Starting phenix.real_space_refine (version: dev) on Tue Feb 28 03:28:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/02_2023/6k4m_9915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/02_2023/6k4m_9915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/02_2023/6k4m_9915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/02_2023/6k4m_9915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/02_2023/6k4m_9915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/02_2023/6k4m_9915_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.051 sd= 0.650 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 Process input model Symmetric amino acids flipped Residue "A ASP 4": "OD1" <-> "OD2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4": "OD1" <-> "OD2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ASP 33": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 9": "OE1" <-> "OE2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E ASP 33": "OD1" <-> "OD2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 4": "OD1" <-> "OD2" Residue "G GLU 9": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "G TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 4": "OD1" <-> "OD2" Residue "H GLU 9": "OE1" <-> "OE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H ASP 60": "OD1" <-> "OD2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "H ASP 139": "OD1" <-> "OD2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 4": "OD1" <-> "OD2" Residue "I GLU 9": "OE1" <-> "OE2" Residue "I ASP 60": "OD1" <-> "OD2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I ASP 99": "OD1" <-> "OD2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 4": "OD1" <-> "OD2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J GLU 85": "OE1" <-> "OE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J ASP 99": "OD1" <-> "OD2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ASP 60": "OD1" <-> "OD2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K ASP 139": "OD1" <-> "OD2" Residue "K TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 4": "OD1" <-> "OD2" Residue "L ASP 33": "OD1" <-> "OD2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "L ASP 99": "OD1" <-> "OD2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L ASP 132": "OD1" <-> "OD2" Residue "L TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 4": "OD1" <-> "OD2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ASP 60": "OD1" <-> "OD2" Residue "M GLU 85": "OE1" <-> "OE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M ASP 99": "OD1" <-> "OD2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "M TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 4": "OD1" <-> "OD2" Residue "N GLU 85": "OE1" <-> "OE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "N ASP 99": "OD1" <-> "OD2" Residue "N GLU 121": "OE1" <-> "OE2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "N GLU 128": "OE1" <-> "OE2" Residue "N TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 4": "OD1" <-> "OD2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O GLU 51": "OE1" <-> "OE2" Residue "O GLU 56": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 92": "OE1" <-> "OE2" Residue "O ASP 99": "OD1" <-> "OD2" Residue "O GLU 121": "OE1" <-> "OE2" Residue "O GLU 128": "OE1" <-> "OE2" Residue "O ASP 132": "OD1" <-> "OD2" Residue "O TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 18": "OE1" <-> "OE2" Residue "P ASP 33": "OD1" <-> "OD2" Residue "P ASP 60": "OD1" <-> "OD2" Residue "P GLU 92": "OE1" <-> "OE2" Residue "P GLU 96": "OE1" <-> "OE2" Residue "P ASP 99": "OD1" <-> "OD2" Residue "P ASP 113": "OD1" <-> "OD2" Residue "P ASP 132": "OD1" <-> "OD2" Residue "P TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 60": "OD1" <-> "OD2" Residue "Q GLU 85": "OE1" <-> "OE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q ASP 99": "OD1" <-> "OD2" Residue "Q ASP 139": "OD1" <-> "OD2" Residue "Q TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 33": "OD1" <-> "OD2" Residue "R ASP 60": "OD1" <-> "OD2" Residue "R GLU 85": "OE1" <-> "OE2" Residue "R GLU 92": "OE1" <-> "OE2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 4": "OD1" <-> "OD2" Residue "S ASP 33": "OD1" <-> "OD2" Residue "S GLU 92": "OE1" <-> "OE2" Residue "S ASP 99": "OD1" <-> "OD2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T GLU 92": "OE1" <-> "OE2" Residue "T GLU 96": "OE1" <-> "OE2" Residue "T ASP 113": "OD1" <-> "OD2" Residue "T GLU 121": "OE1" <-> "OE2" Residue "T ASP 139": "OD1" <-> "OD2" Residue "T TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 4": "OD1" <-> "OD2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U ASP 33": "OD1" <-> "OD2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "U GLU 85": "OE1" <-> "OE2" Residue "U GLU 92": "OE1" <-> "OE2" Residue "U ASP 99": "OD1" <-> "OD2" Residue "U GLU 121": "OE1" <-> "OE2" Residue "U ASP 132": "OD1" <-> "OD2" Residue "U ASP 139": "OD1" <-> "OD2" Residue "U TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 4": "OD1" <-> "OD2" Residue "V ASP 50": "OD1" <-> "OD2" Residue "V ASP 60": "OD1" <-> "OD2" Residue "V GLU 85": "OE1" <-> "OE2" Residue "V GLU 92": "OE1" <-> "OE2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "V ASP 99": "OD1" <-> "OD2" Residue "V ASP 113": "OD1" <-> "OD2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V ASP 139": "OD1" <-> "OD2" Residue "V TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 33": "OD1" <-> "OD2" Residue "W ASP 50": "OD1" <-> "OD2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 96": "OE1" <-> "OE2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "W ASP 132": "OD1" <-> "OD2" Residue "W ASP 139": "OD1" <-> "OD2" Residue "W TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 4": "OD1" <-> "OD2" Residue "X ASP 33": "OD1" <-> "OD2" Residue "X ASP 50": "OD1" <-> "OD2" Residue "X ASP 60": "OD1" <-> "OD2" Residue "X GLU 92": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X ASP 99": "OD1" <-> "OD2" Residue "X GLU 121": "OE1" <-> "OE2" Residue "X GLU 128": "OE1" <-> "OE2" Residue "X ASP 139": "OD1" <-> "OD2" Residue "X TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31508 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: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 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: "G" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1301 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} 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: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.58, per 1000 atoms: 0.53 Number of scatterers: 31508 At special positions: 0 Unit cell: (133.2, 132.09, 133.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 36 26.01 S 96 16.00 O 6054 8.00 N 5375 7.00 C 19947 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=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.38 Conformation dependent library (CDL) restraints added in 4.8 seconds 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 0 sheets defined 77.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 5 through 34 removed outlier: 3.741A pdb=" N GLN A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.793A pdb=" N PHE A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 111 removed outlier: 3.652A pdb=" N PHE A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 144 removed outlier: 3.519A pdb=" N VAL A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 133 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.090A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 removed outlier: 3.607A pdb=" N GLN B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 64 removed outlier: 3.545A pdb=" N PHE B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 111 removed outlier: 3.675A pdb=" N ASP B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 144 removed outlier: 3.514A pdb=" N ASP B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR B 133 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.855A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 32 removed outlier: 3.792A pdb=" N GLN C 14 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 64 removed outlier: 3.989A pdb=" N PHE C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 56 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG C 61 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 111 removed outlier: 3.717A pdb=" N ARG C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU C 106 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 144 removed outlier: 3.992A pdb=" N VAL C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR C 133 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.990A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 34 removed outlier: 3.797A pdb=" N GLN D 14 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 64 removed outlier: 3.804A pdb=" N ASP D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG D 61 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 111 removed outlier: 3.906A pdb=" N ARG D 91 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU D 106 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 144 removed outlier: 3.604A pdb=" N ASP D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR D 133 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 134 " --> pdb=" O HIS D 130 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 152 removed outlier: 4.019A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 32 removed outlier: 3.919A pdb=" N GLN F 14 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 64 removed outlier: 3.734A pdb=" N PHE F 49 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU F 51 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL F 57 " --> pdb=" O ARG F 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 58 " --> pdb=" O HIS F 54 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 62 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 63 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 111 removed outlier: 3.555A pdb=" N ASP F 90 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG F 91 " --> pdb=" O PHE F 87 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU F 92 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU F 106 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 144 removed outlier: 3.661A pdb=" N ALA F 122 " --> pdb=" O ASN F 118 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR F 133 " --> pdb=" O HIS F 129 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU F 138 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 140 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 152 removed outlier: 4.055A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 34 removed outlier: 3.761A pdb=" N GLN E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR E 16 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA E 17 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 64 removed outlier: 3.826A pdb=" N PHE E 49 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU E 51 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 58 " --> pdb=" O HIS E 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 63 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.899A pdb=" N ARG E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU E 92 " --> pdb=" O GLN E 88 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG E 100 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 144 removed outlier: 3.775A pdb=" N ASP E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 128 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR E 133 " --> pdb=" O HIS E 129 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU E 140 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.150A pdb=" N THR E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 34 removed outlier: 3.616A pdb=" N GLN G 14 " --> pdb=" O PHE G 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR G 16 " --> pdb=" O ASN G 12 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 64 removed outlier: 3.763A pdb=" N PHE G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU G 58 " --> pdb=" O HIS G 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 111 removed outlier: 3.855A pdb=" N ARG G 91 " --> pdb=" O PHE G 87 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG G 100 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU G 106 " --> pdb=" O ARG G 102 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL G 107 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 144 removed outlier: 4.065A pdb=" N ASP G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP G 132 " --> pdb=" O GLU G 128 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR G 133 " --> pdb=" O HIS G 129 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 152 removed outlier: 3.859A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 34 removed outlier: 3.710A pdb=" N GLN H 14 " --> pdb=" O PHE H 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 64 removed outlier: 3.767A pdb=" N PHE H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU H 51 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL H 57 " --> pdb=" O ARG H 53 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU H 63 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.833A pdb=" N ARG H 91 " --> pdb=" O PHE H 87 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE H 98 " --> pdb=" O GLU H 94 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG H 100 " --> pdb=" O GLU H 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL H 107 " --> pdb=" O ARG H 103 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 144 removed outlier: 3.719A pdb=" N ASP H 126 " --> pdb=" O ALA H 122 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR H 133 " --> pdb=" O HIS H 129 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 140 " --> pdb=" O THR H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 152 removed outlier: 4.013A pdb=" N THR H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 removed outlier: 3.670A pdb=" N ALA I 17 " --> pdb=" O GLU I 13 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR I 20 " --> pdb=" O THR I 16 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN I 23 " --> pdb=" O LEU I 19 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 64 removed outlier: 3.754A pdb=" N PHE I 49 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP I 50 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU I 51 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL I 57 " --> pdb=" O ARG I 53 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 58 " --> pdb=" O HIS I 54 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU I 63 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 111 removed outlier: 3.655A pdb=" N ASP I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG I 91 " --> pdb=" O PHE I 87 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU I 92 " --> pdb=" O GLN I 88 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE I 98 " --> pdb=" O GLU I 94 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP I 99 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I 105 " --> pdb=" O LEU I 101 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL I 107 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 128 removed outlier: 3.558A pdb=" N VAL I 119 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.746A pdb=" N ASP I 139 " --> pdb=" O GLU I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 152 removed outlier: 3.863A pdb=" N THR I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 35 removed outlier: 3.731A pdb=" N GLN J 14 " --> pdb=" O PHE J 10 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA J 17 " --> pdb=" O GLU J 13 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN J 23 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS J 34 " --> pdb=" O LYS J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 64 removed outlier: 3.677A pdb=" N PHE J 49 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU J 51 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL J 57 " --> pdb=" O ARG J 53 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU J 58 " --> pdb=" O HIS J 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG J 61 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE J 62 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU J 63 " --> pdb=" O THR J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 110 removed outlier: 3.883A pdb=" N ASP J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG J 91 " --> pdb=" O PHE J 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU J 92 " --> pdb=" O GLN J 88 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE J 98 " --> pdb=" O GLU J 94 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP J 99 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG J 100 " --> pdb=" O GLU J 96 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE J 105 " --> pdb=" O LEU J 101 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU J 106 " --> pdb=" O ARG J 102 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 142 removed outlier: 3.504A pdb=" N ALA J 122 " --> pdb=" O ASN J 118 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP J 132 " --> pdb=" O GLU J 128 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR J 133 " --> pdb=" O HIS J 129 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU J 140 " --> pdb=" O THR J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 152 removed outlier: 3.859A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 removed outlier: 3.809A pdb=" N GLN K 14 " --> pdb=" O PHE K 10 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN K 23 " --> pdb=" O LEU K 19 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 64 removed outlier: 3.636A pdb=" N PHE K 49 " --> pdb=" O ARG K 45 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU K 51 " --> pdb=" O GLU K 47 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU K 63 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.844A pdb=" N ARG K 91 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU K 92 " --> pdb=" O GLN K 88 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE K 98 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP K 99 " --> pdb=" O LEU K 95 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG K 100 " --> pdb=" O GLU K 96 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE K 105 " --> pdb=" O LEU K 101 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU K 106 " --> pdb=" O ARG K 102 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL K 107 " --> pdb=" O ARG K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 128 removed outlier: 4.126A pdb=" N ASP K 126 " --> pdb=" O ALA K 122 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU K 127 " --> pdb=" O ILE K 123 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 144 removed outlier: 3.637A pdb=" N ASP K 139 " --> pdb=" O GLU K 135 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 152 removed outlier: 3.970A pdb=" N THR K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 removed outlier: 3.606A pdb=" N PHE L 10 " --> pdb=" O GLU L 6 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN L 23 " --> pdb=" O LEU L 19 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 64 removed outlier: 3.601A pdb=" N PHE L 49 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU L 51 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU L 58 " --> pdb=" O HIS L 54 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU L 63 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 111 removed outlier: 3.792A pdb=" N ARG L 91 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU L 92 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU L 106 " --> pdb=" O ARG L 102 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 144 removed outlier: 3.621A pdb=" N VAL L 119 " --> pdb=" O THR L 115 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP L 126 " --> pdb=" O ALA L 122 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU L 127 " --> pdb=" O ILE L 123 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS L 129 " --> pdb=" O ALA L 125 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR L 133 " --> pdb=" O HIS L 129 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP L 139 " --> pdb=" O GLU L 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU L 140 " --> pdb=" O THR L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 152 removed outlier: 3.934A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 34 removed outlier: 3.632A pdb=" N PHE M 10 " --> pdb=" O GLU M 6 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN M 14 " --> pdb=" O PHE M 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA M 17 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN M 23 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 64 removed outlier: 3.919A pdb=" N ASP M 50 " --> pdb=" O ALA M 46 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU M 63 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 111 removed outlier: 3.899A pdb=" N ARG M 91 " --> pdb=" O PHE M 87 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU M 92 " --> pdb=" O GLN M 88 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP M 99 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG M 100 " --> pdb=" O GLU M 96 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE M 105 " --> pdb=" O LEU M 101 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU M 106 " --> pdb=" O ARG M 102 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL M 107 " --> pdb=" O ARG M 103 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 144 removed outlier: 3.530A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU M 127 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP M 132 " --> pdb=" O GLU M 128 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR M 133 " --> pdb=" O HIS M 129 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP M 139 " --> pdb=" O GLU M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 152 removed outlier: 3.857A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 34 removed outlier: 3.616A pdb=" N PHE N 10 " --> pdb=" O GLU N 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA N 17 " --> pdb=" O GLU N 13 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 64 removed outlier: 3.981A pdb=" N PHE N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP N 50 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU N 51 " --> pdb=" O GLU N 47 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL N 57 " --> pdb=" O ARG N 53 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU N 58 " --> pdb=" O HIS N 54 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE N 62 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU N 63 " --> pdb=" O THR N 59 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.705A pdb=" N ARG N 91 " --> pdb=" O PHE N 87 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU N 92 " --> pdb=" O GLN N 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE N 98 " --> pdb=" O GLU N 94 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU N 106 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL N 107 " --> pdb=" O ARG N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 144 removed outlier: 3.869A pdb=" N ASP N 126 " --> pdb=" O ALA N 122 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP N 132 " --> pdb=" O GLU N 128 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR N 133 " --> pdb=" O HIS N 129 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU N 134 " --> pdb=" O HIS N 130 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP N 139 " --> pdb=" O GLU N 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU N 140 " --> pdb=" O THR N 136 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU N 144 " --> pdb=" O LEU N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 152 removed outlier: 4.054A pdb=" N THR N 152 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 34 removed outlier: 3.542A pdb=" N GLN O 14 " --> pdb=" O PHE O 10 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA O 17 " --> pdb=" O GLU O 13 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN O 24 " --> pdb=" O THR O 20 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 64 removed outlier: 3.881A pdb=" N PHE O 49 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP O 50 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU O 51 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU O 56 " --> pdb=" O MET O 52 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL O 57 " --> pdb=" O ARG O 53 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU O 58 " --> pdb=" O HIS O 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU O 63 " --> pdb=" O THR O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 111 removed outlier: 3.726A pdb=" N PHE O 87 " --> pdb=" O VAL O 83 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG O 91 " --> pdb=" O PHE O 87 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU O 92 " --> pdb=" O GLN O 88 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE O 98 " --> pdb=" O GLU O 94 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP O 99 " --> pdb=" O LEU O 95 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG O 100 " --> pdb=" O GLU O 96 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU O 106 " --> pdb=" O ARG O 102 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL O 107 " --> pdb=" O ARG O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 144 removed outlier: 3.911A pdb=" N ASP O 126 " --> pdb=" O ALA O 122 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP O 132 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR O 133 " --> pdb=" O HIS O 129 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU O 134 " --> pdb=" O HIS O 130 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP O 139 " --> pdb=" O GLU O 135 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU O 144 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 152 removed outlier: 4.070A pdb=" N THR O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 35 removed outlier: 3.820A pdb=" N GLN P 14 " --> pdb=" O PHE P 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP P 33 " --> pdb=" O ALA P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 64 removed outlier: 3.599A pdb=" N PHE P 49 " --> pdb=" O ARG P 45 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU P 51 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU P 56 " --> pdb=" O MET P 52 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL P 57 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU P 58 " --> pdb=" O HIS P 54 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU P 63 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU P 64 " --> pdb=" O ASP P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 111 removed outlier: 3.557A pdb=" N ASP P 90 " --> pdb=" O MET P 86 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU P 92 " --> pdb=" O GLN P 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE P 98 " --> pdb=" O GLU P 94 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG P 100 " --> pdb=" O GLU P 96 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE P 105 " --> pdb=" O LEU P 101 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU P 106 " --> pdb=" O ARG P 102 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL P 107 " --> pdb=" O ARG P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 144 removed outlier: 4.040A pdb=" N ASP P 126 " --> pdb=" O ALA P 122 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU P 127 " --> pdb=" O ILE P 123 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP P 132 " --> pdb=" O GLU P 128 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR P 133 " --> pdb=" O HIS P 129 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP P 139 " --> pdb=" O GLU P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 152 removed outlier: 3.881A pdb=" N THR P 152 " --> pdb=" O LEU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 34 removed outlier: 3.524A pdb=" N PHE Q 10 " --> pdb=" O GLU Q 6 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN Q 14 " --> pdb=" O PHE Q 10 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA Q 21 " --> pdb=" O ALA Q 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE Q 22 " --> pdb=" O GLU Q 18 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 64 removed outlier: 3.734A pdb=" N PHE Q 49 " --> pdb=" O ARG Q 45 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU Q 63 " --> pdb=" O THR Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 111 removed outlier: 3.905A pdb=" N ARG Q 91 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU Q 92 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE Q 98 " --> pdb=" O GLU Q 94 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG Q 100 " --> pdb=" O GLU Q 96 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE Q 105 " --> pdb=" O LEU Q 101 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU Q 106 " --> pdb=" O ARG Q 102 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 144 removed outlier: 3.506A pdb=" N VAL Q 119 " --> pdb=" O THR Q 115 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP Q 126 " --> pdb=" O ALA Q 122 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP Q 132 " --> pdb=" O GLU Q 128 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR Q 133 " --> pdb=" O HIS Q 129 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP Q 139 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 152 removed outlier: 4.064A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 34 removed outlier: 3.608A pdb=" N PHE R 10 " --> pdb=" O GLU R 6 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN R 14 " --> pdb=" O PHE R 10 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA R 17 " --> pdb=" O GLU R 13 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 64 removed outlier: 3.502A pdb=" N PHE R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL R 57 " --> pdb=" O ARG R 53 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG R 61 " --> pdb=" O VAL R 57 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE R 62 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU R 64 " --> pdb=" O ASP R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 111 removed outlier: 3.773A pdb=" N ASP R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG R 91 " --> pdb=" O PHE R 87 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU R 92 " --> pdb=" O GLN R 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP R 99 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG R 100 " --> pdb=" O GLU R 96 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU R 106 " --> pdb=" O ARG R 102 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 144 removed outlier: 3.909A pdb=" N ASP R 126 " --> pdb=" O ALA R 122 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS R 129 " --> pdb=" O ALA R 125 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP R 132 " --> pdb=" O GLU R 128 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR R 133 " --> pdb=" O HIS R 129 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP R 139 " --> pdb=" O GLU R 135 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 152 removed outlier: 3.978A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 34 removed outlier: 3.829A pdb=" N GLN S 14 " --> pdb=" O PHE S 10 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA S 17 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 64 removed outlier: 3.945A pdb=" N PHE S 49 " --> pdb=" O ARG S 45 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP S 50 " --> pdb=" O ALA S 46 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU S 51 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU S 56 " --> pdb=" O MET S 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL S 57 " --> pdb=" O ARG S 53 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG S 61 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU S 63 " --> pdb=" O THR S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 3.763A pdb=" N ASP S 90 " --> pdb=" O MET S 86 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG S 91 " --> pdb=" O PHE S 87 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU S 92 " --> pdb=" O GLN S 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE S 98 " --> pdb=" O GLU S 94 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP S 99 " --> pdb=" O LEU S 95 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG S 100 " --> pdb=" O GLU S 96 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE S 105 " --> pdb=" O LEU S 101 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU S 106 " --> pdb=" O ARG S 102 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL S 107 " --> pdb=" O ARG S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 144 removed outlier: 3.549A pdb=" N VAL S 119 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA S 122 " --> pdb=" O ASN S 118 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP S 132 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR S 133 " --> pdb=" O HIS S 129 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP S 139 " --> pdb=" O GLU S 135 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU S 144 " --> pdb=" O LEU S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 152 removed outlier: 4.022A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 34 removed outlier: 3.777A pdb=" N ALA T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR T 20 " --> pdb=" O THR T 16 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 64 removed outlier: 3.924A pdb=" N PHE T 49 " --> pdb=" O ARG T 45 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU T 51 " --> pdb=" O GLU T 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL T 57 " --> pdb=" O ARG T 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU T 58 " --> pdb=" O HIS T 54 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE T 62 " --> pdb=" O LEU T 58 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU T 63 " --> pdb=" O THR T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 111 removed outlier: 3.884A pdb=" N PHE T 87 " --> pdb=" O VAL T 83 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG T 91 " --> pdb=" O PHE T 87 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU T 92 " --> pdb=" O GLN T 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE T 98 " --> pdb=" O GLU T 94 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP T 99 " --> pdb=" O LEU T 95 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG T 100 " --> pdb=" O GLU T 96 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU T 106 " --> pdb=" O ARG T 102 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL T 107 " --> pdb=" O ARG T 103 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS T 111 " --> pdb=" O VAL T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 144 removed outlier: 3.823A pdb=" N ASP T 126 " --> pdb=" O ALA T 122 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP T 132 " --> pdb=" O GLU T 128 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR T 133 " --> pdb=" O HIS T 129 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP T 139 " --> pdb=" O GLU T 135 " (cutoff:3.500A) Processing helix chain 'T' and resid 147 through 152 removed outlier: 4.049A pdb=" N THR T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 35 removed outlier: 3.642A pdb=" N GLN U 14 " --> pdb=" O PHE U 10 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR U 20 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE U 22 " --> pdb=" O GLU U 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 64 removed outlier: 3.530A pdb=" N PHE U 49 " --> pdb=" O ARG U 45 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU U 51 " --> pdb=" O GLU U 47 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL U 57 " --> pdb=" O ARG U 53 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU U 58 " --> pdb=" O HIS U 54 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU U 63 " --> pdb=" O THR U 59 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.660A pdb=" N ASP U 90 " --> pdb=" O MET U 86 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG U 91 " --> pdb=" O PHE U 87 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU U 92 " --> pdb=" O GLN U 88 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE U 98 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP U 99 " --> pdb=" O LEU U 95 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU U 106 " --> pdb=" O ARG U 102 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL U 107 " --> pdb=" O ARG U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 115 through 144 removed outlier: 3.638A pdb=" N ASP U 126 " --> pdb=" O ALA U 122 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP U 132 " --> pdb=" O GLU U 128 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR U 133 " --> pdb=" O HIS U 129 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU U 134 " --> pdb=" O HIS U 130 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU U 144 " --> pdb=" O LEU U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 152 removed outlier: 3.895A pdb=" N THR U 152 " --> pdb=" O LEU U 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 32 removed outlier: 3.613A pdb=" N PHE V 10 " --> pdb=" O GLU V 6 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA V 17 " --> pdb=" O GLU V 13 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR V 20 " --> pdb=" O THR V 16 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN V 23 " --> pdb=" O LEU V 19 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 64 removed outlier: 3.555A pdb=" N PHE V 49 " --> pdb=" O ARG V 45 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP V 50 " --> pdb=" O ALA V 46 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU V 51 " --> pdb=" O GLU V 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU V 58 " --> pdb=" O HIS V 54 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE V 62 " --> pdb=" O LEU V 58 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU V 63 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU V 64 " --> pdb=" O ASP V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 83 through 111 removed outlier: 3.708A pdb=" N ARG V 91 " --> pdb=" O PHE V 87 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU V 92 " --> pdb=" O GLN V 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE V 98 " --> pdb=" O GLU V 94 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP V 99 " --> pdb=" O LEU V 95 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG V 100 " --> pdb=" O GLU V 96 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU V 106 " --> pdb=" O ARG V 102 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL V 107 " --> pdb=" O ARG V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 144 removed outlier: 3.605A pdb=" N VAL V 119 " --> pdb=" O THR V 115 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP V 132 " --> pdb=" O GLU V 128 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR V 133 " --> pdb=" O HIS V 129 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP V 139 " --> pdb=" O GLU V 135 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU V 144 " --> pdb=" O LEU V 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 152 removed outlier: 3.970A pdb=" N THR V 152 " --> pdb=" O LEU V 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 35 removed outlier: 3.575A pdb=" N PHE W 10 " --> pdb=" O GLU W 6 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR W 20 " --> pdb=" O THR W 16 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA W 21 " --> pdb=" O ALA W 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS W 28 " --> pdb=" O GLN W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 64 removed outlier: 3.695A pdb=" N PHE W 49 " --> pdb=" O ARG W 45 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP W 50 " --> pdb=" O ALA W 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU W 51 " --> pdb=" O GLU W 47 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU W 56 " --> pdb=" O MET W 52 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL W 57 " --> pdb=" O ARG W 53 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU W 58 " --> pdb=" O HIS W 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE W 62 " --> pdb=" O LEU W 58 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU W 63 " --> pdb=" O THR W 59 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU W 64 " --> pdb=" O ASP W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 111 removed outlier: 3.846A pdb=" N ASP W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG W 91 " --> pdb=" O PHE W 87 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU W 92 " --> pdb=" O GLN W 88 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE W 98 " --> pdb=" O GLU W 94 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP W 99 " --> pdb=" O LEU W 95 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG W 100 " --> pdb=" O GLU W 96 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU W 106 " --> pdb=" O ARG W 102 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL W 107 " --> pdb=" O ARG W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 144 removed outlier: 3.518A pdb=" N VAL W 119 " --> pdb=" O THR W 115 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP W 126 " --> pdb=" O ALA W 122 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP W 132 " --> pdb=" O GLU W 128 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR W 133 " --> pdb=" O HIS W 129 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU W 134 " --> pdb=" O HIS W 130 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU W 144 " --> pdb=" O LEU W 140 " (cutoff:3.500A) Processing helix chain 'W' and resid 146 through 152 removed outlier: 3.818A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 34 removed outlier: 3.602A pdb=" N PHE X 10 " --> pdb=" O GLU X 6 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR X 20 " --> pdb=" O THR X 16 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS X 28 " --> pdb=" O GLN X 24 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP X 33 " --> pdb=" O ALA X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 64 removed outlier: 3.760A pdb=" N PHE X 49 " --> pdb=" O ARG X 45 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP X 50 " --> pdb=" O ALA X 46 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL X 57 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU X 58 " --> pdb=" O HIS X 54 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG X 61 " --> pdb=" O VAL X 57 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE X 62 " --> pdb=" O LEU X 58 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU X 63 " --> pdb=" O THR X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 111 removed outlier: 3.894A pdb=" N ARG X 91 " --> pdb=" O PHE X 87 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU X 92 " --> pdb=" O GLN X 88 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE X 98 " --> pdb=" O GLU X 94 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG X 100 " --> pdb=" O GLU X 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE X 105 " --> pdb=" O LEU X 101 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU X 106 " --> pdb=" O ARG X 102 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL X 107 " --> pdb=" O ARG X 103 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 144 removed outlier: 3.547A pdb=" N ALA X 122 " --> pdb=" O ASN X 118 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP X 126 " --> pdb=" O ALA X 122 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP X 132 " --> pdb=" O GLU X 128 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR X 133 " --> pdb=" O HIS X 129 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP X 139 " --> pdb=" O GLU X 135 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU X 144 " --> pdb=" O LEU X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 152 removed outlier: 3.837A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 1785 hydrogen bonds defined for protein. 5355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.62 Time building geometry restraints manager: 14.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 13390 1.40 - 1.58: 18442 1.58 - 1.76: 0 1.76 - 1.94: 192 1.94 - 2.12: 48 Bond restraints: 32072 Sorted by residual: bond pdb=" C VAL D 153 " pdb=" N ILE D 154 " ideal model delta sigma weight residual 1.329 1.310 0.019 1.07e-02 8.73e+03 3.24e+00 bond pdb=" C VAL U 153 " pdb=" N ILE U 154 " ideal model delta sigma weight residual 1.327 1.310 0.017 9.50e-03 1.11e+04 3.19e+00 bond pdb=" C ASP J 113 " pdb=" N ILE J 114 " ideal model delta sigma weight residual 1.332 1.316 0.016 1.16e-02 7.43e+03 1.96e+00 bond pdb=" CA LEU V 65 " pdb=" C LEU V 65 " ideal model delta sigma weight residual 1.523 1.503 0.019 1.41e-02 5.03e+03 1.87e+00 bond pdb=" C VAL W 153 " pdb=" N ILE W 154 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.26e-02 6.30e+03 1.81e+00 ... (remaining 32067 not shown) Histogram of bond angle deviations from ideal: 86.07 - 104.64: 271 104.64 - 123.20: 41694 123.20 - 141.76: 1511 141.76 - 160.33: 0 160.33 - 178.89: 24 Bond angle restraints: 43500 Sorted by residual: angle pdb=" N VAL P 153 " pdb=" CA VAL P 153 " pdb=" C VAL P 153 " ideal model delta sigma weight residual 113.10 107.69 5.41 9.70e-01 1.06e+00 3.11e+01 angle pdb=" N VAL K 153 " pdb=" CA VAL K 153 " pdb=" C VAL K 153 " ideal model delta sigma weight residual 113.22 107.71 5.51 1.23e+00 6.61e-01 2.00e+01 angle pdb=" N ILE D 114 " pdb=" CA ILE D 114 " pdb=" C ILE D 114 " ideal model delta sigma weight residual 112.96 108.99 3.97 1.00e+00 1.00e+00 1.58e+01 angle pdb=" N VAL L 153 " pdb=" CA VAL L 153 " pdb=" C VAL L 153 " ideal model delta sigma weight residual 112.29 108.66 3.63 9.40e-01 1.13e+00 1.49e+01 angle pdb=" N LYS T 111 " pdb=" CA LYS T 111 " pdb=" C LYS T 111 " ideal model delta sigma weight residual 110.44 114.20 -3.76 1.20e+00 6.94e-01 9.82e+00 ... (remaining 43495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16493 17.96 - 35.92: 2160 35.92 - 53.88: 293 53.88 - 71.84: 161 71.84 - 89.79: 73 Dihedral angle restraints: 19180 sinusoidal: 8002 harmonic: 11178 Sorted by residual: dihedral pdb=" CA LYS M 111 " pdb=" C LYS M 111 " pdb=" N HIS M 112 " pdb=" CA HIS M 112 " ideal model delta harmonic sigma weight residual 180.00 146.97 33.03 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" CA LYS J 111 " pdb=" C LYS J 111 " pdb=" N HIS J 112 " pdb=" CA HIS J 112 " ideal model delta harmonic sigma weight residual 180.00 147.35 32.65 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA TRP J 37 " pdb=" C TRP J 37 " pdb=" N THR J 38 " pdb=" CA THR J 38 " ideal model delta harmonic sigma weight residual -180.00 -147.41 -32.59 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 19177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3546 0.044 - 0.088: 988 0.088 - 0.132: 237 0.132 - 0.177: 49 0.177 - 0.221: 9 Chirality restraints: 4829 Sorted by residual: chirality pdb=" CB ILE S 98 " pdb=" CA ILE S 98 " pdb=" CG1 ILE S 98 " pdb=" CG2 ILE S 98 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL P 153 " pdb=" CA VAL P 153 " pdb=" CG1 VAL P 153 " pdb=" CG2 VAL P 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CG LEU T 58 " pdb=" CB LEU T 58 " pdb=" CD1 LEU T 58 " pdb=" CD2 LEU T 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4826 not shown) Planarity restraints: 5615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 150 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C LEU A 150 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 150 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 151 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 120 " -0.011 2.00e-02 2.50e+03 1.25e-02 2.75e+00 pdb=" CG PHE F 120 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE F 120 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE F 120 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE F 120 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 120 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 120 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE W 114 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C ILE W 114 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE W 114 " 0.010 2.00e-02 2.50e+03 pdb=" N THR W 115 " 0.009 2.00e-02 2.50e+03 ... (remaining 5612 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8839 2.79 - 3.32: 33421 3.32 - 3.84: 55026 3.84 - 4.37: 66194 4.37 - 4.90: 98221 Nonbonded interactions: 261701 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OG SER R 116 " model vdw 2.258 2.440 nonbonded pdb=" OD2 ASP B 113 " pdb=" OG SER B 116 " model vdw 2.262 2.440 nonbonded pdb=" OD2 ASP W 113 " pdb=" OG SER W 116 " model vdw 2.270 2.440 nonbonded pdb=" OE1 GLN X 137 " pdb=" OH TYR X 149 " model vdw 2.272 2.440 nonbonded pdb=" OE1 GLN E 137 " pdb=" OH TYR E 149 " model vdw 2.273 2.440 ... (remaining 261696 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 157) selection = (chain 'B' and resid 1 through 157) selection = (chain 'C' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'D' and resid 1 through 157) selection = (chain 'E' and resid 1 through 157) selection = (chain 'F' and resid 1 through 157) selection = (chain 'G' and resid 1 through 157) selection = (chain 'H' and resid 1 through 157) selection = (chain 'I' and resid 1 through 157) selection = (chain 'J' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'K' and resid 1 through 157) selection = (chain 'L' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'M' and resid 1 through 157) selection = (chain 'N' and resid 1 through 157) selection = (chain 'O' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'P' and resid 1 through 157) selection = (chain 'Q' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'R' and resid 1 through 157) selection = (chain 'S' and resid 1 through 157) selection = (chain 'T' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'U' and resid 1 through 157) selection = (chain 'V' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'W' and resid 1 through 157) selection = (chain 'X' and resid 1 through 157) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 36 7.16 5 S 96 5.16 5 C 19947 2.51 5 N 5375 2.21 5 O 6054 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 6.390 Check model and map are aligned: 0.490 Process input model: 77.230 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.310 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 0.006 0.074 32072 Z= 0.377 Angle : 1.009 12.419 43500 Z= 0.563 Chirality : 0.045 0.221 4829 Planarity : 0.004 0.031 5615 Dihedral : 17.743 89.795 11888 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.61 (0.09), residues: 3742 helix: -2.80 (0.06), residues: 2792 sheet: None (None), residues: 0 loop : -3.11 (0.15), residues: 950 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1683 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1665 time to evaluate : 3.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 1672 average time/residue: 0.5195 time to fit residues: 1276.4106 Evaluate side-chains 1203 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1200 time to evaluate : 4.423 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2661 time to fit residues: 6.9112 ------------------------------------------------------------------------------- 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: 6.9990 chunk 272 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 28 HIS A 34 HIS A 76 HIS A 130 HIS B 76 HIS C 28 HIS ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 76 HIS F 130 HIS ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS G 32 GLN G 76 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS H 76 HIS ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS J 32 GLN J 76 HIS J 130 HIS K 32 GLN K 76 HIS L 130 HIS ** M 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS O 130 HIS P 14 GLN P 23 ASN P 118 ASN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS Q 156 GLN R 130 HIS ** R 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 129 HIS ** T 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 HIS ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 HIS V 34 HIS ** V 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 28 HIS W 130 HIS ** X 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 130 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 32072 Z= 0.233 Angle : 0.707 16.285 43500 Z= 0.353 Chirality : 0.038 0.228 4829 Planarity : 0.004 0.036 5615 Dihedral : 8.530 89.204 4222 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 3742 helix: -0.39 (0.08), residues: 2973 sheet: None (None), residues: 0 loop : -2.75 (0.20), residues: 769 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1651 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1626 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 4 residues processed: 1638 average time/residue: 0.5315 time to fit residues: 1275.7655 Evaluate side-chains 1204 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1200 time to evaluate : 3.804 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3120 time to fit residues: 7.2710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 5.9990 chunk 353 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 262 optimal weight: 0.5980 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN E 34 HIS E 118 ASN E 129 HIS E 130 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS H 129 HIS J 156 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 ASN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 HIS L 130 HIS L 156 GLN M 129 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS O 76 HIS P 118 ASN P 130 HIS Q 34 HIS Q 76 HIS Q 156 GLN ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 HIS S 129 HIS S 130 HIS S 156 GLN ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 HIS T 156 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS ** V 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 156 GLN ** W 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 HIS ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 129 HIS ** X 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 156 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 32072 Z= 0.236 Angle : 0.708 16.649 43500 Z= 0.347 Chirality : 0.038 0.196 4829 Planarity : 0.004 0.066 5615 Dihedral : 8.246 88.080 4222 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3742 helix: 0.19 (0.09), residues: 3023 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 719 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1569 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1557 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 1565 average time/residue: 0.5406 time to fit residues: 1251.2149 Evaluate side-chains 1152 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1148 time to evaluate : 3.728 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3504 time to fit residues: 7.3226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 9.9990 chunk 246 optimal weight: 0.0370 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 328 optimal weight: 8.9990 chunk 347 optimal weight: 6.9990 chunk 171 optimal weight: 0.4980 chunk 311 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 34 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 76 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS I 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 HIS L 76 HIS M 76 HIS M 156 GLN N 129 HIS N 130 HIS N 156 GLN O 34 HIS O 130 HIS P 76 HIS Q 34 HIS Q 130 HIS Q 156 GLN R 76 HIS R 130 HIS R 156 GLN ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 HIS S 34 HIS S 76 HIS S 156 GLN T 34 HIS T 156 GLN U 70 ASN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS ** V 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 HIS V 130 HIS V 156 GLN W 34 HIS ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 HIS X 34 HIS ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 HIS X 156 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 32072 Z= 0.191 Angle : 0.667 12.088 43500 Z= 0.321 Chirality : 0.039 0.207 4829 Planarity : 0.003 0.054 5615 Dihedral : 8.075 87.850 4222 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 3742 helix: 0.32 (0.09), residues: 3018 sheet: None (None), residues: 0 loop : -2.49 (0.20), residues: 724 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1620 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1602 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 1614 average time/residue: 0.5200 time to fit residues: 1240.8529 Evaluate side-chains 1173 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1166 time to evaluate : 3.875 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3169 time to fit residues: 9.1926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 5 optimal weight: 0.0370 chunk 259 optimal weight: 30.0000 chunk 143 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS B 130 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 118 ASN D 129 HIS ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 118 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS G 129 HIS H 34 HIS H 130 HIS ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 HIS J 118 ASN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN M 130 HIS ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 ASN ** N 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS ** P 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 HIS Q 34 HIS Q 130 HIS Q 156 GLN ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 HIS S 130 HIS S 156 GLN T 34 HIS T 76 HIS T 130 HIS T 156 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 118 ASN V 129 HIS V 130 HIS V 156 GLN ** W 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 HIS W 129 HIS W 130 HIS ** X 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 HIS X 118 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 32072 Z= 0.263 Angle : 0.771 18.758 43500 Z= 0.365 Chirality : 0.040 0.230 4829 Planarity : 0.004 0.046 5615 Dihedral : 8.121 89.492 4222 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 3742 helix: 0.39 (0.09), residues: 2961 sheet: None (None), residues: 0 loop : -1.96 (0.21), residues: 781 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1513 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1504 time to evaluate : 3.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 9 outliers final: 3 residues processed: 1509 average time/residue: 0.5097 time to fit residues: 1144.4302 Evaluate side-chains 1087 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1084 time to evaluate : 3.772 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3030 time to fit residues: 6.7387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 68 optimal weight: 0.1980 chunk 204 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 34 HIS ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS H 34 HIS ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN M 34 HIS M 130 HIS ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 ASN N 129 HIS P 23 ASN P 130 HIS P 156 GLN Q 23 ASN Q 34 HIS ** Q 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 HIS R 130 HIS S 23 ASN S 34 HIS S 130 HIS S 156 GLN T 34 HIS T 129 HIS T 156 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS V 130 HIS V 156 GLN W 34 HIS W 130 HIS X 34 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 32072 Z= 0.236 Angle : 0.735 16.535 43500 Z= 0.355 Chirality : 0.040 0.196 4829 Planarity : 0.004 0.045 5615 Dihedral : 8.086 89.919 4222 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.24 % 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: -0.23 (0.13), residues: 3742 helix: 0.38 (0.09), residues: 3018 sheet: None (None), residues: 0 loop : -2.10 (0.21), residues: 724 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1545 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1537 time to evaluate : 3.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 1538 average time/residue: 0.5405 time to fit residues: 1242.3196 Evaluate side-chains 1083 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1083 time to evaluate : 3.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 254 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 293 optimal weight: 0.3980 chunk 194 optimal weight: 0.4980 chunk 346 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS F 12 ASN ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 130 HIS E 156 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS H 130 HIS ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 HIS ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN M 34 HIS N 23 ASN ** P 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 HIS R 130 HIS S 34 HIS S 130 HIS S 156 GLN T 34 HIS ** U 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS V 129 HIS V 130 HIS V 156 GLN ** W 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 HIS ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 HIS X 130 HIS X 156 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 32072 Z= 0.246 Angle : 0.775 16.086 43500 Z= 0.372 Chirality : 0.041 0.199 4829 Planarity : 0.004 0.060 5615 Dihedral : 8.039 89.010 4222 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 3742 helix: 0.35 (0.09), residues: 2999 sheet: None (None), residues: 0 loop : -1.93 (0.21), residues: 743 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1517 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 1518 average time/residue: 0.5137 time to fit residues: 1160.5683 Evaluate side-chains 1095 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1092 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2854 time to fit residues: 6.6024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 207 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 chunk 236 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS F 129 HIS F 156 GLN E 34 HIS E 156 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS H 34 HIS ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 HIS I 129 HIS I 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 HIS J 156 GLN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 HIS N 129 HIS N 130 HIS O 129 HIS O 130 HIS ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 ASN P 156 GLN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 HIS Q 156 GLN R 129 HIS R 130 HIS S 23 ASN S 34 HIS S 130 HIS S 156 GLN T 34 HIS U 130 HIS U 156 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS V 130 HIS ** V 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 HIS W 129 HIS X 23 ASN ** X 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 HIS X 156 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 32072 Z= 0.242 Angle : 0.799 18.342 43500 Z= 0.377 Chirality : 0.042 0.202 4829 Planarity : 0.004 0.046 5615 Dihedral : 7.897 88.254 4222 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 3742 helix: 0.28 (0.09), residues: 3007 sheet: None (None), residues: 0 loop : -1.83 (0.22), residues: 735 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1522 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 9 outliers final: 1 residues processed: 1523 average time/residue: 0.5210 time to fit residues: 1184.8549 Evaluate side-chains 1085 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1084 time to evaluate : 3.844 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2649 time to fit residues: 5.6609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.9980 chunk 332 optimal weight: 20.0000 chunk 303 optimal weight: 0.9990 chunk 323 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 322 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 129 HIS F 12 ASN ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN E 34 HIS E 156 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS H 34 HIS H 130 HIS ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 HIS I 129 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN N 156 GLN O 129 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN Q 34 HIS Q 156 GLN R 130 HIS ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 HIS T 34 HIS U 130 HIS U 156 GLN V 34 HIS V 129 HIS V 130 HIS W 34 HIS X 34 HIS X 129 HIS X 156 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.7360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.126 32072 Z= 0.243 Angle : 0.813 21.114 43500 Z= 0.385 Chirality : 0.042 0.201 4829 Planarity : 0.004 0.052 5615 Dihedral : 7.918 87.430 4222 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 3742 helix: 0.26 (0.09), residues: 3000 sheet: None (None), residues: 0 loop : -1.87 (0.22), residues: 742 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1522 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1515 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 7 outliers final: 0 residues processed: 1515 average time/residue: 0.5079 time to fit residues: 1149.8084 Evaluate side-chains 1082 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1082 time to evaluate : 3.879 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 208 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 358 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 285 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 70 ASN A 156 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS C 156 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 118 ASN F 129 HIS F 156 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 156 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS ** H 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 HIS I 130 HIS J 112 HIS J 129 HIS ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN M 23 ASN N 129 HIS N 156 GLN O 129 HIS O 130 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 HIS Q 156 GLN ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 HIS R 130 HIS S 23 ASN ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 HIS S 156 GLN T 34 HIS U 118 ASN U 130 HIS U 156 GLN V 34 HIS V 129 HIS V 130 HIS ** W 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 HIS W 129 HIS W 130 HIS X 34 HIS X 156 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 32072 Z= 0.278 Angle : 0.854 21.708 43500 Z= 0.408 Chirality : 0.043 0.230 4829 Planarity : 0.005 0.059 5615 Dihedral : 8.067 86.619 4222 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 3742 helix: 0.18 (0.09), residues: 2978 sheet: None (None), residues: 0 loop : -1.81 (0.21), residues: 764 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1464 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 1464 average time/residue: 0.5127 time to fit residues: 1126.8257 Evaluate side-chains 1063 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1061 time to evaluate : 3.975 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3285 time to fit residues: 6.3476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 4.9990 chunk 304 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 286 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 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 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 118 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 156 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS ** H 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 HIS ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 HIS Q 156 GLN ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS S 34 HIS S 130 HIS T 34 HIS U 118 ASN U 129 HIS U 130 HIS V 34 HIS V 129 HIS V 130 HIS ** W 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 HIS X 34 HIS X 129 HIS X 156 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.063783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.045573 restraints weight = 150452.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.047220 restraints weight = 116161.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.048589 restraints weight = 94430.617| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.7587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.109 32072 Z= 0.264 Angle : 0.852 22.021 43500 Z= 0.403 Chirality : 0.043 0.203 4829 Planarity : 0.004 0.053 5615 Dihedral : 8.102 86.526 4222 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.15 % 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: -0.40 (0.13), residues: 3742 helix: 0.16 (0.09), residues: 2963 sheet: None (None), residues: 0 loop : -1.51 (0.22), residues: 779 =============================================================================== Job complete usr+sys time: 14483.94 seconds wall clock time: 258 minutes 4.54 seconds (15484.54 seconds total)