: 0.8551 (mtp85) cc_final: 0.7988 (ttm110) REVERT: I 1 MET cc_start: 0.4956 (mtm) cc_final: 0.3444 (mtm) REVERT: I 130 HIS cc_start: 0.7620 (t-90) cc_final: 0.6944 (m170) REVERT: J 78 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8003 (ttm110) REVERT: K 32 GLN cc_start: 0.9098 (mt0) cc_final: 0.8869 (mt0) REVERT: K 126 ASP cc_start: 0.8134 (m-30) cc_final: 0.7596 (t0) REVERT: K 128 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: K 130 HIS cc_start: 0.7589 (t-90) cc_final: 0.6965 (m170) REVERT: M 137 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8686 (tp40) REVERT: N 78 ARG cc_start: 0.8512 (mtp85) cc_final: 0.7905 (ttm110) REVERT: N 130 HIS cc_start: 0.7653 (t-90) cc_final: 0.6887 (m170) REVERT: O 1 MET cc_start: 0.4892 (mtm) cc_final: 0.3424 (ttp) REVERT: O 130 HIS cc_start: 0.7744 (t-90) cc_final: 0.6896 (m170) REVERT: R 137 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8665 (tp40) REVERT: S 128 GLU cc_start: 0.8271 (tp30) cc_final: 0.8048 (mm-30) REVERT: S 130 HIS cc_start: 0.7823 (t70) cc_final: 0.6846 (m170) REVERT: T 130 HIS cc_start: 0.7623 (t-90) cc_final: 0.7016 (m170) REVERT: U 130 HIS cc_start: 0.7728 (t-90) cc_final: 0.6958 (m170) REVERT: W 128 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7804 (tp30) REVERT: X 130 HIS cc_start: 0.7717 (t-90) cc_final: 0.6976 (m170) outliers start: 124 outliers final: 112 residues processed: 716 average time/residue: 0.4067 time to fit residues: 469.1285 Evaluate side-chains 717 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 602 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 28 HIS Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 28 HIS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 28 HIS Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 137 GLN Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 28 HIS Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 28 HIS Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 28 HIS Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 160 ASP Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 6.9990 chunk 257 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 343 optimal weight: 1.9990 chunk 363 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 325 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 28 HIS B 137 GLN D 137 GLN E 28 HIS M 156 GLN N 137 GLN N 156 GLN O 28 HIS O 137 GLN S 137 GLN T 137 GLN U 156 GLN X 137 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32384 Z= 0.203 Angle : 0.567 20.579 43936 Z= 0.266 Chirality : 0.033 0.130 4876 Planarity : 0.002 0.016 5680 Dihedral : 6.983 89.939 4280 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.41 % Allowed : 17.61 % Favored : 78.98 % 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: 3.89 (0.14), residues: 3792 helix: 4.06 (0.08), residues: 2920 sheet: None (None), residues: 0 loop : -3.29 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 37 HIS 0.008 0.001 HIS C 28 PHE 0.016 0.001 PHE M 26 TYR 0.006 0.001 TYR O 149 ARG 0.003 0.000 ARG U 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 614 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5050 (mtm) cc_final: 0.4843 (ptm) REVERT: A 132 ASP cc_start: 0.9040 (t70) cc_final: 0.8587 (t0) REVERT: C 130 HIS cc_start: 0.7654 (t-90) cc_final: 0.6916 (m170) REVERT: D 132 ASP cc_start: 0.9036 (t70) cc_final: 0.8539 (t0) REVERT: F 1 MET cc_start: 0.4894 (mtm) cc_final: 0.4661 (ptm) REVERT: F 130 HIS cc_start: 0.7650 (t70) cc_final: 0.6804 (m170) REVERT: E 78 ARG cc_start: 0.8459 (mtp85) cc_final: 0.7946 (ttm110) REVERT: E 132 ASP cc_start: 0.9049 (t70) cc_final: 0.8551 (t0) REVERT: G 1 MET cc_start: 0.5012 (mtm) cc_final: 0.4679 (ptm) REVERT: G 53 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.7556 (mtm110) REVERT: H 78 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7957 (ttm110) REVERT: I 130 HIS cc_start: 0.7616 (t-90) cc_final: 0.6934 (m170) REVERT: I 132 ASP cc_start: 0.8980 (t70) cc_final: 0.8467 (t0) REVERT: J 78 ARG cc_start: 0.8563 (mtp85) cc_final: 0.8024 (ttm110) REVERT: K 126 ASP cc_start: 0.8074 (m-30) cc_final: 0.7631 (t0) REVERT: K 128 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: L 1 MET cc_start: 0.6744 (mmm) cc_final: 0.6496 (mmm) REVERT: L 130 HIS cc_start: 0.7785 (t-90) cc_final: 0.6938 (m170) REVERT: N 78 ARG cc_start: 0.8494 (mtp85) cc_final: 0.7952 (ttm110) REVERT: N 130 HIS cc_start: 0.7600 (t-90) cc_final: 0.6943 (m170) REVERT: O 73 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8494 (mtm-85) REVERT: O 130 HIS cc_start: 0.7785 (t-90) cc_final: 0.6942 (m170) REVERT: R 130 HIS cc_start: 0.7706 (t70) cc_final: 0.6854 (m170) REVERT: S 22 ILE cc_start: 0.8890 (mt) cc_final: 0.8676 (mm) REVERT: S 130 HIS cc_start: 0.7552 (t70) cc_final: 0.6765 (m170) REVERT: T 130 HIS cc_start: 0.7726 (t-90) cc_final: 0.7050 (m170) REVERT: T 132 ASP cc_start: 0.8994 (t70) cc_final: 0.8525 (t0) REVERT: U 1 MET cc_start: 0.5172 (mtm) cc_final: 0.4483 (ptm) REVERT: V 130 HIS cc_start: 0.7709 (t-90) cc_final: 0.6884 (m170) outliers start: 114 outliers final: 94 residues processed: 662 average time/residue: 0.4128 time to fit residues: 440.1523 Evaluate side-chains 684 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 588 time to evaluate : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 152 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN D 156 GLN J 158 GLN P 156 GLN T 158 GLN U 156 GLN X 137 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 32384 Z= 0.340 Angle : 0.677 25.131 43936 Z= 0.328 Chirality : 0.035 0.131 4876 Planarity : 0.003 0.022 5680 Dihedral : 6.875 88.525 4272 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.19 % Allowed : 18.00 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.13), residues: 3792 helix: 3.49 (0.08), residues: 2932 sheet: None (None), residues: 0 loop : -3.45 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 37 HIS 0.004 0.001 HIS H 34 PHE 0.017 0.001 PHE M 26 TYR 0.008 0.001 TYR I 149 ARG 0.003 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 649 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.7702 (m-30) cc_final: 0.7471 (t0) REVERT: A 132 ASP cc_start: 0.9077 (t70) cc_final: 0.8636 (t0) REVERT: B 4 ASP cc_start: 0.7727 (m-30) cc_final: 0.7486 (t0) REVERT: B 126 ASP cc_start: 0.8816 (t0) cc_final: 0.8601 (t0) REVERT: C 116 SER cc_start: 0.7463 (OUTLIER) cc_final: 0.6918 (p) REVERT: C 120 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7635 (m-10) REVERT: D 4 ASP cc_start: 0.7742 (m-30) cc_final: 0.7464 (t0) REVERT: D 126 ASP cc_start: 0.8786 (t0) cc_final: 0.8558 (t0) REVERT: F 120 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7526 (m-10) REVERT: F 126 ASP cc_start: 0.8785 (t0) cc_final: 0.8574 (t0) REVERT: E 4 ASP cc_start: 0.7762 (m-30) cc_final: 0.7470 (t0) REVERT: E 126 ASP cc_start: 0.8825 (t0) cc_final: 0.8620 (t0) REVERT: G 4 ASP cc_start: 0.7759 (m-30) cc_final: 0.7474 (t0) REVERT: G 53 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.7537 (mtm110) REVERT: H 126 ASP cc_start: 0.8751 (t0) cc_final: 0.8473 (t0) REVERT: I 126 ASP cc_start: 0.8796 (t0) cc_final: 0.8549 (t0) REVERT: J 4 ASP cc_start: 0.7765 (m-30) cc_final: 0.7532 (t0) REVERT: J 78 ARG cc_start: 0.8516 (mtp85) cc_final: 0.7994 (ttm110) REVERT: K 4 ASP cc_start: 0.7813 (m-30) cc_final: 0.7558 (t0) REVERT: K 126 ASP cc_start: 0.8271 (m-30) cc_final: 0.7728 (t0) REVERT: L 18 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: M 52 MET cc_start: 0.8787 (mtm) cc_final: 0.8542 (ttm) REVERT: M 126 ASP cc_start: 0.8709 (t0) cc_final: 0.8455 (t0) REVERT: N 120 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7571 (m-10) REVERT: N 126 ASP cc_start: 0.8736 (t0) cc_final: 0.8516 (t0) REVERT: O 73 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8735 (mtm-85) REVERT: O 108 MET cc_start: 0.8510 (ttm) cc_final: 0.8171 (ttp) REVERT: O 126 ASP cc_start: 0.8810 (t0) cc_final: 0.8572 (t0) REVERT: P 4 ASP cc_start: 0.7801 (m-30) cc_final: 0.7568 (t0) REVERT: P 126 ASP cc_start: 0.8743 (t0) cc_final: 0.8530 (t0) REVERT: Q 116 SER cc_start: 0.7578 (OUTLIER) cc_final: 0.6953 (p) REVERT: Q 126 ASP cc_start: 0.8679 (t0) cc_final: 0.8443 (t0) REVERT: R 4 ASP cc_start: 0.7771 (m-30) cc_final: 0.7510 (t0) REVERT: R 116 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.7045 (p) REVERT: S 120 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: T 4 ASP cc_start: 0.7729 (m-30) cc_final: 0.7492 (t0) REVERT: T 130 HIS cc_start: 0.7892 (t-90) cc_final: 0.7076 (m170) REVERT: W 4 ASP cc_start: 0.7770 (m-30) cc_final: 0.7512 (t0) REVERT: W 116 SER cc_start: 0.7474 (OUTLIER) cc_final: 0.7002 (p) REVERT: X 120 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7658 (m-10) outliers start: 140 outliers final: 116 residues processed: 738 average time/residue: 0.4359 time to fit residues: 520.5710 Evaluate side-chains 736 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 609 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 120 PHE Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 152 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain S residue 120 PHE Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 152 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 116 SER Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain U residue 156 GLN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 120 PHE Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 8.9990 chunk 327 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 89 optimal weight: 0.0010 chunk 363 optimal weight: 10.0000 chunk 301 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN E 137 GLN N 137 GLN N 156 GLN S 137 GLN U 156 GLN X 137 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32384 Z= 0.198 Angle : 0.564 19.976 43936 Z= 0.268 Chirality : 0.033 0.136 4876 Planarity : 0.002 0.025 5680 Dihedral : 6.892 87.989 4272 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.20 % Allowed : 19.59 % Favored : 77.21 % 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: 3.89 (0.14), residues: 3792 helix: 4.04 (0.08), residues: 2932 sheet: None (None), residues: 0 loop : -3.32 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 37 HIS 0.004 0.001 HIS W 130 PHE 0.019 0.001 PHE O 26 TYR 0.004 0.001 TYR A 25 ARG 0.004 0.000 ARG U 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 600 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 132 ASP cc_start: 0.9021 (t70) cc_final: 0.8601 (t0) REVERT: B 126 ASP cc_start: 0.8591 (t0) cc_final: 0.8301 (t0) REVERT: B 130 HIS cc_start: 0.7679 (t70) cc_final: 0.6797 (m170) REVERT: C 130 HIS cc_start: 0.7737 (t-90) cc_final: 0.6905 (m170) REVERT: D 52 MET cc_start: 0.8907 (mtm) cc_final: 0.8701 (mtt) REVERT: D 130 HIS cc_start: 0.7606 (t-90) cc_final: 0.6872 (m170) REVERT: F 126 ASP cc_start: 0.8620 (t0) cc_final: 0.8310 (t0) REVERT: F 130 HIS cc_start: 0.7777 (t-90) cc_final: 0.6811 (m170) REVERT: E 126 ASP cc_start: 0.8589 (t0) cc_final: 0.8291 (t0) REVERT: E 130 HIS cc_start: 0.7826 (t-90) cc_final: 0.6866 (m170) REVERT: E 132 ASP cc_start: 0.9039 (t70) cc_final: 0.8551 (t0) REVERT: G 53 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.7505 (mtm110) REVERT: G 130 HIS cc_start: 0.7681 (t70) cc_final: 0.6701 (m170) REVERT: H 18 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: H 130 HIS cc_start: 0.7723 (t70) cc_final: 0.6656 (m170) REVERT: I 4 ASP cc_start: 0.7327 (t0) cc_final: 0.6675 (m-30) REVERT: I 130 HIS cc_start: 0.7672 (t-90) cc_final: 0.6893 (m170) REVERT: I 132 ASP cc_start: 0.9043 (t70) cc_final: 0.8557 (t0) REVERT: J 72 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8396 (tm-30) REVERT: J 130 HIS cc_start: 0.7697 (t70) cc_final: 0.6762 (m170) REVERT: K 126 ASP cc_start: 0.7975 (m-30) cc_final: 0.7459 (t0) REVERT: K 130 HIS cc_start: 0.7685 (t-90) cc_final: 0.6861 (m170) REVERT: K 135 GLU cc_start: 0.8009 (tt0) cc_final: 0.7659 (tt0) REVERT: L 18 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: L 120 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7395 (m-10) REVERT: N 126 ASP cc_start: 0.8581 (t0) cc_final: 0.8275 (t0) REVERT: N 130 HIS cc_start: 0.7718 (t-90) cc_final: 0.6859 (m170) REVERT: O 4 ASP cc_start: 0.7692 (m-30) cc_final: 0.6968 (t0) REVERT: O 18 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: O 73 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8442 (mtm-85) REVERT: O 126 ASP cc_start: 0.8690 (t0) cc_final: 0.8460 (t0) REVERT: P 126 ASP cc_start: 0.8570 (t0) cc_final: 0.8257 (t0) REVERT: P 130 HIS cc_start: 0.7632 (t70) cc_final: 0.6686 (m170) REVERT: Q 126 ASP cc_start: 0.8512 (t0) cc_final: 0.8162 (t0) REVERT: R 52 MET cc_start: 0.8796 (mtm) cc_final: 0.8551 (ttm) REVERT: R 60 ASP cc_start: 0.8468 (t70) cc_final: 0.8223 (t70) REVERT: R 126 ASP cc_start: 0.8672 (t0) cc_final: 0.8305 (t0) REVERT: R 130 HIS cc_start: 0.7637 (t-90) cc_final: 0.6807 (m170) REVERT: S 130 HIS cc_start: 0.7683 (t-90) cc_final: 0.6835 (m170) REVERT: T 1 MET cc_start: 0.6469 (mmm) cc_final: 0.6221 (ptm) REVERT: T 4 ASP cc_start: 0.7539 (m-30) cc_final: 0.7239 (t0) REVERT: T 130 HIS cc_start: 0.7766 (t-90) cc_final: 0.7022 (m170) REVERT: T 132 ASP cc_start: 0.8973 (t70) cc_final: 0.8529 (t0) REVERT: U 130 HIS cc_start: 0.7783 (t-90) cc_final: 0.6857 (m170) REVERT: U 132 ASP cc_start: 0.8995 (t70) cc_final: 0.8541 (t0) REVERT: W 126 ASP cc_start: 0.8547 (t0) cc_final: 0.8210 (t0) REVERT: W 130 HIS cc_start: 0.7676 (t70) cc_final: 0.6736 (m170) REVERT: X 128 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: X 130 HIS cc_start: 0.7828 (t-90) cc_final: 0.6906 (m170) outliers start: 107 outliers final: 84 residues processed: 641 average time/residue: 0.4061 time to fit residues: 421.5244 Evaluate side-chains 671 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 581 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 152 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 128 GLU Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 306 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 362 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN E 137 GLN H 137 GLN N 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 32384 Z= 0.255 Angle : 0.626 22.097 43936 Z= 0.294 Chirality : 0.034 0.131 4876 Planarity : 0.003 0.023 5680 Dihedral : 6.837 87.173 4272 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.59 % Allowed : 20.81 % Favored : 75.60 % 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: 3.66 (0.14), residues: 3792 helix: 3.85 (0.08), residues: 2944 sheet: None (None), residues: 0 loop : -3.38 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 37 HIS 0.004 0.001 HIS Q 130 PHE 0.015 0.001 PHE N 26 TYR 0.007 0.001 TYR I 149 ARG 0.004 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 572 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.7665 (m-30) cc_final: 0.7391 (t0) REVERT: A 72 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8394 (tm-30) REVERT: A 132 ASP cc_start: 0.9041 (t70) cc_final: 0.8633 (t0) REVERT: C 120 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: D 130 HIS cc_start: 0.7717 (t-90) cc_final: 0.6930 (m170) REVERT: F 120 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7497 (m-10) REVERT: E 126 ASP cc_start: 0.8727 (t0) cc_final: 0.8524 (t0) REVERT: E 132 ASP cc_start: 0.9074 (t70) cc_final: 0.8603 (t0) REVERT: G 53 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.7457 (mtm110) REVERT: H 18 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: H 126 ASP cc_start: 0.8770 (t0) cc_final: 0.8491 (t0) REVERT: I 126 ASP cc_start: 0.8751 (t0) cc_final: 0.8445 (t0) REVERT: I 130 HIS cc_start: 0.7751 (t-90) cc_final: 0.6950 (m170) REVERT: J 116 SER cc_start: 0.6812 (OUTLIER) cc_final: 0.6013 (p) REVERT: K 126 ASP cc_start: 0.8088 (m-30) cc_final: 0.7546 (t0) REVERT: L 18 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: L 120 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7659 (m-10) REVERT: M 126 ASP cc_start: 0.8663 (t0) cc_final: 0.8383 (t0) REVERT: N 78 ARG cc_start: 0.8489 (mtp85) cc_final: 0.7865 (ttm110) REVERT: N 126 ASP cc_start: 0.8698 (t0) cc_final: 0.8478 (t0) REVERT: N 132 ASP cc_start: 0.9012 (t70) cc_final: 0.8543 (t0) REVERT: O 4 ASP cc_start: 0.7820 (m-30) cc_final: 0.7138 (t0) REVERT: O 18 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: O 73 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8557 (mtm-85) REVERT: O 126 ASP cc_start: 0.8808 (t0) cc_final: 0.8582 (t0) REVERT: P 126 ASP cc_start: 0.8719 (t0) cc_final: 0.8495 (t0) REVERT: Q 116 SER cc_start: 0.6748 (OUTLIER) cc_final: 0.6055 (p) REVERT: Q 126 ASP cc_start: 0.8635 (t0) cc_final: 0.8324 (t0) REVERT: R 52 MET cc_start: 0.8908 (mtm) cc_final: 0.8577 (ttm) REVERT: R 60 ASP cc_start: 0.8667 (t70) cc_final: 0.8432 (t70) REVERT: R 126 ASP cc_start: 0.8806 (t0) cc_final: 0.8537 (t0) REVERT: T 4 ASP cc_start: 0.7672 (m-30) cc_final: 0.7389 (t0) REVERT: T 130 HIS cc_start: 0.7707 (t-90) cc_final: 0.6972 (m170) REVERT: U 132 ASP cc_start: 0.9031 (t70) cc_final: 0.8579 (t0) REVERT: V 120 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7652 (m-10) REVERT: W 52 MET cc_start: 0.8886 (ttm) cc_final: 0.8628 (ttt) REVERT: X 120 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: X 130 HIS cc_start: 0.7813 (t-90) cc_final: 0.6933 (m170) outliers start: 120 outliers final: 100 residues processed: 626 average time/residue: 0.4126 time to fit residues: 413.3680 Evaluate side-chains 669 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 558 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 152 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 152 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 120 PHE Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 284 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN N 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32384 Z= 0.226 Angle : 0.601 20.915 43936 Z= 0.284 Chirality : 0.033 0.142 4876 Planarity : 0.002 0.028 5680 Dihedral : 6.890 89.897 4272 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.53 % Allowed : 20.78 % Favored : 75.69 % 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: 3.83 (0.14), residues: 3792 helix: 3.97 (0.08), residues: 2932 sheet: None (None), residues: 0 loop : -3.23 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 37 HIS 0.003 0.001 HIS L 129 PHE 0.014 0.001 PHE N 26 TYR 0.005 0.001 TYR I 149 ARG 0.004 0.000 ARG U 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 564 time to evaluate : 4.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.7602 (m-30) cc_final: 0.7343 (t0) REVERT: A 72 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 132 ASP cc_start: 0.9030 (t70) cc_final: 0.8617 (t0) REVERT: C 120 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7486 (m-10) REVERT: C 130 HIS cc_start: 0.7812 (t-90) cc_final: 0.6920 (m170) REVERT: D 130 HIS cc_start: 0.7691 (t-90) cc_final: 0.6914 (m170) REVERT: F 120 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7371 (m-10) REVERT: E 53 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7403 (mtm110) REVERT: E 126 ASP cc_start: 0.8691 (t0) cc_final: 0.8491 (t0) REVERT: G 53 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7450 (mtm110) REVERT: H 18 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: H 126 ASP cc_start: 0.8726 (t0) cc_final: 0.8440 (t0) REVERT: I 52 MET cc_start: 0.8894 (ttm) cc_final: 0.8611 (ttm) REVERT: I 126 ASP cc_start: 0.8642 (t0) cc_final: 0.8336 (t0) REVERT: I 130 HIS cc_start: 0.7748 (t-90) cc_final: 0.6929 (m170) REVERT: I 132 ASP cc_start: 0.9066 (t70) cc_final: 0.8585 (t0) REVERT: J 72 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8431 (tm-30) REVERT: J 108 MET cc_start: 0.8266 (tpp) cc_final: 0.7938 (ttm) REVERT: K 126 ASP cc_start: 0.8068 (m-30) cc_final: 0.7426 (t0) REVERT: K 130 HIS cc_start: 0.7717 (t-90) cc_final: 0.6946 (m170) REVERT: L 18 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: L 120 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7465 (m-10) REVERT: M 126 ASP cc_start: 0.8630 (t0) cc_final: 0.8342 (t0) REVERT: N 78 ARG cc_start: 0.8482 (mtp85) cc_final: 0.7883 (ttm110) REVERT: N 126 ASP cc_start: 0.8632 (t0) cc_final: 0.8355 (t0) REVERT: N 130 HIS cc_start: 0.7779 (t-90) cc_final: 0.6893 (m170) REVERT: N 132 ASP cc_start: 0.8999 (t70) cc_final: 0.8516 (t0) REVERT: O 4 ASP cc_start: 0.7767 (m-30) cc_final: 0.7049 (t0) REVERT: O 18 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: O 73 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8524 (mtm-85) REVERT: O 126 ASP cc_start: 0.8780 (t0) cc_final: 0.8549 (t0) REVERT: P 126 ASP cc_start: 0.8670 (t0) cc_final: 0.8436 (t0) REVERT: Q 116 SER cc_start: 0.6715 (OUTLIER) cc_final: 0.5987 (p) REVERT: Q 126 ASP cc_start: 0.8599 (t0) cc_final: 0.8302 (t0) REVERT: R 52 MET cc_start: 0.8879 (mtm) cc_final: 0.8547 (ttm) REVERT: R 60 ASP cc_start: 0.8646 (t70) cc_final: 0.8391 (t70) REVERT: R 126 ASP cc_start: 0.8765 (t0) cc_final: 0.8503 (t0) REVERT: T 1 MET cc_start: 0.6612 (mmm) cc_final: 0.6171 (ptm) REVERT: T 4 ASP cc_start: 0.7620 (m-30) cc_final: 0.7395 (t0) REVERT: T 130 HIS cc_start: 0.7776 (t-90) cc_final: 0.7029 (m170) REVERT: U 120 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7564 (m-10) REVERT: U 130 HIS cc_start: 0.7897 (t-90) cc_final: 0.6917 (m170) REVERT: U 132 ASP cc_start: 0.9012 (t70) cc_final: 0.8557 (t0) REVERT: V 120 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: X 120 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7188 (m-10) REVERT: X 130 HIS cc_start: 0.7864 (t-90) cc_final: 0.6901 (m170) outliers start: 118 outliers final: 98 residues processed: 611 average time/residue: 0.4145 time to fit residues: 405.8234 Evaluate side-chains 674 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 565 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 152 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 152 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 120 PHE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 120 PHE Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 10.0000 chunk 347 optimal weight: 7.9990 chunk 316 optimal weight: 9.9990 chunk 337 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 336 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN D 156 GLN F 137 GLN N 156 GLN W 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 32384 Z= 0.459 Angle : 0.756 18.718 43936 Z= 0.381 Chirality : 0.038 0.143 4876 Planarity : 0.003 0.031 5680 Dihedral : 7.123 89.530 4272 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.01 % Allowed : 21.05 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.13), residues: 3792 helix: 3.22 (0.08), residues: 2920 sheet: None (None), residues: 0 loop : -3.21 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP S 37 HIS 0.005 0.001 HIS F 34 PHE 0.022 0.002 PHE M 26 TYR 0.011 0.001 TYR H 43 ARG 0.005 0.000 ARG U 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 617 time to evaluate : 4.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.9056 (t70) cc_final: 0.8632 (t0) REVERT: C 22 ILE cc_start: 0.8973 (mt) cc_final: 0.8684 (mm) REVERT: C 120 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7685 (m-10) REVERT: D 53 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7333 (mtm110) REVERT: D 126 ASP cc_start: 0.8792 (t0) cc_final: 0.8586 (t0) REVERT: F 120 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: E 4 ASP cc_start: 0.8002 (m-30) cc_final: 0.7699 (t0) REVERT: E 120 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7678 (m-10) REVERT: G 4 ASP cc_start: 0.7990 (m-30) cc_final: 0.7652 (t0) REVERT: G 53 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.7438 (mtm110) REVERT: G 120 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7658 (m-10) REVERT: H 126 ASP cc_start: 0.8856 (t0) cc_final: 0.8616 (t0) REVERT: I 4 ASP cc_start: 0.7337 (t0) cc_final: 0.6692 (m-30) REVERT: I 52 MET cc_start: 0.8787 (ttm) cc_final: 0.8451 (ttt) REVERT: I 126 ASP cc_start: 0.8814 (t0) cc_final: 0.8600 (t0) REVERT: J 4 ASP cc_start: 0.7278 (t0) cc_final: 0.6918 (m-30) REVERT: K 120 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7693 (m-10) REVERT: K 126 ASP cc_start: 0.8464 (m-30) cc_final: 0.7851 (t0) REVERT: L 18 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: L 120 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7728 (m-10) REVERT: M 4 ASP cc_start: 0.7960 (m-30) cc_final: 0.7508 (t0) REVERT: M 126 ASP cc_start: 0.8787 (t0) cc_final: 0.8530 (t0) REVERT: N 78 ARG cc_start: 0.8480 (mtp85) cc_final: 0.7854 (ttm110) REVERT: N 120 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7802 (m-10) REVERT: O 18 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: O 73 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8732 (mtm-85) REVERT: P 126 ASP cc_start: 0.8845 (t0) cc_final: 0.8634 (t0) REVERT: Q 4 ASP cc_start: 0.8007 (m-30) cc_final: 0.7730 (t0) REVERT: Q 126 ASP cc_start: 0.8793 (t0) cc_final: 0.8520 (t0) REVERT: R 4 ASP cc_start: 0.7965 (m-30) cc_final: 0.7639 (t0) REVERT: R 60 ASP cc_start: 0.8855 (t70) cc_final: 0.8613 (t70) REVERT: R 126 ASP cc_start: 0.8881 (t0) cc_final: 0.8663 (t0) REVERT: S 120 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7813 (m-10) REVERT: T 4 ASP cc_start: 0.7994 (m-30) cc_final: 0.7693 (t0) REVERT: U 4 ASP cc_start: 0.7467 (t0) cc_final: 0.6826 (m-30) REVERT: U 53 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.7441 (mtm110) REVERT: U 120 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7672 (m-10) REVERT: V 120 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7708 (m-10) REVERT: W 4 ASP cc_start: 0.8046 (m-30) cc_final: 0.7669 (t0) REVERT: X 120 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7682 (m-10) outliers start: 134 outliers final: 119 residues processed: 704 average time/residue: 0.4269 time to fit residues: 478.9505 Evaluate side-chains 718 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 585 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 120 PHE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 120 PHE Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 120 PHE Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 152 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 120 PHE Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 152 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 120 PHE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 120 PHE Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 0.8980 chunk 357 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 374 optimal weight: 4.9990 chunk 344 optimal weight: 0.9980 chunk 298 optimal weight: 0.0070 chunk 30 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS D 137 GLN E 54 HIS N 156 GLN V 156 GLN W 137 GLN W 156 GLN X 54 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 32384 Z= 0.193 Angle : 0.603 15.220 43936 Z= 0.290 Chirality : 0.033 0.134 4876 Planarity : 0.003 0.032 5680 Dihedral : 7.131 89.635 4272 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.54 % Allowed : 22.67 % Favored : 74.79 % 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: 3.98 (0.14), residues: 3792 helix: 4.09 (0.08), residues: 2916 sheet: None (None), residues: 0 loop : -3.08 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 37 HIS 0.005 0.001 HIS W 130 PHE 0.018 0.001 PHE G 26 TYR 0.006 0.001 TYR G 25 ARG 0.004 0.000 ARG U 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 594 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8399 (tm-30) REVERT: A 132 ASP cc_start: 0.8947 (t70) cc_final: 0.8542 (t0) REVERT: D 53 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7425 (mtm110) REVERT: D 130 HIS cc_start: 0.7614 (t-90) cc_final: 0.6842 (m170) REVERT: F 53 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.7241 (mtm110) REVERT: E 130 HIS cc_start: 0.7781 (t-90) cc_final: 0.6773 (m170) REVERT: E 132 ASP cc_start: 0.8999 (t70) cc_final: 0.8535 (t0) REVERT: G 78 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8140 (mtp180) REVERT: G 130 HIS cc_start: 0.7643 (t70) cc_final: 0.6696 (m170) REVERT: H 130 HIS cc_start: 0.7665 (t70) cc_final: 0.6695 (m170) REVERT: I 52 MET cc_start: 0.8880 (ttm) cc_final: 0.8593 (ttm) REVERT: I 130 HIS cc_start: 0.7669 (t-90) cc_final: 0.6789 (m170) REVERT: J 72 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8437 (tm-30) REVERT: J 130 HIS cc_start: 0.7606 (t70) cc_final: 0.6679 (m170) REVERT: K 126 ASP cc_start: 0.7943 (m-30) cc_final: 0.7560 (t0) REVERT: K 130 HIS cc_start: 0.7710 (t-90) cc_final: 0.6873 (m170) REVERT: L 18 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: N 130 HIS cc_start: 0.7737 (t-90) cc_final: 0.6838 (m170) REVERT: N 132 ASP cc_start: 0.8803 (t70) cc_final: 0.8241 (t0) REVERT: O 18 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: P 32 GLN cc_start: 0.8888 (mt0) cc_final: 0.8571 (mt0) REVERT: P 53 ARG cc_start: 0.8304 (mtm-85) cc_final: 0.7380 (mtm110) REVERT: P 130 HIS cc_start: 0.7686 (t70) cc_final: 0.6757 (m170) REVERT: R 52 MET cc_start: 0.8968 (mtm) cc_final: 0.8644 (ttm) REVERT: R 130 HIS cc_start: 0.7760 (t-90) cc_final: 0.6786 (m170) REVERT: S 130 HIS cc_start: 0.7750 (t-90) cc_final: 0.6798 (m170) REVERT: T 130 HIS cc_start: 0.7664 (t-90) cc_final: 0.6895 (m170) REVERT: U 53 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.7856 (ttp-110) REVERT: U 130 HIS cc_start: 0.7842 (t-90) cc_final: 0.6879 (m170) REVERT: W 130 HIS cc_start: 0.7640 (t70) cc_final: 0.6615 (m170) REVERT: X 130 HIS cc_start: 0.7753 (t-90) cc_final: 0.6854 (m170) outliers start: 85 outliers final: 80 residues processed: 612 average time/residue: 0.3949 time to fit residues: 397.2319 Evaluate side-chains 638 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 556 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 152 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 10.0000 chunk 317 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 chunk 125 optimal weight: 0.2980 chunk 306 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN N 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130052 restraints weight = 48026.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133668 restraints weight = 27506.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136126 restraints weight = 18152.090| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 32384 Z= 0.210 Angle : 0.635 15.071 43936 Z= 0.294 Chirality : 0.033 0.134 4876 Planarity : 0.003 0.030 5680 Dihedral : 7.035 88.673 4272 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.69 % Allowed : 22.91 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.14), residues: 3792 helix: 4.10 (0.08), residues: 2936 sheet: None (None), residues: 0 loop : -3.02 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 37 HIS 0.003 0.001 HIS L 129 PHE 0.015 0.001 PHE M 26 TYR 0.006 0.001 TYR G 43 ARG 0.004 0.000 ARG O 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7535.39 seconds wall clock time: 135 minutes 32.68 seconds (8132.68 seconds total)