Starting phenix.real_space_refine on Thu Mar 21 23:29:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6g_33640/03_2024/7y6g_33640_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6g_33640/03_2024/7y6g_33640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6g_33640/03_2024/7y6g_33640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6g_33640/03_2024/7y6g_33640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6g_33640/03_2024/7y6g_33640_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6g_33640/03_2024/7y6g_33640_trim_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 59 7.16 5 S 96 5.16 5 C 19886 2.51 5 N 5356 2.21 5 O 6030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 4": "OD1" <-> "OD2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "B ASP 4": "OD1" <-> "OD2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 33": "OD1" <-> "OD2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "F ASP 4": "OD1" <-> "OD2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F ASP 126": "OD1" <-> "OD2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "G GLU 9": "OE1" <-> "OE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G ASP 132": "OD1" <-> "OD2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "H GLU 9": "OE1" <-> "OE2" Residue "H TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H ASP 139": "OD1" <-> "OD2" Residue "I ASP 4": "OD1" <-> "OD2" Residue "I TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "J ASP 4": "OD1" <-> "OD2" Residue "J TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 33": "OD1" <-> "OD2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 50": "OD1" <-> "OD2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J ASP 126": "OD1" <-> "OD2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "K ASP 4": "OD1" <-> "OD2" Residue "K TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 127": "OE1" <-> "OE2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "L PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 56": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "L GLU 135": "OE1" <-> "OE2" Residue "L GLU 146": "OE1" <-> "OE2" Residue "M ASP 33": "OD1" <-> "OD2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ASP 132": "OD1" <-> "OD2" Residue "N TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N ASP 99": "OD1" <-> "OD2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "N GLU 135": "OE1" <-> "OE2" Residue "N ASP 139": "OD1" <-> "OD2" Residue "O PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 33": "OD1" <-> "OD2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O GLU 92": "OE1" <-> "OE2" Residue "O GLU 96": "OE1" <-> "OE2" Residue "O ASP 99": "OD1" <-> "OD2" Residue "O ASP 126": "OD1" <-> "OD2" Residue "O GLU 127": "OE1" <-> "OE2" Residue "O ASP 132": "OD1" <-> "OD2" Residue "O GLU 135": "OE1" <-> "OE2" Residue "O GLU 142": "OE1" <-> "OE2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "P ASP 4": "OD1" <-> "OD2" Residue "P TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P ASP 50": "OD1" <-> "OD2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P ASP 126": "OD1" <-> "OD2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P ASP 132": "OD1" <-> "OD2" Residue "P GLU 135": "OE1" <-> "OE2" Residue "P ASP 139": "OD1" <-> "OD2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 47": "OE1" <-> "OE2" Residue "Q ASP 50": "OD1" <-> "OD2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q ASP 126": "OD1" <-> "OD2" Residue "Q GLU 127": "OE1" <-> "OE2" Residue "Q ASP 132": "OD1" <-> "OD2" Residue "Q GLU 135": "OE1" <-> "OE2" Residue "R ASP 4": "OD1" <-> "OD2" Residue "R GLU 9": "OE1" <-> "OE2" Residue "R GLU 18": "OE1" <-> "OE2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R ASP 50": "OD1" <-> "OD2" Residue "R GLU 92": "OE1" <-> "OE2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R ASP 99": "OD1" <-> "OD2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R ASP 139": "OD1" <-> "OD2" Residue "S TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S ASP 50": "OD1" <-> "OD2" Residue "S GLU 92": "OE1" <-> "OE2" Residue "S ASP 99": "OD1" <-> "OD2" Residue "S GLU 121": "OE1" <-> "OE2" Residue "S GLU 127": "OE1" <-> "OE2" Residue "S GLU 135": "OE1" <-> "OE2" Residue "S GLU 146": "OE1" <-> "OE2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 50": "OD1" <-> "OD2" Residue "T GLU 92": "OE1" <-> "OE2" Residue "T GLU 127": "OE1" <-> "OE2" Residue "T ASP 132": "OD1" <-> "OD2" Residue "T GLU 135": "OE1" <-> "OE2" Residue "U ASP 4": "OD1" <-> "OD2" Residue "U TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 50": "OD1" <-> "OD2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "U GLU 92": "OE1" <-> "OE2" Residue "U GLU 121": "OE1" <-> "OE2" Residue "U ASP 126": "OD1" <-> "OD2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "U GLU 128": "OE1" <-> "OE2" Residue "U GLU 135": "OE1" <-> "OE2" Residue "U ASP 139": "OD1" <-> "OD2" Residue "V GLU 18": "OE1" <-> "OE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ASP 50": "OD1" <-> "OD2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "V GLU 92": "OE1" <-> "OE2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 4": "OD1" <-> "OD2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 50": "OD1" <-> "OD2" Residue "W GLU 85": "OE1" <-> "OE2" Residue "W ASP 99": "OD1" <-> "OD2" Residue "W GLU 127": "OE1" <-> "OE2" Residue "W GLU 135": "OE1" <-> "OE2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "X ASP 4": "OD1" <-> "OD2" Residue "X GLU 18": "OE1" <-> "OE2" Residue "X TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X ASP 50": "OD1" <-> "OD2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "X GLU 92": "OE1" <-> "OE2" Residue "X ASP 99": "OD1" <-> "OD2" Residue "X GLU 127": "OE1" <-> "OE2" Residue "X GLU 135": "OE1" <-> "OE2" Residue "X ASP 139": "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: 31427 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1280 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} 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: "E" 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: 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: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" 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: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" 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: "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: 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: "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: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} 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: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} 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: 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: "T" 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: "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: 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: "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: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.48, per 1000 atoms: 0.49 Number of scatterers: 31427 At special positions: 0 Unit cell: (131.274, 131.274, 131.274, 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 59 26.01 S 96 16.00 O 6030 8.00 N 5356 7.00 C 19886 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.85 Conformation dependent library (CDL) restraints added in 5.5 seconds 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 Processing helix chain 'A' and resid 38 through 65 removed outlier: 3.520A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 111 removed outlier: 3.656A pdb=" N LYS A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 144 Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.132A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 Processing helix chain 'B' and resid 38 through 65 removed outlier: 3.614A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 111 removed outlier: 3.666A 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: 3.944A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 35 Processing helix chain 'C' and resid 38 through 65 removed outlier: 3.500A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 111 removed outlier: 3.654A 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: 4.096A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 35 Processing helix chain 'D' and resid 38 through 65 removed outlier: 3.568A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 111 removed outlier: 3.624A pdb=" N LYS D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 144 Processing helix chain 'D' and resid 146 through 152 removed outlier: 4.014A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 Processing helix chain 'E' and resid 38 through 65 removed outlier: 3.515A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.662A 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: 4.095A pdb=" N THR E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 35 Processing helix chain 'F' and resid 38 through 65 removed outlier: 3.520A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 111 removed outlier: 3.671A 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: 4.066A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 Processing helix chain 'G' and resid 38 through 65 removed outlier: 3.526A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 111 removed outlier: 3.649A 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: 4.094A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 35 Processing helix chain 'H' and resid 38 through 65 removed outlier: 3.508A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.664A 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: 3.976A pdb=" N THR H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 Processing helix chain 'I' and resid 38 through 65 removed outlier: 3.520A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 111 removed outlier: 3.638A pdb=" N LYS I 111 " --> pdb=" O VAL I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 144 Processing helix chain 'I' and resid 146 through 152 removed outlier: 3.929A pdb=" N THR I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 35 Processing helix chain 'J' and resid 38 through 65 removed outlier: 3.520A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 111 removed outlier: 3.628A pdb=" N LYS J 111 " --> pdb=" O VAL J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 144 Processing helix chain 'J' and resid 146 through 152 removed outlier: 4.129A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 Processing helix chain 'K' and resid 38 through 65 removed outlier: 3.616A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.663A 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: 3.957A pdb=" N THR K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 removed outlier: 3.510A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 65 removed outlier: 3.626A pdb=" N ALA L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 111 Processing helix chain 'L' and resid 114 through 144 Processing helix chain 'L' and resid 146 through 152 removed outlier: 4.159A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 35 Processing helix chain 'M' and resid 38 through 65 Processing helix chain 'M' and resid 83 through 111 removed outlier: 3.506A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 144 removed outlier: 3.700A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 152 removed outlier: 3.997A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 35 Processing helix chain 'N' and resid 38 through 65 Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.677A 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: 4.087A pdb=" N THR N 152 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 35 Processing helix chain 'O' and resid 38 through 65 Processing helix chain 'O' and resid 83 through 111 removed outlier: 3.539A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 144 Processing helix chain 'O' and resid 146 through 152 removed outlier: 3.940A pdb=" N THR O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 35 Processing helix chain 'P' and resid 38 through 65 removed outlier: 3.611A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 111 removed outlier: 3.656A 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: 3.890A pdb=" N THR P 152 " --> pdb=" O LEU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 35 Processing helix chain 'Q' and resid 38 through 65 Processing helix chain 'Q' and resid 83 through 111 removed outlier: 3.629A pdb=" N LYS Q 111 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 144 Processing helix chain 'Q' and resid 146 through 152 removed outlier: 4.089A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 35 Processing helix chain 'R' and resid 38 through 65 removed outlier: 3.572A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 111 removed outlier: 3.649A 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: 4.046A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 35 Processing helix chain 'S' and resid 38 through 65 removed outlier: 3.519A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 3.674A 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: 4.074A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 35 Processing helix chain 'T' and resid 38 through 65 removed outlier: 3.520A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 111 removed outlier: 3.654A pdb=" N LYS T 111 " --> pdb=" O VAL T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 144 Processing helix chain 'T' and resid 146 through 152 removed outlier: 4.025A pdb=" N THR T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 35 removed outlier: 3.542A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 65 removed outlier: 3.608A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.657A 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: 4.033A pdb=" N THR U 152 " --> pdb=" O LEU U 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 35 Processing helix chain 'V' and resid 38 through 65 Processing helix chain 'V' and resid 83 through 111 Processing helix chain 'V' and resid 114 through 144 removed outlier: 3.699A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 152 removed outlier: 4.152A pdb=" N THR V 152 " --> pdb=" O LEU V 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 35 Processing helix chain 'W' and resid 38 through 65 removed outlier: 3.969A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 111 removed outlier: 3.652A 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: 4.063A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 35 Processing helix chain 'X' and resid 38 through 65 removed outlier: 3.570A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 111 removed outlier: 3.682A 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: 4.076A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 2466 hydrogen bonds defined for protein. 7398 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: 9.89 Time building geometry restraints manager: 13.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 13351 1.41 - 1.59: 18377 1.59 - 1.78: 6 1.78 - 1.96: 186 1.96 - 2.14: 48 Bond restraints: 31968 Sorted by residual: bond pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 1.335 1.407 -0.072 1.31e-02 5.83e+03 3.01e+01 bond pdb=" C GLU W 13 " pdb=" N GLN W 14 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.89e+01 bond pdb=" CB MET Q 52 " pdb=" CG MET Q 52 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CGA HEM C 203 " pdb=" O2A HEM C 203 " ideal model delta sigma weight residual 1.258 1.288 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" NB HEM S 203 " pdb="FE HEM S 203 " ideal model delta sigma weight residual 2.080 1.975 0.105 7.00e-02 2.04e+02 2.25e+00 ... (remaining 31963 not shown) Histogram of bond angle deviations from ideal: 83.42 - 102.60: 148 102.60 - 121.79: 36583 121.79 - 140.97: 6599 140.97 - 160.15: 2 160.15 - 179.33: 22 Bond angle restraints: 43354 Sorted by residual: angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 83.42 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CB MET X 52 " pdb=" CG MET X 52 " pdb=" SD MET X 52 " ideal model delta sigma weight residual 112.70 93.08 19.62 3.00e+00 1.11e-01 4.28e+01 angle pdb=" CB MET S 52 " pdb=" CG MET S 52 " pdb=" SD MET S 52 " ideal model delta sigma weight residual 112.70 93.25 19.45 3.00e+00 1.11e-01 4.20e+01 angle pdb=" O GLN W 14 " pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.06e+00 8.90e-01 3.92e+01 angle pdb=" CB MET N 52 " pdb=" CG MET N 52 " pdb=" SD MET N 52 " ideal model delta sigma weight residual 112.70 95.16 17.54 3.00e+00 1.11e-01 3.42e+01 ... (remaining 43349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 16867 17.68 - 35.35: 1827 35.35 - 53.03: 296 53.03 - 70.70: 99 70.70 - 88.38: 29 Dihedral angle restraints: 19118 sinusoidal: 7994 harmonic: 11124 Sorted by residual: dihedral pdb=" C2B HEM S 203 " pdb=" C3B HEM S 203 " pdb=" CAB HEM S 203 " pdb=" CBB HEM S 203 " ideal model delta sinusoidal sigma weight residual 0.00 32.74 -32.74 2 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CA GLU Q 51 " pdb=" C GLU Q 51 " pdb=" N MET Q 52 " pdb=" CA MET Q 52 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C2B HEM K 203 " pdb=" C3B HEM K 203 " pdb=" CAB HEM K 203 " pdb=" CBB HEM K 203 " ideal model delta sinusoidal sigma weight residual 0.00 -30.74 30.74 2 1.00e+01 1.00e-02 1.25e+01 ... (remaining 19115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3785 0.034 - 0.069: 722 0.069 - 0.103: 269 0.103 - 0.137: 28 0.137 - 0.172: 2 Chirality restraints: 4806 Sorted by residual: chirality pdb=" CA MET Q 52 " pdb=" N MET Q 52 " pdb=" C MET Q 52 " pdb=" CB MET Q 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PHE F 49 " pdb=" N PHE F 49 " pdb=" C PHE F 49 " pdb=" CB PHE F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA MET C 52 " pdb=" N MET C 52 " pdb=" C MET C 52 " pdb=" CB MET C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 4803 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 45 " -0.450 9.50e-02 1.11e+02 2.02e-01 2.63e+01 pdb=" NE ARG R 45 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG R 45 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG R 45 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG R 45 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 49 " 0.016 2.00e-02 2.50e+03 2.93e-02 1.50e+01 pdb=" CG PHE F 49 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE F 49 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE F 49 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE F 49 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE F 49 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 49 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 203 " 0.011 2.00e-02 2.50e+03 2.11e-02 1.00e+01 pdb=" C2A HEM C 203 " 0.028 2.00e-02 2.50e+03 pdb=" C3A HEM C 203 " 0.010 2.00e-02 2.50e+03 pdb=" C4A HEM C 203 " 0.004 2.00e-02 2.50e+03 pdb=" CAA HEM C 203 " -0.032 2.00e-02 2.50e+03 pdb=" CHA HEM C 203 " 0.017 2.00e-02 2.50e+03 pdb=" CHB HEM C 203 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM C 203 " 0.001 2.00e-02 2.50e+03 pdb=" NA HEM C 203 " -0.041 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 74 2.43 - 3.04: 19765 3.04 - 3.66: 43966 3.66 - 4.28: 68656 4.28 - 4.90: 116050 Nonbonded interactions: 248511 Sorted by model distance: nonbonded pdb=" OE2 GLU H 94 " pdb="FE FE H 202 " model vdw 1.807 2.260 nonbonded pdb=" OE1 GLU G 127 " pdb="FE FE G 202 " model vdw 1.953 2.260 nonbonded pdb=" OE1 GLU T 127 " pdb="FE FE2 T 203 " model vdw 1.972 3.000 nonbonded pdb=" OE1 GLU F 127 " pdb="FE FE2 F 202 " model vdw 1.974 3.000 nonbonded pdb=" OE1 GLU R 127 " pdb="FE FE R 202 " model vdw 2.031 2.260 ... (remaining 248506 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) selection = (chain 'B' and resid 1 through 156) selection = (chain 'C' and resid 1 through 156) selection = (chain 'D' and resid 1 through 156) selection = (chain 'E' and resid 1 through 156) selection = (chain 'F' and resid 1 through 156) selection = (chain 'G' and resid 1 through 156) selection = (chain 'H' and resid 1 through 156) selection = (chain 'I' and resid 1 through 156) selection = (chain 'J' and resid 1 through 156) selection = (chain 'K' and resid 1 through 156) selection = (chain 'L' and resid 1 through 156) selection = (chain 'M' and resid 1 through 156) selection = (chain 'N' and resid 1 through 156) selection = (chain 'O' and resid 1 through 156) selection = (chain 'P' and resid 1 through 156) selection = (chain 'Q' and resid 1 through 156) selection = (chain 'R' and resid 1 through 156) selection = (chain 'S' and resid 1 through 156) selection = (chain 'T' and resid 1 through 156) selection = (chain 'U' and resid 1 through 156) selection = (chain 'V' and resid 1 through 156) selection = (chain 'W' and resid 1 through 156) selection = (chain 'X' and resid 1 through 156) } 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: 0.870 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: 0.020 Extract box with map and model: 5.200 Check model and map are aligned: 0.490 Set scattering table: 0.320 Process input model: 78.940 Find NCS groups from input model: 2.770 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 31968 Z= 0.210 Angle : 0.618 31.860 43354 Z= 0.323 Chirality : 0.033 0.172 4806 Planarity : 0.004 0.202 5596 Dihedral : 15.053 88.377 11862 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 4.11 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 2999 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 37 HIS 0.003 0.001 HIS U 54 PHE 0.062 0.003 PHE F 49 TYR 0.047 0.001 TYR T 71 ARG 0.019 0.000 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 3.776 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 outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.4523 time to fit residues: 333.3363 Evaluate side-chains 208 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 171 optimal weight: 0.0040 chunk 210 optimal weight: 30.0000 chunk 326 optimal weight: 7.9990 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN E 156 GLN J 112 HIS M 137 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 112 HIS S 81 GLN U 156 GLN W 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 31968 Z= 0.231 Angle : 0.629 16.178 43354 Z= 0.290 Chirality : 0.032 0.124 4806 Planarity : 0.003 0.077 5596 Dihedral : 6.840 78.783 4204 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.78 % Allowed : 7.94 % Favored : 91.28 % 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: 4.52 (0.13), residues: 3724 helix: 3.99 (0.08), residues: 3019 sheet: None (None), residues: 0 loop : -2.16 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 37 HIS 0.004 0.001 HIS V 112 PHE 0.031 0.002 PHE F 49 TYR 0.027 0.001 TYR T 71 ARG 0.004 0.000 ARG P 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 238 time to evaluate : 4.073 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 outliers start: 26 outliers final: 4 residues processed: 255 average time/residue: 0.3925 time to fit residues: 167.3116 Evaluate side-chains 193 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain Q residue 52 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 327 optimal weight: 6.9990 chunk 353 optimal weight: 4.9990 chunk 291 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN C 156 GLN M 81 GLN M 156 GLN N 81 GLN O 81 GLN T 81 GLN V 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 31968 Z= 0.272 Angle : 0.616 16.259 43354 Z= 0.289 Chirality : 0.033 0.119 4806 Planarity : 0.002 0.051 5596 Dihedral : 6.962 88.448 4204 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.03 % Allowed : 9.99 % Favored : 88.99 % 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: 4.34 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.03 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 37 HIS 0.003 0.001 HIS L 54 PHE 0.020 0.002 PHE N 26 TYR 0.045 0.001 TYR T 71 ARG 0.007 0.001 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 3.826 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 outliers start: 34 outliers final: 21 residues processed: 212 average time/residue: 0.3656 time to fit residues: 135.3734 Evaluate side-chains 188 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain W residue 98 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 219 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31968 Z= 0.234 Angle : 0.583 14.659 43354 Z= 0.273 Chirality : 0.032 0.121 4806 Planarity : 0.002 0.045 5596 Dihedral : 7.009 85.127 4204 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.00 % Allowed : 9.29 % Favored : 89.71 % 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: 4.40 (0.13), residues: 3724 helix: 3.88 (0.08), residues: 2921 sheet: None (None), residues: 0 loop : -1.19 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 37 HIS 0.003 0.001 HIS A 34 PHE 0.020 0.002 PHE S 26 TYR 0.032 0.001 TYR T 71 ARG 0.008 0.000 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 3.917 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 outliers start: 33 outliers final: 10 residues processed: 188 average time/residue: 0.3667 time to fit residues: 119.4988 Evaluate side-chains 175 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 3.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 6.9990 chunk 197 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 296 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 177 optimal weight: 20.0000 chunk 312 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 130 HIS Q 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31968 Z= 0.223 Angle : 0.586 14.478 43354 Z= 0.270 Chirality : 0.032 0.124 4806 Planarity : 0.002 0.036 5596 Dihedral : 7.077 89.844 4204 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.09 % Allowed : 9.90 % Favored : 89.02 % 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: 4.33 (0.13), residues: 3724 helix: 3.80 (0.08), residues: 2916 sheet: None (None), residues: 0 loop : -1.05 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 37 HIS 0.002 0.001 HIS J 34 PHE 0.019 0.001 PHE S 26 TYR 0.027 0.001 TYR T 71 ARG 0.007 0.000 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 3.881 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 outliers start: 36 outliers final: 20 residues processed: 188 average time/residue: 0.3849 time to fit residues: 124.1801 Evaluate side-chains 184 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain X residue 98 ILE Chi-restraints excluded: chain X residue 154 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 348 optimal weight: 20.0000 chunk 289 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31968 Z= 0.220 Angle : 0.582 14.728 43354 Z= 0.269 Chirality : 0.032 0.116 4806 Planarity : 0.002 0.035 5596 Dihedral : 7.019 88.536 4204 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.63 % Allowed : 11.38 % Favored : 87.99 % 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: 4.23 (0.13), residues: 3724 helix: 3.69 (0.08), residues: 2934 sheet: None (None), residues: 0 loop : -1.04 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 37 HIS 0.002 0.001 HIS G 34 PHE 0.018 0.001 PHE U 26 TYR 0.027 0.001 TYR T 71 ARG 0.006 0.000 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 4.199 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 outliers start: 21 outliers final: 17 residues processed: 183 average time/residue: 0.3751 time to fit residues: 119.2495 Evaluate side-chains 182 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 4.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain X residue 98 ILE Chi-restraints excluded: chain X residue 154 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 346 optimal weight: 20.0000 chunk 217 optimal weight: 30.0000 chunk 211 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS C 130 HIS N 130 HIS P 130 HIS T 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31968 Z= 0.253 Angle : 0.610 15.626 43354 Z= 0.284 Chirality : 0.033 0.117 4806 Planarity : 0.002 0.032 5596 Dihedral : 6.965 87.357 4204 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.06 % Allowed : 12.07 % Favored : 86.87 % 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: 4.09 (0.13), residues: 3724 helix: 3.58 (0.08), residues: 2940 sheet: None (None), residues: 0 loop : -1.07 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 37 HIS 0.003 0.001 HIS B 34 PHE 0.018 0.001 PHE U 26 TYR 0.028 0.001 TYR T 71 ARG 0.005 0.000 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 3.827 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 outliers start: 35 outliers final: 34 residues processed: 176 average time/residue: 0.3640 time to fit residues: 112.3991 Evaluate side-chains 192 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Chi-restraints excluded: chain X residue 154 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 236 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS D 156 GLN N 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31968 Z= 0.235 Angle : 0.605 14.941 43354 Z= 0.277 Chirality : 0.032 0.123 4806 Planarity : 0.002 0.031 5596 Dihedral : 6.926 86.645 4204 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.03 % Allowed : 12.49 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.13), residues: 3724 helix: 3.61 (0.08), residues: 2940 sheet: None (None), residues: 0 loop : -1.07 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 37 HIS 0.002 0.001 HIS V 34 PHE 0.018 0.001 PHE U 26 TYR 0.025 0.001 TYR T 71 ARG 0.004 0.000 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 3.269 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 outliers start: 34 outliers final: 32 residues processed: 189 average time/residue: 0.3409 time to fit residues: 113.4302 Evaluate side-chains 190 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Chi-restraints excluded: chain X residue 154 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 303 optimal weight: 0.2980 chunk 323 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 292 optimal weight: 40.0000 chunk 305 optimal weight: 8.9990 chunk 322 optimal weight: 7.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS D 156 GLN ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31968 Z= 0.205 Angle : 0.586 15.335 43354 Z= 0.266 Chirality : 0.032 0.126 4806 Planarity : 0.002 0.028 5596 Dihedral : 6.882 82.440 4204 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.63 % Allowed : 12.98 % Favored : 86.39 % 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: 4.27 (0.13), residues: 3724 helix: 3.71 (0.09), residues: 2940 sheet: None (None), residues: 0 loop : -1.01 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 37 HIS 0.002 0.001 HIS W 28 PHE 0.016 0.001 PHE U 26 TYR 0.025 0.001 TYR T 71 ARG 0.004 0.000 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 4.236 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 outliers start: 21 outliers final: 21 residues processed: 177 average time/residue: 0.3672 time to fit residues: 115.4061 Evaluate side-chains 185 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain X residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 358 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 chunk 285 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN C 130 HIS D 156 GLN ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS V 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31968 Z= 0.197 Angle : 0.583 15.030 43354 Z= 0.263 Chirality : 0.032 0.115 4806 Planarity : 0.002 0.028 5596 Dihedral : 6.854 83.588 4204 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.66 % Allowed : 13.10 % Favored : 86.24 % 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: 4.30 (0.13), residues: 3724 helix: 3.73 (0.09), residues: 2934 sheet: None (None), residues: 0 loop : -0.94 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 37 HIS 0.002 0.001 HIS L 54 PHE 0.016 0.001 PHE U 26 TYR 0.024 0.001 TYR T 71 ARG 0.004 0.000 ARG M 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 3.475 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 outliers start: 22 outliers final: 18 residues processed: 177 average time/residue: 0.3428 time to fit residues: 106.5084 Evaluate side-chains 178 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain X residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 10.0000 chunk 304 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 286 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 293 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 130 HIS C 130 HIS D 156 GLN P 130 HIS U 130 HIS V 32 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.026691 restraints weight = 209789.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.027687 restraints weight = 134008.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028458 restraints weight = 96345.898| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31968 Z= 0.246 Angle : 0.620 15.787 43354 Z= 0.284 Chirality : 0.033 0.116 4806 Planarity : 0.002 0.033 5596 Dihedral : 6.868 82.971 4204 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.78 % Allowed : 13.07 % Favored : 86.15 % 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: 4.12 (0.13), residues: 3724 helix: 3.60 (0.08), residues: 2940 sheet: None (None), residues: 0 loop : -1.05 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 37 HIS 0.003 0.001 HIS G 34 PHE 0.017 0.001 PHE S 26 TYR 0.026 0.001 TYR T 71 ARG 0.004 0.000 ARG M 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4104.73 seconds wall clock time: 79 minutes 6.20 seconds (4746.20 seconds total)