Starting phenix.real_space_refine on Mon Mar 18 16:05:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aox_15555/03_2024/8aox_15555_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aox_15555/03_2024/8aox_15555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aox_15555/03_2024/8aox_15555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aox_15555/03_2024/8aox_15555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aox_15555/03_2024/8aox_15555_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aox_15555/03_2024/8aox_15555_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 24 6.06 5 S 768 5.16 5 C 52104 2.51 5 N 14520 2.21 5 O 20400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "JA ASP 152": "OD1" <-> "OD2" Residue "JA TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA GLU 283": "OE1" <-> "OE2" Residue "JA TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA ASP 436": "OD1" <-> "OD2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 11": "OD1" <-> "OD2" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C ASP 436": "OD1" <-> "OD2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ASP 146": "OD1" <-> "OD2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G ASP 201": "OD1" <-> "OD2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 322": "OD1" <-> "OD2" Residue "G GLU 349": "OE1" <-> "OE2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "G PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I ASP 152": "OD1" <-> "OD2" Residue "I TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 216": "OD1" <-> "OD2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "K TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 283": "OE1" <-> "OE2" Residue "K TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 353": "OE1" <-> "OE2" Residue "M GLU 26": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 202": "OE1" <-> "OE2" Residue "M TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 322": "OD1" <-> "OD2" Residue "M PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 436": "OD1" <-> "OD2" Residue "M PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 283": "OE1" <-> "OE2" Residue "O TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 436": "OD1" <-> "OD2" Residue "O PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "Q TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 283": "OE1" <-> "OE2" Residue "Q TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 349": "OE1" <-> "OE2" Residue "Q GLU 353": "OE1" <-> "OE2" Residue "Q ASP 436": "OD1" <-> "OD2" Residue "S ASP 11": "OD1" <-> "OD2" Residue "S ASP 152": "OD1" <-> "OD2" Residue "S TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 202": "OE1" <-> "OE2" Residue "S TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 283": "OE1" <-> "OE2" Residue "S TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 436": "OD1" <-> "OD2" Residue "S PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 283": "OE1" <-> "OE2" Residue "V TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 349": "OE1" <-> "OE2" Residue "X ASP 9": "OD1" <-> "OD2" Residue "X ASP 11": "OD1" <-> "OD2" Residue "X GLU 26": "OE1" <-> "OE2" Residue "X GLU 52": "OE1" <-> "OE2" Residue "X GLU 283": "OE1" <-> "OE2" Residue "X TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 322": "OD1" <-> "OD2" Residue "X GLU 405": "OE1" <-> "OE2" Residue "X ASP 436": "OD1" <-> "OD2" Residue "X PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 11": "OD1" <-> "OD2" Residue "Z GLU 26": "OE1" <-> "OE2" Residue "Z TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 202": "OE1" <-> "OE2" Residue "Z TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 283": "OE1" <-> "OE2" Residue "Z PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 349": "OE1" <-> "OE2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA GLU 202": "OE1" <-> "OE2" Residue "BA TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA GLU 349": "OE1" <-> "OE2" Residue "BA PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 26": "OE1" <-> "OE2" Residue "DA ASP 152": "OD1" <-> "OD2" Residue "DA TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 283": "OE1" <-> "OE2" Residue "DA GLU 349": "OE1" <-> "OE2" Residue "DA ASP 436": "OD1" <-> "OD2" Residue "FA GLU 26": "OE1" <-> "OE2" Residue "FA ASP 36": "OD1" <-> "OD2" Residue "FA TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA ASP 11": "OD1" <-> "OD2" Residue "HA GLU 26": "OE1" <-> "OE2" Residue "HA GLU 52": "OE1" <-> "OE2" Residue "HA TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA GLU 349": "OE1" <-> "OE2" Residue "HA ASP 436": "OD1" <-> "OD2" Residue "LA GLU 26": "OE1" <-> "OE2" Residue "LA ASP 63": "OD1" <-> "OD2" Residue "LA GLU 283": "OE1" <-> "OE2" Residue "LA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA ASP 63": "OD1" <-> "OD2" Residue "NA ASP 152": "OD1" <-> "OD2" Residue "NA TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA GLU 202": "OE1" <-> "OE2" Residue "NA GLU 283": "OE1" <-> "OE2" Residue "NA TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA ASP 11": "OD1" <-> "OD2" Residue "PA TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA GLU 202": "OE1" <-> "OE2" Residue "PA GLU 283": "OE1" <-> "OE2" Residue "PA PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA GLU 349": "OE1" <-> "OE2" Residue "PA GLU 353": "OE1" <-> "OE2" Residue "PA PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA ASP 11": "OD1" <-> "OD2" Residue "RA ASP 152": "OD1" <-> "OD2" Residue "RA TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA GLU 202": "OE1" <-> "OE2" Residue "RA TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA GLU 283": "OE1" <-> "OE2" Residue "RA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA GLU 349": "OE1" <-> "OE2" Residue "RA GLU 353": "OE1" <-> "OE2" Residue "TA ASP 11": "OD1" <-> "OD2" Residue "TA GLU 26": "OE1" <-> "OE2" Residue "TA ASP 36": "OD1" <-> "OD2" Residue "TA GLU 52": "OE1" <-> "OE2" Residue "TA PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA ASP 152": "OD1" <-> "OD2" Residue "TA TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA GLU 202": "OE1" <-> "OE2" Residue "TA TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA GLU 283": "OE1" <-> "OE2" Residue "TA TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA ASP 436": "OD1" <-> "OD2" Residue "TA PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA GLU 349": "OE1" <-> "OE2" Residue "VA GLU 353": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 87816 Number of models: 1 Model: "" Number of chains: 72 Chain: "JA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "A" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "C" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "E" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "G" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "I" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "K" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "M" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "O" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "Q" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "S" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "V" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "X" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "Z" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "BA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "DA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "FA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "HA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "LA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "NA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "PA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "RA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "TA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "VA" Number of atoms: 3429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 432, 3356 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3345 Chain: "JA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "DA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "FA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "HA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "LA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "NA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "PA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "RA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "TA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "VA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "JA" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 199 Classifications: {'water': 199} Link IDs: {None: 198} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Chain: "G" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 199 Classifications: {'water': 199} Link IDs: {None: 198} Chain: "I" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Chain: "K" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Chain: "M" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Chain: "O" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "Q" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 199 Classifications: {'water': 199} Link IDs: {None: 198} Chain: "S" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Chain: "V" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Chain: "X" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "Z" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 199 Classifications: {'water': 199} Link IDs: {None: 198} Chain: "BA" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Chain: "DA" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "FA" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Chain: "HA" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "LA" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "NA" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 200 Classifications: {'water': 200} Link IDs: {None: 199} Chain: "PA" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "RA" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "TA" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 201 Classifications: {'water': 201} Link IDs: {None: 200} Chain: "VA" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1030 SG CYSJA 134 179.375 71.768 134.557 1.00 96.75 S ATOM 1082 SG CYSJA 141 178.528 67.931 133.913 1.00 73.14 S ATOM 4459 SG CYS A 134 183.389 114.928 134.506 1.00 87.64 S ATOM 4511 SG CYS A 141 184.567 111.325 133.882 1.00 55.28 S ATOM 7888 SG CYS C 134 165.304 154.336 134.521 1.00 81.03 S ATOM 7940 SG CYS C 141 168.230 151.668 133.886 1.00 63.44 S ATOM 11317 SG CYS E 134 130.012 179.358 134.591 1.00 98.60 S ATOM 11369 SG CYS E 141 133.917 178.575 133.929 1.00 68.59 S ATOM 14746 SG CYS G 134 86.891 183.468 134.584 1.00 87.93 S ATOM 14798 SG CYS G 141 90.653 184.607 133.894 1.00 57.04 S ATOM 18175 SG CYS I 134 47.485 165.597 134.661 1.00 80.92 S ATOM 18227 SG CYS I 141 50.203 168.311 133.865 1.00 65.71 S ATOM 21604 SG CYS K 134 22.392 130.044 134.585 1.00 94.65 S ATOM 21656 SG CYS K 141 23.265 133.853 133.866 1.00 64.39 S ATOM 25033 SG CYS M 134 18.298 86.828 134.530 1.00 84.39 S ATOM 25085 SG CYS M 141 17.217 90.545 133.887 1.00 59.42 S ATOM 28462 SG CYS O 134 36.494 47.427 134.426 1.00 89.81 S ATOM 28514 SG CYS O 141 33.610 50.087 133.895 1.00 58.63 S ATOM 31891 SG CYS Q 134 71.779 22.414 134.551 1.00 96.38 S ATOM 31943 SG CYS Q 141 67.936 23.269 133.910 1.00 66.15 S ATOM 35320 SG CYS S 134 114.855 18.194 134.517 1.00 83.60 S ATOM 35372 SG CYS S 141 111.105 17.209 133.877 1.00 54.68 S ATOM 38749 SG CYS V 134 154.321 36.440 134.547 1.00 85.90 S ATOM 38801 SG CYS V 141 151.692 33.509 133.857 1.00 62.95 S ATOM 42178 SG CYS X 134 179.366 130.031 27.521 1.00 99.40 S ATOM 42230 SG CYS X 141 178.508 133.933 28.170 1.00 77.41 S ATOM 45607 SG CYS Z 134 183.460 86.847 27.550 1.00 90.78 S ATOM 45659 SG CYS Z 141 184.584 90.628 28.218 1.00 52.54 S ATOM 49036 SG CYSBA 134 165.305 47.484 27.550 1.00 93.95 S ATOM 49088 SG CYSBA 141 168.296 50.101 28.213 1.00 56.03 S ATOM 52465 SG CYSDA 134 130.002 22.379 27.545 1.00 92.34 S ATOM 52517 SG CYSDA 141 133.780 23.239 28.182 1.00 76.07 S ATOM 55894 SG CYSFA 134 86.851 18.321 27.512 1.00 90.53 S ATOM 55946 SG CYSFA 141 90.661 17.183 28.241 1.00 59.65 S ATOM 59323 SG CYSHA 134 47.404 36.443 27.517 1.00 86.40 S ATOM 59375 SG CYSHA 141 50.135 33.547 28.213 1.00 62.18 S ATOM 62752 SG CYSLA 134 22.385 71.761 27.520 1.00 97.93 S ATOM 62804 SG CYSLA 141 23.243 68.001 28.192 1.00 67.19 S ATOM 66181 SG CYSNA 134 18.438 114.911 27.632 1.00 90.08 S ATOM 66233 SG CYSNA 141 17.241 111.133 28.193 1.00 47.18 S ATOM 69610 SG CYSPA 134 36.420 154.324 27.525 1.00 86.49 S ATOM 69662 SG CYSPA 141 33.514 151.642 28.224 1.00 67.28 S ATOM 73039 SG CYSRA 134 71.734 179.397 27.569 1.00105.47 S ATOM 73091 SG CYSRA 141 67.905 178.541 28.216 1.00 71.08 S ATOM 76468 SG CYSTA 134 114.951 183.431 27.548 1.00 83.08 S ATOM 76520 SG CYSTA 141 111.181 184.572 28.209 1.00 56.23 S ATOM 79897 SG CYSVA 134 154.329 165.351 27.570 1.00 79.86 S ATOM 79949 SG CYSVA 141 151.640 168.233 28.213 1.00 66.41 S Residues with excluded nonbonded symmetry interactions: 192 residue: pdb=" N AGLNJA 19 " occ=0.44 ... (16 atoms not shown) pdb=" NE2BGLNJA 19 " occ=0.56 residue: pdb=" N ACYSJA 82 " occ=0.61 ... (10 atoms not shown) pdb=" SG BCYSJA 82 " occ=0.39 residue: pdb=" N AGLUJA 234 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLUJA 234 " occ=0.49 residue: pdb=" N AGLUJA 250 " occ=0.57 ... (16 atoms not shown) pdb=" OE2BGLUJA 250 " occ=0.43 residue: pdb=" N AASPJA 310 " occ=0.76 ... (14 atoms not shown) pdb=" OD2BASPJA 310 " occ=0.24 residue: pdb=" N AGLNJA 364 " occ=0.68 ... (16 atoms not shown) pdb=" NE2BGLNJA 364 " occ=0.32 residue: pdb=" N ALYSJA 400 " occ=0.69 ... (16 atoms not shown) pdb=" NZ BLYSJA 400 " occ=0.31 residue: pdb=" N ACYSJA 418 " occ=0.45 ... (10 atoms not shown) pdb=" SG BCYSJA 418 " occ=0.55 residue: pdb=" N AGLN A 19 " occ=0.52 ... (16 atoms not shown) pdb=" NE2BGLN A 19 " occ=0.48 residue: pdb=" N ACYS A 82 " occ=0.65 ... (10 atoms not shown) pdb=" SG BCYS A 82 " occ=0.35 residue: pdb=" N AGLU A 234 " occ=0.56 ... (16 atoms not shown) pdb=" OE2BGLU A 234 " occ=0.44 residue: pdb=" N AGLU A 250 " occ=0.44 ... (16 atoms not shown) pdb=" OE2BGLU A 250 " occ=0.56 ... (remaining 180 not shown) Time building chain proxies: 61.24, per 1000 atoms: 0.70 Number of scatterers: 87816 At special positions: 0 Unit cell: (202.615, 202.615, 162.919, 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) Zn 24 29.99 S 768 16.00 O 20400 8.00 N 14520 7.00 C 52104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.48 Conformation dependent library (CDL) restraints added in 22.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" NE2 HIS M 79 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 134 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 141 " pdb=" ZN O1001 " pdb="ZN ZN O1001 " - pdb=" NE2 HIS O 79 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 134 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 141 " pdb=" ZN Q1001 " pdb="ZN ZN Q1001 " - pdb=" NE2 HIS Q 79 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 134 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 141 " pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" NE2 HIS S 79 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 134 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 141 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" NE2 HIS V 79 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 134 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 141 " pdb=" ZN X1001 " pdb="ZN ZN X1001 " - pdb=" NE2 HIS X 79 " pdb="ZN ZN X1001 " - pdb=" SG CYS X 134 " pdb="ZN ZN X1001 " - pdb=" SG CYS X 141 " pdb=" ZN Z1001 " pdb="ZN ZN Z1001 " - pdb=" NE2 HIS Z 79 " pdb="ZN ZN Z1001 " - pdb=" SG CYS Z 134 " pdb="ZN ZN Z1001 " - pdb=" SG CYS Z 141 " pdb=" ZNBA1001 " pdb="ZN ZNBA1001 " - pdb=" NE2 HISBA 79 " pdb="ZN ZNBA1001 " - pdb=" SG CYSBA 134 " pdb="ZN ZNBA1001 " - pdb=" SG CYSBA 141 " pdb=" ZNDA1001 " pdb="ZN ZNDA1001 " - pdb=" NE2 HISDA 79 " pdb="ZN ZNDA1001 " - pdb=" SG CYSDA 134 " pdb="ZN ZNDA1001 " - pdb=" SG CYSDA 141 " pdb=" ZNFA1001 " pdb="ZN ZNFA1001 " - pdb=" NE2 HISFA 79 " pdb="ZN ZNFA1001 " - pdb=" SG CYSFA 134 " pdb="ZN ZNFA1001 " - pdb=" SG CYSFA 141 " pdb=" ZNHA1001 " pdb="ZN ZNHA1001 " - pdb=" NE2 HISHA 79 " pdb="ZN ZNHA1001 " - pdb=" SG CYSHA 134 " pdb="ZN ZNHA1001 " - pdb=" SG CYSHA 141 " pdb=" ZNJA1001 " pdb="ZN ZNJA1001 " - pdb=" NE2 HISJA 79 " pdb="ZN ZNJA1001 " - pdb=" SG CYSJA 134 " pdb="ZN ZNJA1001 " - pdb=" SG CYSJA 141 " pdb=" ZNLA1001 " pdb="ZN ZNLA1001 " - pdb=" SG CYSLA 134 " pdb="ZN ZNLA1001 " - pdb=" NE2 HISLA 79 " pdb="ZN ZNLA1001 " - pdb=" SG CYSLA 141 " pdb=" ZNNA1001 " pdb="ZN ZNNA1001 " - pdb=" NE2 HISNA 79 " pdb="ZN ZNNA1001 " - pdb=" SG CYSNA 134 " pdb="ZN ZNNA1001 " - pdb=" SG CYSNA 141 " pdb=" ZNPA1001 " pdb="ZN ZNPA1001 " - pdb=" NE2 HISPA 79 " pdb="ZN ZNPA1001 " - pdb=" SG CYSPA 134 " pdb="ZN ZNPA1001 " - pdb=" SG CYSPA 141 " pdb=" ZNRA1001 " pdb="ZN ZNRA1001 " - pdb=" SG CYSRA 134 " pdb="ZN ZNRA1001 " - pdb=" NE2 HISRA 79 " pdb="ZN ZNRA1001 " - pdb=" SG CYSRA 141 " pdb=" ZNTA1001 " pdb="ZN ZNTA1001 " - pdb=" NE2 HISTA 79 " pdb="ZN ZNTA1001 " - pdb=" SG CYSTA 134 " pdb="ZN ZNTA1001 " - pdb=" SG CYSTA 141 " pdb=" ZNVA1001 " pdb="ZN ZNVA1001 " - pdb=" NE2 HISVA 79 " pdb="ZN ZNVA1001 " - pdb=" SG CYSVA 134 " pdb="ZN ZNVA1001 " - pdb=" SG CYSVA 141 " 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 312 helices and 118 sheets defined 28.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.94 Creating SS restraints... Processing helix chain 'JA' and resid 14 through 21 Processing helix chain 'JA' and resid 38 through 54 Processing helix chain 'JA' and resid 89 through 101 Processing helix chain 'JA' and resid 112 through 122 removed outlier: 3.735A pdb=" N GLYJA 117 " --> pdb=" O SERJA 113 " (cutoff:3.500A) Processing helix chain 'JA' and resid 158 through 168 removed outlier: 3.623A pdb=" N LYSJA 168 " --> pdb=" O HISJA 164 " (cutoff:3.500A) Processing helix chain 'JA' and resid 181 through 184 No H-bonds generated for 'chain 'JA' and resid 181 through 184' Processing helix chain 'JA' and resid 193 through 195 No H-bonds generated for 'chain 'JA' and resid 193 through 195' Processing helix chain 'JA' and resid 202 through 204 No H-bonds generated for 'chain 'JA' and resid 202 through 204' Processing helix chain 'JA' and resid 252 through 258 removed outlier: 3.598A pdb=" N TRPJA 258 " --> pdb=" O LEUJA 254 " (cutoff:3.500A) Processing helix chain 'JA' and resid 336 through 342 Processing helix chain 'JA' and resid 345 through 347 No H-bonds generated for 'chain 'JA' and resid 345 through 347' Processing helix chain 'JA' and resid 352 through 363 Processing helix chain 'JA' and resid 381 through 403 Proline residue: JA 385 - end of helix removed outlier: 4.074A pdb=" N ALAJA 395 " --> pdb=" O SERJA 392 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYSJA 398 " --> pdb=" O ALAJA 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 38 through 54 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.605A pdb=" N GLY A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.649A pdb=" N LYS A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.610A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 381 through 403 Proline residue: A 385 - end of helix removed outlier: 4.043A pdb=" N ALA A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 112 through 122 removed outlier: 3.777A pdb=" N GLY C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.766A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 363 Processing helix chain 'C' and resid 381 through 403 Proline residue: C 385 - end of helix removed outlier: 4.139A pdb=" N ALA C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 38 through 54 Processing helix chain 'E' and resid 89 through 101 Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.697A pdb=" N GLY E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 181 through 184 No H-bonds generated for 'chain 'E' and resid 181 through 184' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.599A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 363 Processing helix chain 'E' and resid 381 through 403 Proline residue: E 385 - end of helix removed outlier: 4.109A pdb=" N ALA E 395 " --> pdb=" O SER E 392 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS E 398 " --> pdb=" O ALA E 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 38 through 54 Processing helix chain 'G' and resid 89 through 102 Processing helix chain 'G' and resid 112 through 122 removed outlier: 3.768A pdb=" N GLY G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 168 removed outlier: 3.506A pdb=" N LYS G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.668A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 341 Processing helix chain 'G' and resid 345 through 347 No H-bonds generated for 'chain 'G' and resid 345 through 347' Processing helix chain 'G' and resid 352 through 363 Processing helix chain 'G' and resid 381 through 403 Proline residue: G 385 - end of helix removed outlier: 4.027A pdb=" N ALA G 395 " --> pdb=" O SER G 392 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS G 398 " --> pdb=" O ALA G 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 21 Processing helix chain 'I' and resid 38 through 54 Processing helix chain 'I' and resid 89 through 102 Processing helix chain 'I' and resid 112 through 122 removed outlier: 3.698A pdb=" N GLY I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 168 removed outlier: 3.671A pdb=" N LYS I 168 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 184 No H-bonds generated for 'chain 'I' and resid 181 through 184' Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.749A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 342 Processing helix chain 'I' and resid 345 through 347 No H-bonds generated for 'chain 'I' and resid 345 through 347' Processing helix chain 'I' and resid 352 through 363 Processing helix chain 'I' and resid 381 through 403 Proline residue: I 385 - end of helix removed outlier: 4.084A pdb=" N ALA I 395 " --> pdb=" O SER I 392 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS I 398 " --> pdb=" O ALA I 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 38 through 54 Processing helix chain 'K' and resid 89 through 101 Processing helix chain 'K' and resid 112 through 122 removed outlier: 3.777A pdb=" N GLY K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 168 removed outlier: 3.682A pdb=" N LYS K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 184 No H-bonds generated for 'chain 'K' and resid 181 through 184' Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.682A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 341 Processing helix chain 'K' and resid 345 through 347 No H-bonds generated for 'chain 'K' and resid 345 through 347' Processing helix chain 'K' and resid 352 through 363 Processing helix chain 'K' and resid 381 through 403 Proline residue: K 385 - end of helix removed outlier: 4.064A pdb=" N ALA K 395 " --> pdb=" O SER K 392 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS K 398 " --> pdb=" O ALA K 395 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 Processing helix chain 'M' and resid 38 through 54 Processing helix chain 'M' and resid 89 through 101 Processing helix chain 'M' and resid 112 through 122 removed outlier: 3.724A pdb=" N GLY M 117 " --> pdb=" O SER M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 168 removed outlier: 3.660A pdb=" N LYS M 168 " --> pdb=" O HIS M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 184 No H-bonds generated for 'chain 'M' and resid 181 through 184' Processing helix chain 'M' and resid 193 through 195 No H-bonds generated for 'chain 'M' and resid 193 through 195' Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.634A pdb=" N TRP M 258 " --> pdb=" O LEU M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 342 Processing helix chain 'M' and resid 352 through 363 Processing helix chain 'M' and resid 381 through 403 Proline residue: M 385 - end of helix removed outlier: 4.052A pdb=" N ALA M 395 " --> pdb=" O SER M 392 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS M 398 " --> pdb=" O ALA M 395 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 21 removed outlier: 3.649A pdb=" N LYS O 16 " --> pdb=" O ALA O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 54 Processing helix chain 'O' and resid 89 through 102 Processing helix chain 'O' and resid 112 through 122 removed outlier: 3.693A pdb=" N GLY O 117 " --> pdb=" O SER O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 168 Processing helix chain 'O' and resid 181 through 184 No H-bonds generated for 'chain 'O' and resid 181 through 184' Processing helix chain 'O' and resid 193 through 195 No H-bonds generated for 'chain 'O' and resid 193 through 195' Processing helix chain 'O' and resid 202 through 204 No H-bonds generated for 'chain 'O' and resid 202 through 204' Processing helix chain 'O' and resid 252 through 258 removed outlier: 3.643A pdb=" N TRP O 258 " --> pdb=" O LEU O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 342 Processing helix chain 'O' and resid 345 through 347 No H-bonds generated for 'chain 'O' and resid 345 through 347' Processing helix chain 'O' and resid 352 through 363 Processing helix chain 'O' and resid 381 through 403 Proline residue: O 385 - end of helix removed outlier: 4.088A pdb=" N ALA O 395 " --> pdb=" O SER O 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS O 398 " --> pdb=" O ALA O 395 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 21 Processing helix chain 'Q' and resid 38 through 54 Processing helix chain 'Q' and resid 89 through 101 Processing helix chain 'Q' and resid 112 through 122 removed outlier: 3.741A pdb=" N GLY Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 168 removed outlier: 3.649A pdb=" N LYS Q 168 " --> pdb=" O HIS Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 184 No H-bonds generated for 'chain 'Q' and resid 181 through 184' Processing helix chain 'Q' and resid 193 through 195 No H-bonds generated for 'chain 'Q' and resid 193 through 195' Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 252 through 258 removed outlier: 3.638A pdb=" N TRP Q 258 " --> pdb=" O LEU Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 336 through 342 Processing helix chain 'Q' and resid 345 through 347 No H-bonds generated for 'chain 'Q' and resid 345 through 347' Processing helix chain 'Q' and resid 352 through 363 Processing helix chain 'Q' and resid 381 through 403 Proline residue: Q 385 - end of helix removed outlier: 4.076A pdb=" N ALA Q 395 " --> pdb=" O SER Q 392 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS Q 398 " --> pdb=" O ALA Q 395 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 21 removed outlier: 4.164A pdb=" N ALA S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 54 Processing helix chain 'S' and resid 89 through 101 Processing helix chain 'S' and resid 112 through 122 removed outlier: 3.507A pdb=" N GLY S 117 " --> pdb=" O SER S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 158 through 168 removed outlier: 3.530A pdb=" N LYS S 168 " --> pdb=" O HIS S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 184 No H-bonds generated for 'chain 'S' and resid 181 through 184' Processing helix chain 'S' and resid 193 through 195 No H-bonds generated for 'chain 'S' and resid 193 through 195' Processing helix chain 'S' and resid 202 through 204 No H-bonds generated for 'chain 'S' and resid 202 through 204' Processing helix chain 'S' and resid 252 through 258 removed outlier: 3.727A pdb=" N TRP S 258 " --> pdb=" O LEU S 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 336 through 342 Processing helix chain 'S' and resid 345 through 347 No H-bonds generated for 'chain 'S' and resid 345 through 347' Processing helix chain 'S' and resid 352 through 363 Processing helix chain 'S' and resid 381 through 403 Proline residue: S 385 - end of helix removed outlier: 4.080A pdb=" N ALA S 395 " --> pdb=" O SER S 392 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS S 398 " --> pdb=" O ALA S 395 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 21 Processing helix chain 'V' and resid 38 through 54 Processing helix chain 'V' and resid 89 through 101 Processing helix chain 'V' and resid 112 through 122 removed outlier: 3.702A pdb=" N GLY V 117 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 158 through 168 removed outlier: 3.576A pdb=" N LYS V 168 " --> pdb=" O HIS V 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 181 through 184 No H-bonds generated for 'chain 'V' and resid 181 through 184' Processing helix chain 'V' and resid 193 through 195 No H-bonds generated for 'chain 'V' and resid 193 through 195' Processing helix chain 'V' and resid 202 through 204 No H-bonds generated for 'chain 'V' and resid 202 through 204' Processing helix chain 'V' and resid 252 through 258 removed outlier: 3.628A pdb=" N TRP V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 336 through 342 Processing helix chain 'V' and resid 345 through 347 No H-bonds generated for 'chain 'V' and resid 345 through 347' Processing helix chain 'V' and resid 352 through 363 Processing helix chain 'V' and resid 381 through 403 Proline residue: V 385 - end of helix removed outlier: 4.083A pdb=" N ALA V 395 " --> pdb=" O SER V 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N CYS V 398 " --> pdb=" O ALA V 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 21 Processing helix chain 'X' and resid 38 through 54 Processing helix chain 'X' and resid 89 through 101 Processing helix chain 'X' and resid 112 through 122 removed outlier: 3.733A pdb=" N GLY X 117 " --> pdb=" O SER X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 166 Processing helix chain 'X' and resid 181 through 184 No H-bonds generated for 'chain 'X' and resid 181 through 184' Processing helix chain 'X' and resid 193 through 195 No H-bonds generated for 'chain 'X' and resid 193 through 195' Processing helix chain 'X' and resid 202 through 204 No H-bonds generated for 'chain 'X' and resid 202 through 204' Processing helix chain 'X' and resid 252 through 258 removed outlier: 3.643A pdb=" N TRP X 258 " --> pdb=" O LEU X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 336 through 342 Processing helix chain 'X' and resid 345 through 347 No H-bonds generated for 'chain 'X' and resid 345 through 347' Processing helix chain 'X' and resid 352 through 363 Processing helix chain 'X' and resid 381 through 403 Proline residue: X 385 - end of helix removed outlier: 4.086A pdb=" N ALA X 395 " --> pdb=" O SER X 392 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS X 398 " --> pdb=" O ALA X 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 14 through 21 Processing helix chain 'Z' and resid 38 through 53 Processing helix chain 'Z' and resid 89 through 101 Processing helix chain 'Z' and resid 112 through 122 removed outlier: 3.801A pdb=" N GLY Z 117 " --> pdb=" O SER Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 158 through 168 removed outlier: 3.686A pdb=" N LYS Z 168 " --> pdb=" O HIS Z 164 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 184 No H-bonds generated for 'chain 'Z' and resid 181 through 184' Processing helix chain 'Z' and resid 193 through 195 No H-bonds generated for 'chain 'Z' and resid 193 through 195' Processing helix chain 'Z' and resid 202 through 204 No H-bonds generated for 'chain 'Z' and resid 202 through 204' Processing helix chain 'Z' and resid 252 through 258 removed outlier: 3.658A pdb=" N TRP Z 258 " --> pdb=" O LEU Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 336 through 341 Processing helix chain 'Z' and resid 345 through 347 No H-bonds generated for 'chain 'Z' and resid 345 through 347' Processing helix chain 'Z' and resid 352 through 363 Processing helix chain 'Z' and resid 381 through 403 Proline residue: Z 385 - end of helix removed outlier: 4.076A pdb=" N ALA Z 395 " --> pdb=" O SER Z 392 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS Z 398 " --> pdb=" O ALA Z 395 " (cutoff:3.500A) Processing helix chain 'BA' and resid 14 through 21 Processing helix chain 'BA' and resid 38 through 54 Processing helix chain 'BA' and resid 89 through 102 Processing helix chain 'BA' and resid 112 through 122 removed outlier: 3.755A pdb=" N GLYBA 117 " --> pdb=" O SERBA 113 " (cutoff:3.500A) Processing helix chain 'BA' and resid 158 through 168 removed outlier: 3.706A pdb=" N LYSBA 168 " --> pdb=" O HISBA 164 " (cutoff:3.500A) Processing helix chain 'BA' and resid 181 through 184 No H-bonds generated for 'chain 'BA' and resid 181 through 184' Processing helix chain 'BA' and resid 193 through 195 No H-bonds generated for 'chain 'BA' and resid 193 through 195' Processing helix chain 'BA' and resid 202 through 204 No H-bonds generated for 'chain 'BA' and resid 202 through 204' Processing helix chain 'BA' and resid 252 through 258 removed outlier: 3.642A pdb=" N TRPBA 258 " --> pdb=" O LEUBA 254 " (cutoff:3.500A) Processing helix chain 'BA' and resid 336 through 342 Processing helix chain 'BA' and resid 352 through 363 Processing helix chain 'BA' and resid 381 through 403 Proline residue: BA 385 - end of helix removed outlier: 4.093A pdb=" N ALABA 395 " --> pdb=" O SERBA 392 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYSBA 398 " --> pdb=" O ALABA 395 " (cutoff:3.500A) Processing helix chain 'DA' and resid 14 through 21 Processing helix chain 'DA' and resid 38 through 54 Processing helix chain 'DA' and resid 68 through 71 Processing helix chain 'DA' and resid 89 through 101 Processing helix chain 'DA' and resid 112 through 122 removed outlier: 3.741A pdb=" N GLYDA 117 " --> pdb=" O SERDA 113 " (cutoff:3.500A) Processing helix chain 'DA' and resid 158 through 168 removed outlier: 3.670A pdb=" N LYSDA 168 " --> pdb=" O HISDA 164 " (cutoff:3.500A) Processing helix chain 'DA' and resid 181 through 184 No H-bonds generated for 'chain 'DA' and resid 181 through 184' Processing helix chain 'DA' and resid 193 through 195 No H-bonds generated for 'chain 'DA' and resid 193 through 195' Processing helix chain 'DA' and resid 202 through 204 No H-bonds generated for 'chain 'DA' and resid 202 through 204' Processing helix chain 'DA' and resid 252 through 258 removed outlier: 3.670A pdb=" N TRPDA 258 " --> pdb=" O LEUDA 254 " (cutoff:3.500A) Processing helix chain 'DA' and resid 336 through 342 Processing helix chain 'DA' and resid 345 through 347 No H-bonds generated for 'chain 'DA' and resid 345 through 347' Processing helix chain 'DA' and resid 352 through 363 Processing helix chain 'DA' and resid 381 through 403 Proline residue: DA 385 - end of helix removed outlier: 4.126A pdb=" N ALADA 395 " --> pdb=" O SERDA 392 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYSDA 398 " --> pdb=" O ALADA 395 " (cutoff:3.500A) Processing helix chain 'FA' and resid 14 through 21 Processing helix chain 'FA' and resid 38 through 54 Processing helix chain 'FA' and resid 89 through 101 Processing helix chain 'FA' and resid 112 through 122 removed outlier: 3.706A pdb=" N GLYFA 117 " --> pdb=" O SERFA 113 " (cutoff:3.500A) Processing helix chain 'FA' and resid 158 through 168 Processing helix chain 'FA' and resid 181 through 184 No H-bonds generated for 'chain 'FA' and resid 181 through 184' Processing helix chain 'FA' and resid 193 through 195 No H-bonds generated for 'chain 'FA' and resid 193 through 195' Processing helix chain 'FA' and resid 202 through 204 No H-bonds generated for 'chain 'FA' and resid 202 through 204' Processing helix chain 'FA' and resid 252 through 258 removed outlier: 3.621A pdb=" N TRPFA 258 " --> pdb=" O LEUFA 254 " (cutoff:3.500A) Processing helix chain 'FA' and resid 336 through 342 Processing helix chain 'FA' and resid 345 through 347 No H-bonds generated for 'chain 'FA' and resid 345 through 347' Processing helix chain 'FA' and resid 352 through 363 Processing helix chain 'FA' and resid 381 through 403 Proline residue: FA 385 - end of helix removed outlier: 4.211A pdb=" N ALAFA 395 " --> pdb=" O SERFA 392 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYSFA 398 " --> pdb=" O ALAFA 395 " (cutoff:3.500A) Processing helix chain 'HA' and resid 13 through 21 removed outlier: 3.721A pdb=" N LYSHA 16 " --> pdb=" O ALAHA 13 " (cutoff:3.500A) Processing helix chain 'HA' and resid 38 through 54 Processing helix chain 'HA' and resid 89 through 102 Processing helix chain 'HA' and resid 112 through 122 removed outlier: 3.830A pdb=" N GLYHA 117 " --> pdb=" O SERHA 113 " (cutoff:3.500A) Processing helix chain 'HA' and resid 158 through 166 Processing helix chain 'HA' and resid 181 through 184 No H-bonds generated for 'chain 'HA' and resid 181 through 184' Processing helix chain 'HA' and resid 193 through 195 No H-bonds generated for 'chain 'HA' and resid 193 through 195' Processing helix chain 'HA' and resid 202 through 204 No H-bonds generated for 'chain 'HA' and resid 202 through 204' Processing helix chain 'HA' and resid 252 through 258 removed outlier: 3.623A pdb=" N TRPHA 258 " --> pdb=" O LEUHA 254 " (cutoff:3.500A) Processing helix chain 'HA' and resid 336 through 342 Processing helix chain 'HA' and resid 345 through 347 No H-bonds generated for 'chain 'HA' and resid 345 through 347' Processing helix chain 'HA' and resid 352 through 363 Processing helix chain 'HA' and resid 381 through 403 Proline residue: HA 385 - end of helix removed outlier: 4.047A pdb=" N ALAHA 395 " --> pdb=" O SERHA 392 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYSHA 398 " --> pdb=" O ALAHA 395 " (cutoff:3.500A) Processing helix chain 'LA' and resid 14 through 21 Processing helix chain 'LA' and resid 38 through 54 Processing helix chain 'LA' and resid 89 through 101 Processing helix chain 'LA' and resid 112 through 122 removed outlier: 3.624A pdb=" N GLYLA 117 " --> pdb=" O SERLA 113 " (cutoff:3.500A) Processing helix chain 'LA' and resid 158 through 168 removed outlier: 3.725A pdb=" N LYSLA 168 " --> pdb=" O HISLA 164 " (cutoff:3.500A) Processing helix chain 'LA' and resid 181 through 184 No H-bonds generated for 'chain 'LA' and resid 181 through 184' Processing helix chain 'LA' and resid 193 through 195 No H-bonds generated for 'chain 'LA' and resid 193 through 195' Processing helix chain 'LA' and resid 202 through 204 No H-bonds generated for 'chain 'LA' and resid 202 through 204' Processing helix chain 'LA' and resid 252 through 258 removed outlier: 3.654A pdb=" N TRPLA 258 " --> pdb=" O LEULA 254 " (cutoff:3.500A) Processing helix chain 'LA' and resid 336 through 341 Processing helix chain 'LA' and resid 345 through 347 No H-bonds generated for 'chain 'LA' and resid 345 through 347' Processing helix chain 'LA' and resid 352 through 363 Processing helix chain 'LA' and resid 381 through 403 Proline residue: LA 385 - end of helix removed outlier: 4.096A pdb=" N ALALA 395 " --> pdb=" O SERLA 392 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N CYSLA 398 " --> pdb=" O ALALA 395 " (cutoff:3.500A) Processing helix chain 'NA' and resid 14 through 21 Processing helix chain 'NA' and resid 38 through 54 Processing helix chain 'NA' and resid 89 through 102 Processing helix chain 'NA' and resid 112 through 122 removed outlier: 3.662A pdb=" N GLYNA 117 " --> pdb=" O SERNA 113 " (cutoff:3.500A) Processing helix chain 'NA' and resid 158 through 168 removed outlier: 3.553A pdb=" N LYSNA 168 " --> pdb=" O HISNA 164 " (cutoff:3.500A) Processing helix chain 'NA' and resid 181 through 184 No H-bonds generated for 'chain 'NA' and resid 181 through 184' Processing helix chain 'NA' and resid 193 through 195 No H-bonds generated for 'chain 'NA' and resid 193 through 195' Processing helix chain 'NA' and resid 202 through 204 No H-bonds generated for 'chain 'NA' and resid 202 through 204' Processing helix chain 'NA' and resid 252 through 258 removed outlier: 3.635A pdb=" N TRPNA 258 " --> pdb=" O LEUNA 254 " (cutoff:3.500A) Processing helix chain 'NA' and resid 336 through 342 Processing helix chain 'NA' and resid 345 through 347 No H-bonds generated for 'chain 'NA' and resid 345 through 347' Processing helix chain 'NA' and resid 352 through 363 Processing helix chain 'NA' and resid 381 through 403 Proline residue: NA 385 - end of helix removed outlier: 4.133A pdb=" N ALANA 395 " --> pdb=" O SERNA 392 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYSNA 398 " --> pdb=" O ALANA 395 " (cutoff:3.500A) Processing helix chain 'PA' and resid 14 through 21 Processing helix chain 'PA' and resid 38 through 54 Processing helix chain 'PA' and resid 68 through 71 Processing helix chain 'PA' and resid 89 through 101 Processing helix chain 'PA' and resid 112 through 122 removed outlier: 3.700A pdb=" N GLYPA 117 " --> pdb=" O SERPA 113 " (cutoff:3.500A) Processing helix chain 'PA' and resid 158 through 166 Processing helix chain 'PA' and resid 181 through 185 Processing helix chain 'PA' and resid 193 through 195 No H-bonds generated for 'chain 'PA' and resid 193 through 195' Processing helix chain 'PA' and resid 202 through 204 No H-bonds generated for 'chain 'PA' and resid 202 through 204' Processing helix chain 'PA' and resid 252 through 258 removed outlier: 3.614A pdb=" N TRPPA 258 " --> pdb=" O LEUPA 254 " (cutoff:3.500A) Processing helix chain 'PA' and resid 336 through 342 Processing helix chain 'PA' and resid 345 through 347 No H-bonds generated for 'chain 'PA' and resid 345 through 347' Processing helix chain 'PA' and resid 352 through 363 Processing helix chain 'PA' and resid 381 through 403 Proline residue: PA 385 - end of helix removed outlier: 4.126A pdb=" N ALAPA 395 " --> pdb=" O SERPA 392 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYSPA 398 " --> pdb=" O ALAPA 395 " (cutoff:3.500A) Processing helix chain 'RA' and resid 14 through 21 Processing helix chain 'RA' and resid 38 through 54 Processing helix chain 'RA' and resid 89 through 101 Processing helix chain 'RA' and resid 112 through 122 removed outlier: 3.879A pdb=" N GLYRA 117 " --> pdb=" O SERRA 113 " (cutoff:3.500A) Processing helix chain 'RA' and resid 158 through 168 removed outlier: 3.613A pdb=" N LYSRA 168 " --> pdb=" O HISRA 164 " (cutoff:3.500A) Processing helix chain 'RA' and resid 181 through 184 No H-bonds generated for 'chain 'RA' and resid 181 through 184' Processing helix chain 'RA' and resid 193 through 195 No H-bonds generated for 'chain 'RA' and resid 193 through 195' Processing helix chain 'RA' and resid 202 through 204 No H-bonds generated for 'chain 'RA' and resid 202 through 204' Processing helix chain 'RA' and resid 252 through 258 removed outlier: 3.597A pdb=" N TRPRA 258 " --> pdb=" O LEURA 254 " (cutoff:3.500A) Processing helix chain 'RA' and resid 336 through 342 Processing helix chain 'RA' and resid 345 through 347 No H-bonds generated for 'chain 'RA' and resid 345 through 347' Processing helix chain 'RA' and resid 352 through 363 Processing helix chain 'RA' and resid 381 through 403 Proline residue: RA 385 - end of helix removed outlier: 4.114A pdb=" N ALARA 395 " --> pdb=" O SERRA 392 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYSRA 398 " --> pdb=" O ALARA 395 " (cutoff:3.500A) Processing helix chain 'TA' and resid 14 through 21 Processing helix chain 'TA' and resid 38 through 54 Processing helix chain 'TA' and resid 89 through 101 Processing helix chain 'TA' and resid 112 through 122 removed outlier: 3.554A pdb=" N GLYTA 117 " --> pdb=" O SERTA 113 " (cutoff:3.500A) Processing helix chain 'TA' and resid 158 through 168 removed outlier: 3.530A pdb=" N LYSTA 168 " --> pdb=" O HISTA 164 " (cutoff:3.500A) Processing helix chain 'TA' and resid 181 through 184 No H-bonds generated for 'chain 'TA' and resid 181 through 184' Processing helix chain 'TA' and resid 193 through 195 No H-bonds generated for 'chain 'TA' and resid 193 through 195' Processing helix chain 'TA' and resid 202 through 204 No H-bonds generated for 'chain 'TA' and resid 202 through 204' Processing helix chain 'TA' and resid 252 through 258 removed outlier: 3.688A pdb=" N TRPTA 258 " --> pdb=" O LEUTA 254 " (cutoff:3.500A) Processing helix chain 'TA' and resid 336 through 341 Processing helix chain 'TA' and resid 345 through 347 No H-bonds generated for 'chain 'TA' and resid 345 through 347' Processing helix chain 'TA' and resid 352 through 363 Processing helix chain 'TA' and resid 381 through 403 Proline residue: TA 385 - end of helix removed outlier: 4.098A pdb=" N ALATA 395 " --> pdb=" O SERTA 392 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYSTA 398 " --> pdb=" O ALATA 395 " (cutoff:3.500A) Processing helix chain 'VA' and resid 14 through 21 Processing helix chain 'VA' and resid 38 through 54 Processing helix chain 'VA' and resid 89 through 101 Processing helix chain 'VA' and resid 112 through 122 removed outlier: 3.727A pdb=" N GLYVA 117 " --> pdb=" O SERVA 113 " (cutoff:3.500A) Processing helix chain 'VA' and resid 158 through 168 removed outlier: 3.603A pdb=" N LYSVA 168 " --> pdb=" O HISVA 164 " (cutoff:3.500A) Processing helix chain 'VA' and resid 181 through 184 No H-bonds generated for 'chain 'VA' and resid 181 through 184' Processing helix chain 'VA' and resid 193 through 195 No H-bonds generated for 'chain 'VA' and resid 193 through 195' Processing helix chain 'VA' and resid 202 through 204 No H-bonds generated for 'chain 'VA' and resid 202 through 204' Processing helix chain 'VA' and resid 252 through 258 removed outlier: 3.650A pdb=" N TRPVA 258 " --> pdb=" O LEUVA 254 " (cutoff:3.500A) Processing helix chain 'VA' and resid 336 through 342 Processing helix chain 'VA' and resid 345 through 347 No H-bonds generated for 'chain 'VA' and resid 345 through 347' Processing helix chain 'VA' and resid 352 through 363 Processing helix chain 'VA' and resid 381 through 403 Proline residue: VA 385 - end of helix removed outlier: 4.118A pdb=" N ALAVA 395 " --> pdb=" O SERVA 392 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYSVA 398 " --> pdb=" O ALAVA 395 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'JA' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'JA' and resid 78 through 80 removed outlier: 6.863A pdb=" N ILEJA 61 " --> pdb=" O HISJA 79 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VALJA 147 " --> pdb=" O LEUJA 62 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEUJA 172 " --> pdb=" O ALAJA 148 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYRJA 150 " --> pdb=" O LEUJA 172 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYRJA 174 " --> pdb=" O TYRJA 150 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARGJA 289 " --> pdb=" O THRJA 278 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N THRJA 278 " --> pdb=" O ARGJA 289 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THRJA 291 " --> pdb=" O CYSJA 276 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N CYSJA 276 " --> pdb=" O THRJA 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'JA' and resid 189 through 192 Processing sheet with id= D, first strand: chain 'JA' and resid 303 through 308 removed outlier: 3.935A pdb=" N THRJA 437 " --> pdb=" O HISJA 308 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'JA' and resid 324 through 334 Processing sheet with id= F, first strand: chain 'A' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'A' and resid 78 through 80 removed outlier: 6.874A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 189 through 192 Processing sheet with id= I, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.891A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 324 through 334 Processing sheet with id= K, first strand: chain 'C' and resid 4 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.850A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 189 through 192 Processing sheet with id= N, first strand: chain 'C' and resid 303 through 308 removed outlier: 3.934A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 324 through 334 Processing sheet with id= P, first strand: chain 'E' and resid 78 through 80 removed outlier: 6.825A pdb=" N ILE E 61 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 189 through 192 Processing sheet with id= R, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.918A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 324 through 334 Processing sheet with id= T, first strand: chain 'G' and resid 4 through 6 Processing sheet with id= U, first strand: chain 'G' and resid 78 through 80 removed outlier: 6.935A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 189 through 192 Processing sheet with id= W, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.930A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 324 through 334 Processing sheet with id= Y, first strand: chain 'I' and resid 4 through 6 Processing sheet with id= Z, first strand: chain 'I' and resid 78 through 80 removed outlier: 6.857A pdb=" N ILE I 61 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 189 through 192 Processing sheet with id= AB, first strand: chain 'I' and resid 303 through 308 removed outlier: 3.880A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 324 through 334 Processing sheet with id= AD, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= AE, first strand: chain 'K' and resid 78 through 80 removed outlier: 6.962A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL K 147 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 189 through 192 Processing sheet with id= AG, first strand: chain 'K' and resid 303 through 308 removed outlier: 3.932A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 324 through 334 Processing sheet with id= AI, first strand: chain 'M' and resid 4 through 6 Processing sheet with id= AJ, first strand: chain 'M' and resid 78 through 80 removed outlier: 6.880A pdb=" N ILE M 61 " --> pdb=" O HIS M 79 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL M 147 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU M 172 " --> pdb=" O ALA M 148 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N TYR M 150 " --> pdb=" O LEU M 172 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR M 174 " --> pdb=" O TYR M 150 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG M 289 " --> pdb=" O THR M 278 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR M 278 " --> pdb=" O ARG M 289 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR M 291 " --> pdb=" O CYS M 276 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N CYS M 276 " --> pdb=" O THR M 291 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 189 through 192 Processing sheet with id= AL, first strand: chain 'M' and resid 303 through 308 removed outlier: 3.900A pdb=" N THR M 437 " --> pdb=" O HIS M 308 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 324 through 334 Processing sheet with id= AN, first strand: chain 'O' and resid 4 through 6 Processing sheet with id= AO, first strand: chain 'O' and resid 78 through 80 removed outlier: 6.815A pdb=" N ILE O 61 " --> pdb=" O HIS O 79 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL O 147 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU O 172 " --> pdb=" O ALA O 148 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N TYR O 150 " --> pdb=" O LEU O 172 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR O 174 " --> pdb=" O TYR O 150 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG O 289 " --> pdb=" O THR O 278 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N THR O 278 " --> pdb=" O ARG O 289 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR O 291 " --> pdb=" O CYS O 276 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N CYS O 276 " --> pdb=" O THR O 291 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'O' and resid 430 through 433 removed outlier: 6.743A pdb=" N ALA O 189 " --> pdb=" O CYS O 331 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N TYR O 333 " --> pdb=" O ALA O 189 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA O 191 " --> pdb=" O TYR O 333 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'O' and resid 303 through 308 removed outlier: 3.861A pdb=" N THR O 437 " --> pdb=" O HIS O 308 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id= AS, first strand: chain 'Q' and resid 78 through 80 removed outlier: 6.852A pdb=" N ILE Q 61 " --> pdb=" O HIS Q 79 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL Q 147 " --> pdb=" O LEU Q 62 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU Q 172 " --> pdb=" O ALA Q 148 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR Q 150 " --> pdb=" O LEU Q 172 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR Q 174 " --> pdb=" O TYR Q 150 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG Q 289 " --> pdb=" O THR Q 278 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N THR Q 278 " --> pdb=" O ARG Q 289 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR Q 291 " --> pdb=" O CYS Q 276 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N CYS Q 276 " --> pdb=" O THR Q 291 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 189 through 192 Processing sheet with id= AU, first strand: chain 'Q' and resid 303 through 308 removed outlier: 3.916A pdb=" N THR Q 437 " --> pdb=" O HIS Q 308 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 324 through 334 Processing sheet with id= AW, first strand: chain 'S' and resid 4 through 6 Processing sheet with id= AX, first strand: chain 'S' and resid 78 through 80 removed outlier: 6.862A pdb=" N ILE S 61 " --> pdb=" O HIS S 79 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL S 147 " --> pdb=" O LEU S 62 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU S 172 " --> pdb=" O ALA S 148 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR S 150 " --> pdb=" O LEU S 172 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR S 174 " --> pdb=" O TYR S 150 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG S 289 " --> pdb=" O THR S 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N THR S 278 " --> pdb=" O ARG S 289 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR S 291 " --> pdb=" O CYS S 276 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N CYS S 276 " --> pdb=" O THR S 291 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'S' and resid 189 through 192 Processing sheet with id= AZ, first strand: chain 'S' and resid 303 through 308 removed outlier: 3.907A pdb=" N THR S 437 " --> pdb=" O HIS S 308 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'S' and resid 324 through 334 Processing sheet with id= BB, first strand: chain 'V' and resid 4 through 6 Processing sheet with id= BC, first strand: chain 'V' and resid 78 through 80 removed outlier: 6.894A pdb=" N ILE V 61 " --> pdb=" O HIS V 79 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL V 147 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU V 172 " --> pdb=" O ALA V 148 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N TYR V 150 " --> pdb=" O LEU V 172 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR V 174 " --> pdb=" O TYR V 150 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG V 289 " --> pdb=" O THR V 278 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR V 278 " --> pdb=" O ARG V 289 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR V 291 " --> pdb=" O CYS V 276 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N CYS V 276 " --> pdb=" O THR V 291 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'V' and resid 189 through 192 Processing sheet with id= BE, first strand: chain 'V' and resid 303 through 308 removed outlier: 3.872A pdb=" N THR V 437 " --> pdb=" O HIS V 308 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'V' and resid 324 through 334 Processing sheet with id= BG, first strand: chain 'X' and resid 4 through 6 Processing sheet with id= BH, first strand: chain 'X' and resid 78 through 80 removed outlier: 6.873A pdb=" N ILE X 61 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL X 147 " --> pdb=" O LEU X 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU X 172 " --> pdb=" O ALA X 148 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TYR X 150 " --> pdb=" O LEU X 172 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR X 174 " --> pdb=" O TYR X 150 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG X 289 " --> pdb=" O THR X 278 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR X 278 " --> pdb=" O ARG X 289 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR X 291 " --> pdb=" O CYS X 276 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N CYS X 276 " --> pdb=" O THR X 291 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'X' and resid 189 through 192 Processing sheet with id= BJ, first strand: chain 'X' and resid 303 through 308 removed outlier: 3.911A pdb=" N THR X 437 " --> pdb=" O HIS X 308 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'X' and resid 324 through 334 Processing sheet with id= BL, first strand: chain 'Z' and resid 4 through 6 Processing sheet with id= BM, first strand: chain 'Z' and resid 78 through 80 removed outlier: 6.929A pdb=" N ILE Z 61 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL Z 147 " --> pdb=" O LEU Z 62 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE Z 64 " --> pdb=" O VAL Z 147 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE Z 149 " --> pdb=" O ILE Z 64 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU Z 172 " --> pdb=" O ALA Z 148 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR Z 150 " --> pdb=" O LEU Z 172 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR Z 174 " --> pdb=" O TYR Z 150 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG Z 289 " --> pdb=" O THR Z 278 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR Z 278 " --> pdb=" O ARG Z 289 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR Z 291 " --> pdb=" O CYS Z 276 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N CYS Z 276 " --> pdb=" O THR Z 291 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'Z' and resid 189 through 192 Processing sheet with id= BO, first strand: chain 'Z' and resid 303 through 308 removed outlier: 3.894A pdb=" N THR Z 437 " --> pdb=" O HIS Z 308 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Z' and resid 324 through 334 Processing sheet with id= BQ, first strand: chain 'BA' and resid 4 through 6 Processing sheet with id= BR, first strand: chain 'BA' and resid 78 through 80 removed outlier: 6.852A pdb=" N ILEBA 61 " --> pdb=" O HISBA 79 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VALBA 147 " --> pdb=" O LEUBA 62 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEUBA 172 " --> pdb=" O ALABA 148 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYRBA 150 " --> pdb=" O LEUBA 172 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYRBA 174 " --> pdb=" O TYRBA 150 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARGBA 289 " --> pdb=" O THRBA 278 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THRBA 278 " --> pdb=" O ARGBA 289 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THRBA 291 " --> pdb=" O CYSBA 276 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYSBA 276 " --> pdb=" O THRBA 291 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'BA' and resid 189 through 192 Processing sheet with id= BT, first strand: chain 'BA' and resid 303 through 308 removed outlier: 3.835A pdb=" N THRBA 437 " --> pdb=" O HISBA 308 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'BA' and resid 324 through 334 Processing sheet with id= BV, first strand: chain 'DA' and resid 4 through 6 Processing sheet with id= BW, first strand: chain 'DA' and resid 78 through 80 removed outlier: 6.857A pdb=" N ILEDA 61 " --> pdb=" O HISDA 79 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VALDA 147 " --> pdb=" O LEUDA 62 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEUDA 172 " --> pdb=" O ALADA 148 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYRDA 150 " --> pdb=" O LEUDA 172 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYRDA 174 " --> pdb=" O TYRDA 150 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARGDA 289 " --> pdb=" O THRDA 278 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THRDA 278 " --> pdb=" O ARGDA 289 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N THRDA 291 " --> pdb=" O CYSDA 276 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYSDA 276 " --> pdb=" O THRDA 291 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'DA' and resid 189 through 192 Processing sheet with id= BY, first strand: chain 'DA' and resid 303 through 308 removed outlier: 3.914A pdb=" N THRDA 437 " --> pdb=" O HISDA 308 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'DA' and resid 324 through 334 Processing sheet with id= CA, first strand: chain 'FA' and resid 4 through 6 Processing sheet with id= CB, first strand: chain 'FA' and resid 78 through 80 removed outlier: 6.812A pdb=" N ILEFA 61 " --> pdb=" O HISFA 79 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VALFA 147 " --> pdb=" O LEUFA 62 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEUFA 172 " --> pdb=" O ALAFA 148 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYRFA 150 " --> pdb=" O LEUFA 172 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYRFA 174 " --> pdb=" O TYRFA 150 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARGFA 289 " --> pdb=" O THRFA 278 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THRFA 278 " --> pdb=" O ARGFA 289 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THRFA 291 " --> pdb=" O CYSFA 276 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N CYSFA 276 " --> pdb=" O THRFA 291 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'FA' and resid 189 through 192 Processing sheet with id= CD, first strand: chain 'FA' and resid 303 through 308 removed outlier: 3.907A pdb=" N THRFA 437 " --> pdb=" O HISFA 308 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'FA' and resid 324 through 334 Processing sheet with id= CF, first strand: chain 'HA' and resid 4 through 6 Processing sheet with id= CG, first strand: chain 'HA' and resid 78 through 80 removed outlier: 6.846A pdb=" N ILEHA 61 " --> pdb=" O HISHA 79 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VALHA 147 " --> pdb=" O LEUHA 62 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEUHA 172 " --> pdb=" O ALAHA 148 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYRHA 150 " --> pdb=" O LEUHA 172 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYRHA 174 " --> pdb=" O TYRHA 150 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARGHA 289 " --> pdb=" O THRHA 278 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THRHA 278 " --> pdb=" O ARGHA 289 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THRHA 291 " --> pdb=" O CYSHA 276 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N CYSHA 276 " --> pdb=" O THRHA 291 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'HA' and resid 189 through 192 Processing sheet with id= CI, first strand: chain 'HA' and resid 303 through 308 removed outlier: 3.914A pdb=" N THRHA 437 " --> pdb=" O HISHA 308 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'HA' and resid 324 through 334 Processing sheet with id= CK, first strand: chain 'LA' and resid 4 through 6 Processing sheet with id= CL, first strand: chain 'LA' and resid 78 through 80 removed outlier: 6.793A pdb=" N ILELA 61 " --> pdb=" O HISLA 79 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VALLA 147 " --> pdb=" O LEULA 62 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEULA 172 " --> pdb=" O ALALA 148 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N TYRLA 150 " --> pdb=" O LEULA 172 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYRLA 174 " --> pdb=" O TYRLA 150 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARGLA 289 " --> pdb=" O THRLA 278 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N THRLA 278 " --> pdb=" O ARGLA 289 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THRLA 291 " --> pdb=" O CYSLA 276 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N CYSLA 276 " --> pdb=" O THRLA 291 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'LA' and resid 189 through 192 Processing sheet with id= CN, first strand: chain 'LA' and resid 303 through 308 removed outlier: 3.935A pdb=" N THRLA 437 " --> pdb=" O HISLA 308 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'LA' and resid 324 through 334 Processing sheet with id= CP, first strand: chain 'NA' and resid 4 through 6 Processing sheet with id= CQ, first strand: chain 'NA' and resid 78 through 80 removed outlier: 6.910A pdb=" N ILENA 61 " --> pdb=" O HISNA 79 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VALNA 147 " --> pdb=" O LEUNA 62 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEUNA 172 " --> pdb=" O ALANA 148 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N TYRNA 150 " --> pdb=" O LEUNA 172 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYRNA 174 " --> pdb=" O TYRNA 150 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARGNA 289 " --> pdb=" O THRNA 278 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THRNA 278 " --> pdb=" O ARGNA 289 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THRNA 291 " --> pdb=" O CYSNA 276 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N CYSNA 276 " --> pdb=" O THRNA 291 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'NA' and resid 189 through 192 removed outlier: 3.516A pdb=" N THRNA 246 " --> pdb=" O VALNA 243 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'NA' and resid 303 through 308 removed outlier: 3.870A pdb=" N THRNA 437 " --> pdb=" O HISNA 308 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'NA' and resid 324 through 334 Processing sheet with id= CU, first strand: chain 'PA' and resid 4 through 6 Processing sheet with id= CV, first strand: chain 'PA' and resid 78 through 80 removed outlier: 6.763A pdb=" N ILEPA 61 " --> pdb=" O HISPA 79 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VALPA 147 " --> pdb=" O LEUPA 62 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEUPA 172 " --> pdb=" O ALAPA 148 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYRPA 150 " --> pdb=" O LEUPA 172 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYRPA 174 " --> pdb=" O TYRPA 150 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARGPA 289 " --> pdb=" O THRPA 278 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THRPA 278 " --> pdb=" O ARGPA 289 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THRPA 291 " --> pdb=" O CYSPA 276 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N CYSPA 276 " --> pdb=" O THRPA 291 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'PA' and resid 189 through 192 Processing sheet with id= CX, first strand: chain 'PA' and resid 303 through 308 removed outlier: 3.861A pdb=" N THRPA 437 " --> pdb=" O HISPA 308 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'PA' and resid 324 through 334 Processing sheet with id= CZ, first strand: chain 'RA' and resid 4 through 6 Processing sheet with id= DA, first strand: chain 'RA' and resid 78 through 80 removed outlier: 6.781A pdb=" N ILERA 61 " --> pdb=" O HISRA 79 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VALRA 147 " --> pdb=" O LEURA 62 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEURA 172 " --> pdb=" O ALARA 148 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N TYRRA 150 " --> pdb=" O LEURA 172 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYRRA 174 " --> pdb=" O TYRRA 150 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARGRA 289 " --> pdb=" O THRRA 278 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THRRA 278 " --> pdb=" O ARGRA 289 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THRRA 291 " --> pdb=" O CYSRA 276 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N CYSRA 276 " --> pdb=" O THRRA 291 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'RA' and resid 189 through 192 Processing sheet with id= DC, first strand: chain 'RA' and resid 303 through 308 removed outlier: 3.888A pdb=" N THRRA 437 " --> pdb=" O HISRA 308 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'RA' and resid 324 through 334 Processing sheet with id= DE, first strand: chain 'TA' and resid 4 through 6 Processing sheet with id= DF, first strand: chain 'TA' and resid 78 through 80 removed outlier: 6.919A pdb=" N ILETA 61 " --> pdb=" O HISTA 79 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VALTA 147 " --> pdb=" O LEUTA 62 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEUTA 172 " --> pdb=" O ALATA 148 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N TYRTA 150 " --> pdb=" O LEUTA 172 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYRTA 174 " --> pdb=" O TYRTA 150 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARGTA 289 " --> pdb=" O THRTA 278 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THRTA 278 " --> pdb=" O ARGTA 289 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N THRTA 291 " --> pdb=" O CYSTA 276 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N CYSTA 276 " --> pdb=" O THRTA 291 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'TA' and resid 189 through 192 Processing sheet with id= DH, first strand: chain 'TA' and resid 303 through 308 removed outlier: 3.919A pdb=" N THRTA 437 " --> pdb=" O HISTA 308 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'TA' and resid 324 through 334 Processing sheet with id= DJ, first strand: chain 'VA' and resid 4 through 6 Processing sheet with id= DK, first strand: chain 'VA' and resid 78 through 80 removed outlier: 6.869A pdb=" N ILEVA 61 " --> pdb=" O HISVA 79 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VALVA 147 " --> pdb=" O LEUVA 62 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEUVA 172 " --> pdb=" O ALAVA 148 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYRVA 150 " --> pdb=" O LEUVA 172 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYRVA 174 " --> pdb=" O TYRVA 150 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARGVA 289 " --> pdb=" O THRVA 278 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THRVA 278 " --> pdb=" O ARGVA 289 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THRVA 291 " --> pdb=" O CYSVA 276 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N CYSVA 276 " --> pdb=" O THRVA 291 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'VA' and resid 189 through 192 Processing sheet with id= DM, first strand: chain 'VA' and resid 303 through 308 removed outlier: 3.891A pdb=" N THRVA 437 " --> pdb=" O HISVA 308 " (cutoff:3.500A) Processing sheet with id= DN, first strand: chain 'VA' and resid 324 through 334 2787 hydrogen bonds defined for protein. 6826 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: 40.62 Time building geometry restraints manager: 35.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.19: 2 1.19 - 1.48: 47951 1.48 - 1.78: 35834 1.78 - 2.07: 1076 2.07 - 2.37: 1 Bond restraints: 84864 Sorted by residual: bond pdb=" CG PRO S 57 " pdb=" CD PRO S 57 " ideal model delta sigma weight residual 1.503 0.891 0.612 3.40e-02 8.65e+02 3.24e+02 bond pdb=" CB PRO S 57 " pdb=" CG PRO S 57 " ideal model delta sigma weight residual 1.492 2.370 -0.878 5.00e-02 4.00e+02 3.08e+02 bond pdb=" C ASP S 56 " pdb=" O ASP S 56 " ideal model delta sigma weight residual 1.239 1.122 0.118 1.23e-02 6.61e+03 9.14e+01 bond pdb=" CA PRO S 57 " pdb=" C PRO S 57 " ideal model delta sigma weight residual 1.516 1.408 0.109 1.72e-02 3.38e+03 3.99e+01 bond pdb=" N PRO S 57 " pdb=" CD PRO S 57 " ideal model delta sigma weight residual 1.473 1.408 0.065 1.40e-02 5.10e+03 2.18e+01 ... (remaining 84859 not shown) Histogram of bond angle deviations from ideal: 0.04 - 31.18: 1 31.18 - 62.31: 0 62.31 - 93.45: 4 93.45 - 124.59: 113880 124.59 - 155.73: 1459 Bond angle restraints: 115344 Sorted by residual: angle pdb=" CB PRO S 57 " pdb=" CG PRO S 57 " pdb=" CD PRO S 57 " ideal model delta sigma weight residual 106.10 0.04 106.06 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO S 57 " pdb=" N PRO S 57 " pdb=" CD PRO S 57 " ideal model delta sigma weight residual 112.00 83.40 28.60 1.40e+00 5.10e-01 4.17e+02 angle pdb=" N PRO S 57 " pdb=" CA PRO S 57 " pdb=" CB PRO S 57 " ideal model delta sigma weight residual 103.30 82.74 20.56 1.12e+00 7.97e-01 3.37e+02 angle pdb=" CA PRO S 57 " pdb=" CB PRO S 57 " pdb=" CG PRO S 57 " ideal model delta sigma weight residual 104.50 77.89 26.61 1.90e+00 2.77e-01 1.96e+02 angle pdb=" CA ASP S 56 " pdb=" C ASP S 56 " pdb=" N PRO S 57 " ideal model delta sigma weight residual 118.83 128.58 -9.75 8.70e-01 1.32e+00 1.26e+02 ... (remaining 115339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.29: 46224 20.29 - 40.57: 4732 40.57 - 60.86: 1162 60.86 - 81.15: 88 81.15 - 101.44: 42 Dihedral angle restraints: 52248 sinusoidal: 20976 harmonic: 31272 Sorted by residual: dihedral pdb=" N PRO S 57 " pdb=" C PRO S 57 " pdb=" CA PRO S 57 " pdb=" CB PRO S 57 " ideal model delta harmonic sigma weight residual 115.10 91.00 24.10 0 2.50e+00 1.60e-01 9.29e+01 dihedral pdb=" C PRO S 57 " pdb=" N PRO S 57 " pdb=" CA PRO S 57 " pdb=" CB PRO S 57 " ideal model delta harmonic sigma weight residual -120.70 -105.66 -15.04 0 2.50e+00 1.60e-01 3.62e+01 dihedral pdb=" CA PRO S 57 " pdb=" CB PRO S 57 " pdb=" CG PRO S 57 " pdb=" CD PRO S 57 " ideal model delta sinusoidal sigma weight residual 38.00 139.44 -101.44 1 2.00e+01 2.50e-03 2.88e+01 ... (remaining 52245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 8958 0.039 - 0.078: 2670 0.078 - 0.117: 1189 0.117 - 0.156: 163 0.156 - 0.195: 28 Chirality restraints: 13008 Sorted by residual: chirality pdb=" C2' SAM K1002 " pdb=" C1' SAM K1002 " pdb=" C3' SAM K1002 " pdb=" O2' SAM K1002 " both_signs ideal model delta sigma weight residual False -2.76 -2.56 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" C2' SAM Q1002 " pdb=" C1' SAM Q1002 " pdb=" C3' SAM Q1002 " pdb=" O2' SAM Q1002 " both_signs ideal model delta sigma weight residual False -2.76 -2.56 -0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" C2' SAMNA1002 " pdb=" C1' SAMNA1002 " pdb=" C3' SAMNA1002 " pdb=" O2' SAMNA1002 " both_signs ideal model delta sigma weight residual False -2.76 -2.56 -0.19 2.00e-01 2.50e+01 9.27e-01 ... (remaining 13005 not shown) Planarity restraints: 14808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP S 56 " -0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ASP S 56 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP S 56 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO S 57 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 56 " 0.057 5.00e-02 4.00e+02 7.32e-02 8.56e+00 pdb=" N PRO S 57 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO S 57 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO S 57 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARGDA 275 " 0.086 9.50e-02 1.11e+02 4.39e-02 6.39e+00 pdb=" NE ARGDA 275 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARGDA 275 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARGDA 275 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARGDA 275 " -0.010 2.00e-02 2.50e+03 ... (remaining 14805 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 1297 2.41 - 3.04: 53379 3.04 - 3.66: 147500 3.66 - 4.28: 227898 4.28 - 4.90: 365141 Nonbonded interactions: 795215 Sorted by model distance: nonbonded pdb=" NH1 ARG X 20 " pdb=" O HOH X1101 " model vdw 1.792 2.520 nonbonded pdb=" OE1 GLU K 91 " pdb=" NE ARG M 275 " model vdw 1.956 2.520 nonbonded pdb=" OD1 ASPTA 152 " pdb=" OH TYRTA 285 " model vdw 1.973 2.440 nonbonded pdb=" OD1 ASPFA 152 " pdb=" OH TYRFA 285 " model vdw 2.036 2.440 nonbonded pdb=" OE2 GLU K 129 " pdb="ZN ZN K1001 " model vdw 2.043 2.230 ... (remaining 795210 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 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'BA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'C' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'DA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'E' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'FA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'G' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'HA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'I' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'JA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'K' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'LA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'M' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'NA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'O' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'PA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'Q' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'RA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'S' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'TA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'V' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'VA' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 2 \ 33 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resi \ d 1001 through 1002)) selection = (chain 'X' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) selection = (chain 'Z' and (resid 3 through 18 or resid 20 through 81 or resid 83 through 23 \ 3 or resid 235 through 249 or resid 251 through 309 or resid 311 through 363 or \ resid 377 through 398 or resid 401 through 417 or resid 419 through 447 or resid \ 1001 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.09 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.110 Extract box with map and model: 9.660 Check model and map are aligned: 0.980 Set scattering table: 0.610 Process input model: 251.340 Find NCS groups from input model: 5.440 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 280.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.005 0.878 84864 Z= 0.399 Angle : 0.727 106.063 115344 Z= 0.346 Chirality : 0.045 0.195 13008 Planarity : 0.004 0.073 14808 Dihedral : 16.817 101.437 32088 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.25 % Allowed : 19.93 % Favored : 78.82 % Cbeta Deviations : 0.01 % 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: -1.25 (0.08), residues: 10752 helix: 0.04 (0.09), residues: 3288 sheet: -0.61 (0.11), residues: 2112 loop : -1.45 (0.08), residues: 5352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 258 HIS 0.010 0.001 HISJA 79 PHE 0.011 0.002 PHE C 183 TYR 0.016 0.001 TYR S 382 ARG 0.041 0.001 ARGDA 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 973 time to evaluate : 7.259 Fit side-chains REVERT: O 49 LYS cc_start: 0.6539 (mmmm) cc_final: 0.6083 (mmpt) REVERT: O 402 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6898 (mtp) REVERT: Z 342 MET cc_start: 0.8078 (mmm) cc_final: 0.7609 (mmm) REVERT: PA 70 ARG cc_start: 0.5464 (OUTLIER) cc_final: 0.5045 (mtp85) REVERT: RA 396 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7977 (tmtt) outliers start: 61 outliers final: 45 residues processed: 1012 average time/residue: 1.3918 time to fit residues: 2002.4623 Evaluate side-chains 1007 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 959 time to evaluate : 7.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain JA residue 123 MET Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 384 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain Q residue 53 GLN Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain Z residue 72 MET Chi-restraints excluded: chain Z residue 350 VAL Chi-restraints excluded: chain BA residue 112 ILE Chi-restraints excluded: chain BA residue 123 MET Chi-restraints excluded: chain BA residue 384 ILE Chi-restraints excluded: chain DA residue 44 SER Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 396 LYS Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain HA residue 112 ILE Chi-restraints excluded: chain HA residue 384 ILE Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 123 MET Chi-restraints excluded: chain PA residue 70 ARG Chi-restraints excluded: chain PA residue 112 ILE Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 123 MET Chi-restraints excluded: chain RA residue 318 THR Chi-restraints excluded: chain RA residue 396 LYS Chi-restraints excluded: chain VA residue 112 ILE Chi-restraints excluded: chain VA residue 123 MET Chi-restraints excluded: chain VA residue 384 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 871 optimal weight: 30.0000 chunk 782 optimal weight: 8.9990 chunk 434 optimal weight: 6.9990 chunk 267 optimal weight: 0.8980 chunk 527 optimal weight: 8.9990 chunk 417 optimal weight: 10.0000 chunk 808 optimal weight: 0.0070 chunk 313 optimal weight: 5.9990 chunk 491 optimal weight: 10.0000 chunk 602 optimal weight: 30.0000 chunk 937 optimal weight: 1.9990 overall best weight: 3.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN C 53 GLN E 429 HIS G 389 GLN I 143 GLN I 186 ASN I 389 GLN M 186 ASN M 389 GLN O 53 GLN O 389 GLN PA 186 ASN PA 389 GLN PA 429 HIS RA 53 GLN VA 389 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 84864 Z= 0.234 Angle : 0.577 17.099 115344 Z= 0.294 Chirality : 0.045 0.158 13008 Planarity : 0.005 0.047 14808 Dihedral : 7.989 60.452 12609 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.04 % Allowed : 18.09 % Favored : 78.88 % 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: -1.18 (0.08), residues: 10752 helix: 0.24 (0.09), residues: 3288 sheet: -0.54 (0.11), residues: 2112 loop : -1.54 (0.08), residues: 5352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 258 HIS 0.006 0.001 HISFA 164 PHE 0.019 0.002 PHEPA 183 TYR 0.016 0.002 TYR M 382 ARG 0.007 0.001 ARGJA 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 944 time to evaluate : 7.622 Fit side-chains revert: symmetry clash REVERT: A 49 LYS cc_start: 0.6471 (mmmm) cc_final: 0.6183 (mmtm) REVERT: A 389 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7104 (tp-100) REVERT: A 402 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7364 (mtp) REVERT: C 389 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7355 (tp-100) REVERT: E 184 MET cc_start: 0.8326 (mmm) cc_final: 0.7902 (tpp) REVERT: G 36 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6374 (p0) REVERT: G 357 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7531 (mttm) REVERT: G 389 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7570 (tp40) REVERT: I 345 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7105 (tp) REVERT: I 402 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6839 (mtp) REVERT: K 314 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7021 (tpt) REVERT: M 389 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7286 (tp-100) REVERT: O 292 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5218 (tpp) REVERT: O 389 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7434 (tp-100) REVERT: O 396 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7854 (tmtt) REVERT: Q 292 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.5867 (mpp) REVERT: S 389 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7072 (tp-100) REVERT: V 292 MET cc_start: 0.6083 (OUTLIER) cc_final: 0.5064 (tpp) REVERT: DA 275 ARG cc_start: 0.5877 (OUTLIER) cc_final: 0.5563 (mtp180) REVERT: FA 389 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7085 (tp-100) REVERT: HA 389 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7235 (tp-100) REVERT: HA 402 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6791 (mtt) REVERT: LA 184 MET cc_start: 0.8146 (mmm) cc_final: 0.7573 (tpp) REVERT: LA 389 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7282 (tp-100) REVERT: NA 389 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7225 (tp-100) REVERT: PA 292 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5285 (tpp) REVERT: RA 184 MET cc_start: 0.8140 (mmm) cc_final: 0.7617 (tpp) REVERT: RA 389 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6930 (mm-40) REVERT: TA 389 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7142 (tp-100) outliers start: 221 outliers final: 74 residues processed: 1064 average time/residue: 1.4079 time to fit residues: 2129.0183 Evaluate side-chains 1017 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 918 time to evaluate : 7.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 314 MET Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 389 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 217 LEU Chi-restraints excluded: chain O residue 292 MET Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 389 GLN Chi-restraints excluded: chain O residue 396 LYS Chi-restraints excluded: chain O residue 424 LYS Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 292 MET Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain S residue 63 ASP Chi-restraints excluded: chain S residue 134 CYS Chi-restraints excluded: chain S residue 313 LEU Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain S residue 389 GLN Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 72 MET Chi-restraints excluded: chain V residue 292 MET Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain BA residue 63 ASP Chi-restraints excluded: chain BA residue 112 ILE Chi-restraints excluded: chain BA residue 345 ILE Chi-restraints excluded: chain BA residue 350 VAL Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 112 ILE Chi-restraints excluded: chain DA residue 275 ARG Chi-restraints excluded: chain DA residue 386 VAL Chi-restraints excluded: chain FA residue 53 GLN Chi-restraints excluded: chain FA residue 63 ASP Chi-restraints excluded: chain FA residue 217 LEU Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain FA residue 389 GLN Chi-restraints excluded: chain HA residue 53 GLN Chi-restraints excluded: chain HA residue 63 ASP Chi-restraints excluded: chain HA residue 112 ILE Chi-restraints excluded: chain HA residue 345 ILE Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain HA residue 389 GLN Chi-restraints excluded: chain HA residue 402 MET Chi-restraints excluded: chain LA residue 53 GLN Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 384 ILE Chi-restraints excluded: chain LA residue 389 GLN Chi-restraints excluded: chain NA residue 53 GLN Chi-restraints excluded: chain NA residue 63 ASP Chi-restraints excluded: chain NA residue 134 CYS Chi-restraints excluded: chain NA residue 389 GLN Chi-restraints excluded: chain PA residue 63 ASP Chi-restraints excluded: chain PA residue 292 MET Chi-restraints excluded: chain PA residue 345 ILE Chi-restraints excluded: chain PA residue 350 VAL Chi-restraints excluded: chain PA residue 384 ILE Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 389 GLN Chi-restraints excluded: chain TA residue 313 LEU Chi-restraints excluded: chain TA residue 389 GLN Chi-restraints excluded: chain TA residue 402 MET Chi-restraints excluded: chain VA residue 63 ASP Chi-restraints excluded: chain VA residue 345 ILE Chi-restraints excluded: chain VA residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 520 optimal weight: 5.9990 chunk 290 optimal weight: 0.9990 chunk 779 optimal weight: 5.9990 chunk 638 optimal weight: 0.7980 chunk 258 optimal weight: 20.0000 chunk 938 optimal weight: 5.9990 chunk 1014 optimal weight: 9.9990 chunk 836 optimal weight: 9.9990 chunk 931 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 753 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: JA 429 HIS C 53 GLN C 186 ASN C 444 GLN G 389 GLN G 429 HIS G 444 GLN I 186 ASN I 444 GLN M 186 ASN O 53 GLN O 444 GLN V 186 ASN V 444 GLN Z 429 HIS Z 444 GLN FA 444 GLN HA 426 GLN PA 186 ASN PA 389 GLN VA 444 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 84864 Z= 0.250 Angle : 0.586 8.253 115344 Z= 0.298 Chirality : 0.045 0.150 13008 Planarity : 0.005 0.052 14808 Dihedral : 7.647 59.813 12540 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.49 % Allowed : 17.83 % Favored : 78.67 % 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: -1.23 (0.08), residues: 10752 helix: 0.24 (0.09), residues: 3288 sheet: -0.55 (0.11), residues: 2112 loop : -1.61 (0.08), residues: 5352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.008 0.001 HISFA 164 PHE 0.019 0.002 PHE V 183 TYR 0.016 0.002 TYR M 382 ARG 0.006 0.001 ARGJA 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 907 time to evaluate : 7.304 Fit side-chains revert: symmetry clash REVERT: JA 240 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7562 (mm) REVERT: A 49 LYS cc_start: 0.6471 (mmmm) cc_final: 0.6171 (mmtm) REVERT: A 389 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7111 (tp-100) REVERT: C 389 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7367 (tp-100) REVERT: E 184 MET cc_start: 0.8254 (mmm) cc_final: 0.7845 (tpp) REVERT: E 292 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.5570 (mmt) REVERT: E 389 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7461 (tp-100) REVERT: G 36 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6341 (p0) REVERT: G 49 LYS cc_start: 0.6516 (mmmm) cc_final: 0.6252 (mmtm) REVERT: G 357 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7549 (mttm) REVERT: I 345 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7168 (tp) REVERT: I 402 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6853 (mtp) REVERT: K 240 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7521 (mm) REVERT: K 314 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7015 (tpt) REVERT: K 441 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7100 (mt0) REVERT: O 292 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5242 (tpp) REVERT: O 345 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7120 (tp) REVERT: O 396 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7842 (tmtt) REVERT: Q 85 ARG cc_start: 0.4019 (mtt-85) cc_final: 0.3759 (ttp-170) REVERT: Q 389 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6981 (mm-40) REVERT: S 389 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7098 (tp-100) REVERT: V 292 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.5130 (tpp) REVERT: V 402 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6827 (mtt) REVERT: X 184 MET cc_start: 0.8130 (mmm) cc_final: 0.7547 (tpp) REVERT: Z 73 MET cc_start: 0.4563 (mpm) cc_final: 0.2961 (mtm) REVERT: DA 184 MET cc_start: 0.8272 (mmm) cc_final: 0.7862 (tpp) REVERT: DA 240 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7591 (mm) REVERT: FA 389 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7091 (tp-100) REVERT: HA 389 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7243 (tp-100) REVERT: HA 402 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6807 (mtt) REVERT: LA 184 MET cc_start: 0.8213 (mmm) cc_final: 0.7652 (tpp) REVERT: LA 240 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7550 (mm) REVERT: LA 389 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7443 (tp-100) REVERT: NA 389 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7224 (tp-100) REVERT: PA 84 MET cc_start: 0.3795 (OUTLIER) cc_final: 0.3340 (mmt) REVERT: PA 345 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7134 (tp) REVERT: RA 184 MET cc_start: 0.8248 (mmm) cc_final: 0.7750 (tpp) REVERT: RA 389 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6958 (mm-40) REVERT: TA 389 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7167 (tp-100) REVERT: VA 345 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7131 (tp) REVERT: VA 402 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6800 (mtt) outliers start: 261 outliers final: 111 residues processed: 1067 average time/residue: 1.4362 time to fit residues: 2162.3822 Evaluate side-chains 1042 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 899 time to evaluate : 7.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain JA residue 240 LEU Chi-restraints excluded: chain JA residue 255 LEU Chi-restraints excluded: chain JA residue 384 ILE Chi-restraints excluded: chain JA residue 386 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 314 MET Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 134 CYS Chi-restraints excluded: chain O residue 217 LEU Chi-restraints excluded: chain O residue 292 MET Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 396 LYS Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 313 LEU Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 389 GLN Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain S residue 63 ASP Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 313 LEU Chi-restraints excluded: chain S residue 386 VAL Chi-restraints excluded: chain S residue 389 GLN Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 292 MET Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 384 ILE Chi-restraints excluded: chain V residue 386 VAL Chi-restraints excluded: chain V residue 402 MET Chi-restraints excluded: chain X residue 53 GLN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 217 LEU Chi-restraints excluded: chain Z residue 386 VAL Chi-restraints excluded: chain BA residue 44 SER Chi-restraints excluded: chain BA residue 63 ASP Chi-restraints excluded: chain BA residue 112 ILE Chi-restraints excluded: chain BA residue 345 ILE Chi-restraints excluded: chain BA residue 386 VAL Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 93 LEU Chi-restraints excluded: chain DA residue 112 ILE Chi-restraints excluded: chain DA residue 226 SER Chi-restraints excluded: chain DA residue 240 LEU Chi-restraints excluded: chain DA residue 291 THR Chi-restraints excluded: chain DA residue 384 ILE Chi-restraints excluded: chain DA residue 386 VAL Chi-restraints excluded: chain FA residue 53 GLN Chi-restraints excluded: chain FA residue 217 LEU Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain FA residue 386 VAL Chi-restraints excluded: chain FA residue 389 GLN Chi-restraints excluded: chain HA residue 53 GLN Chi-restraints excluded: chain HA residue 63 ASP Chi-restraints excluded: chain HA residue 112 ILE Chi-restraints excluded: chain HA residue 345 ILE Chi-restraints excluded: chain HA residue 350 VAL Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain HA residue 389 GLN Chi-restraints excluded: chain HA residue 402 MET Chi-restraints excluded: chain LA residue 53 GLN Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 146 ASP Chi-restraints excluded: chain LA residue 240 LEU Chi-restraints excluded: chain LA residue 255 LEU Chi-restraints excluded: chain LA residue 384 ILE Chi-restraints excluded: chain LA residue 389 GLN Chi-restraints excluded: chain NA residue 53 GLN Chi-restraints excluded: chain NA residue 63 ASP Chi-restraints excluded: chain NA residue 93 LEU Chi-restraints excluded: chain NA residue 134 CYS Chi-restraints excluded: chain NA residue 389 GLN Chi-restraints excluded: chain PA residue 63 ASP Chi-restraints excluded: chain PA residue 84 MET Chi-restraints excluded: chain PA residue 112 ILE Chi-restraints excluded: chain PA residue 345 ILE Chi-restraints excluded: chain PA residue 384 ILE Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 218 THR Chi-restraints excluded: chain RA residue 255 LEU Chi-restraints excluded: chain RA residue 345 ILE Chi-restraints excluded: chain RA residue 384 ILE Chi-restraints excluded: chain RA residue 389 GLN Chi-restraints excluded: chain TA residue 63 ASP Chi-restraints excluded: chain TA residue 313 LEU Chi-restraints excluded: chain TA residue 386 VAL Chi-restraints excluded: chain TA residue 389 GLN Chi-restraints excluded: chain TA residue 402 MET Chi-restraints excluded: chain VA residue 63 ASP Chi-restraints excluded: chain VA residue 345 ILE Chi-restraints excluded: chain VA residue 350 VAL Chi-restraints excluded: chain VA residue 386 VAL Chi-restraints excluded: chain VA residue 402 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 927 optimal weight: 5.9990 chunk 705 optimal weight: 0.8980 chunk 487 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 448 optimal weight: 9.9990 chunk 630 optimal weight: 20.0000 chunk 942 optimal weight: 10.0000 chunk 997 optimal weight: 20.0000 chunk 492 optimal weight: 10.0000 chunk 892 optimal weight: 5.9990 chunk 268 optimal weight: 40.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN C 53 GLN C 186 ASN C 444 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 GLN G 444 GLN I 186 ASN I 429 HIS I 444 GLN K 429 HIS M 186 ASN M 389 GLN M 429 HIS M 444 GLN O 444 GLN S 444 GLN V 186 ASN V 429 HIS V 444 GLN X 45 HIS X 151 GLN ** X 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 429 HIS Z 444 GLN BA 186 ASN BA 429 HIS DA 45 HIS ** DA 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 444 GLN HA 186 ASN HA 429 HIS LA 429 HIS NA 444 GLN PA 186 ASN ** RA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 444 GLN VA 444 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 84864 Z= 0.381 Angle : 0.708 9.098 115344 Z= 0.361 Chirality : 0.050 0.216 13008 Planarity : 0.006 0.084 14808 Dihedral : 8.294 58.771 12538 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.69 % Allowed : 18.09 % Favored : 78.23 % 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: -1.50 (0.08), residues: 10752 helix: 0.01 (0.09), residues: 3288 sheet: -0.67 (0.11), residues: 2136 loop : -1.79 (0.08), residues: 5328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPFA 394 HIS 0.011 0.002 HISFA 164 PHE 0.021 0.003 PHE V 183 TYR 0.022 0.003 TYR G 285 ARG 0.006 0.001 ARG Z 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 901 time to evaluate : 7.981 Fit side-chains revert: symmetry clash REVERT: JA 217 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8250 (mp) REVERT: JA 240 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7568 (mm) REVERT: A 389 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7150 (tp-100) REVERT: C 389 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7437 (tp-100) REVERT: C 402 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6837 (mtp) REVERT: E 184 MET cc_start: 0.8268 (mmm) cc_final: 0.7867 (tpp) REVERT: E 232 LYS cc_start: 0.6340 (ptpt) cc_final: 0.6111 (ptpp) REVERT: E 240 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7592 (mm) REVERT: E 389 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7272 (tp-100) REVERT: G 36 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6335 (p0) REVERT: G 73 MET cc_start: 0.4480 (OUTLIER) cc_final: 0.3954 (mmp) REVERT: G 389 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7633 (tp40) REVERT: I 345 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7230 (tp) REVERT: I 402 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7004 (mtp) REVERT: K 85 ARG cc_start: 0.4027 (mtt180) cc_final: 0.3785 (ttp-170) REVERT: K 217 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8236 (mp) REVERT: K 240 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7571 (mm) REVERT: K 314 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8000 (tpp) REVERT: O 292 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5435 (tpp) REVERT: O 345 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7168 (tp) REVERT: O 396 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7858 (tmtt) REVERT: Q 85 ARG cc_start: 0.4069 (mtt-85) cc_final: 0.3780 (ttp-170) REVERT: Q 184 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7540 (tpp) REVERT: Q 389 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6992 (mm-40) REVERT: S 73 MET cc_start: 0.4569 (OUTLIER) cc_final: 0.4011 (mmp) REVERT: S 389 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7183 (tp-100) REVERT: V 93 LEU cc_start: 0.4371 (OUTLIER) cc_final: 0.4150 (mp) REVERT: V 292 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5163 (tpp) REVERT: V 345 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7346 (tp) REVERT: V 402 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6999 (mtt) REVERT: X 85 ARG cc_start: 0.4102 (mtt-85) cc_final: 0.3865 (ttp-170) REVERT: X 184 MET cc_start: 0.8203 (mmm) cc_final: 0.7510 (tpp) REVERT: X 345 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7209 (tp) REVERT: X 441 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6876 (mt0) REVERT: BA 345 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7304 (tp) REVERT: BA 402 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6870 (mtp) REVERT: DA 184 MET cc_start: 0.8272 (mmm) cc_final: 0.7862 (tpp) REVERT: DA 217 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8301 (mp) REVERT: DA 240 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7643 (mm) REVERT: FA 389 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7161 (tp-100) REVERT: HA 345 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7344 (tp) REVERT: HA 389 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7324 (tp-100) REVERT: HA 402 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6820 (mtt) REVERT: LA 217 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8266 (mp) REVERT: LA 240 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7615 (mm) REVERT: LA 389 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7444 (tp-100) REVERT: NA 73 MET cc_start: 0.4418 (OUTLIER) cc_final: 0.3901 (mmp) REVERT: NA 389 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7228 (tp-100) REVERT: PA 402 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6991 (mtp) REVERT: RA 85 ARG cc_start: 0.4042 (mtt180) cc_final: 0.3840 (ttp-170) REVERT: RA 345 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7472 (tp) REVERT: RA 389 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6939 (mm-40) REVERT: TA 389 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7263 (tp-100) REVERT: VA 389 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7407 (tp-100) outliers start: 279 outliers final: 124 residues processed: 1064 average time/residue: 1.4448 time to fit residues: 2161.7060 Evaluate side-chains 1054 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 884 time to evaluate : 7.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain JA residue 217 LEU Chi-restraints excluded: chain JA residue 240 LEU Chi-restraints excluded: chain JA residue 255 LEU Chi-restraints excluded: chain JA residue 386 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 314 MET Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 134 CYS Chi-restraints excluded: chain O residue 217 LEU Chi-restraints excluded: chain O residue 226 SER Chi-restraints excluded: chain O residue 292 MET Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 396 LYS Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 184 MET Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 389 GLN Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 63 ASP Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 134 CYS Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 313 LEU Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain S residue 386 VAL Chi-restraints excluded: chain S residue 389 GLN Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 253 LYS Chi-restraints excluded: chain V residue 292 MET Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 384 ILE Chi-restraints excluded: chain V residue 386 VAL Chi-restraints excluded: chain V residue 402 MET Chi-restraints excluded: chain X residue 53 GLN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 123 MET Chi-restraints excluded: chain X residue 218 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 441 GLN Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 217 LEU Chi-restraints excluded: chain Z residue 313 LEU Chi-restraints excluded: chain Z residue 386 VAL Chi-restraints excluded: chain BA residue 44 SER Chi-restraints excluded: chain BA residue 63 ASP Chi-restraints excluded: chain BA residue 112 ILE Chi-restraints excluded: chain BA residue 217 LEU Chi-restraints excluded: chain BA residue 345 ILE Chi-restraints excluded: chain BA residue 386 VAL Chi-restraints excluded: chain BA residue 402 MET Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 112 ILE Chi-restraints excluded: chain DA residue 156 VAL Chi-restraints excluded: chain DA residue 217 LEU Chi-restraints excluded: chain DA residue 240 LEU Chi-restraints excluded: chain DA residue 291 THR Chi-restraints excluded: chain DA residue 386 VAL Chi-restraints excluded: chain FA residue 53 GLN Chi-restraints excluded: chain FA residue 63 ASP Chi-restraints excluded: chain FA residue 217 LEU Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain FA residue 386 VAL Chi-restraints excluded: chain FA residue 389 GLN Chi-restraints excluded: chain HA residue 9 ASP Chi-restraints excluded: chain HA residue 63 ASP Chi-restraints excluded: chain HA residue 112 ILE Chi-restraints excluded: chain HA residue 345 ILE Chi-restraints excluded: chain HA residue 350 VAL Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain HA residue 389 GLN Chi-restraints excluded: chain HA residue 402 MET Chi-restraints excluded: chain LA residue 53 GLN Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 146 ASP Chi-restraints excluded: chain LA residue 217 LEU Chi-restraints excluded: chain LA residue 240 LEU Chi-restraints excluded: chain LA residue 255 LEU Chi-restraints excluded: chain LA residue 384 ILE Chi-restraints excluded: chain LA residue 389 GLN Chi-restraints excluded: chain NA residue 53 GLN Chi-restraints excluded: chain NA residue 63 ASP Chi-restraints excluded: chain NA residue 73 MET Chi-restraints excluded: chain NA residue 93 LEU Chi-restraints excluded: chain NA residue 134 CYS Chi-restraints excluded: chain NA residue 217 LEU Chi-restraints excluded: chain NA residue 345 ILE Chi-restraints excluded: chain NA residue 386 VAL Chi-restraints excluded: chain NA residue 389 GLN Chi-restraints excluded: chain PA residue 63 ASP Chi-restraints excluded: chain PA residue 112 ILE Chi-restraints excluded: chain PA residue 123 MET Chi-restraints excluded: chain PA residue 226 SER Chi-restraints excluded: chain PA residue 291 THR Chi-restraints excluded: chain PA residue 350 VAL Chi-restraints excluded: chain PA residue 386 VAL Chi-restraints excluded: chain PA residue 402 MET Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 218 THR Chi-restraints excluded: chain RA residue 255 LEU Chi-restraints excluded: chain RA residue 345 ILE Chi-restraints excluded: chain RA residue 384 ILE Chi-restraints excluded: chain RA residue 389 GLN Chi-restraints excluded: chain TA residue 63 ASP Chi-restraints excluded: chain TA residue 313 LEU Chi-restraints excluded: chain TA residue 386 VAL Chi-restraints excluded: chain TA residue 389 GLN Chi-restraints excluded: chain TA residue 402 MET Chi-restraints excluded: chain VA residue 63 ASP Chi-restraints excluded: chain VA residue 112 ILE Chi-restraints excluded: chain VA residue 350 VAL Chi-restraints excluded: chain VA residue 386 VAL Chi-restraints excluded: chain VA residue 389 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 830 optimal weight: 6.9990 chunk 566 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 742 optimal weight: 8.9990 chunk 411 optimal weight: 5.9990 chunk 851 optimal weight: 5.9990 chunk 689 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 509 optimal weight: 5.9990 chunk 895 optimal weight: 2.9990 chunk 251 optimal weight: 0.0030 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN C 53 GLN C 186 ASN C 444 GLN G 186 ASN G 389 GLN G 444 GLN I 186 ASN I 444 GLN M 186 ASN M 389 GLN M 444 GLN O 444 GLN S 444 GLN V 186 ASN V 444 GLN X 151 GLN Z 444 GLN BA 186 ASN BA 444 GLN FA 444 GLN HA 186 ASN NA 186 ASN NA 444 GLN PA 444 GLN TA 186 ASN TA 444 GLN VA 444 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 84864 Z= 0.237 Angle : 0.583 10.232 115344 Z= 0.297 Chirality : 0.045 0.165 13008 Planarity : 0.005 0.043 14808 Dihedral : 7.592 59.768 12538 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.33 % Allowed : 18.63 % Favored : 78.05 % 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: -1.37 (0.08), residues: 10752 helix: 0.14 (0.09), residues: 3288 sheet: -0.65 (0.11), residues: 2136 loop : -1.70 (0.08), residues: 5328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 258 HIS 0.009 0.001 HISFA 164 PHE 0.017 0.002 PHEPA 183 TYR 0.016 0.002 TYRNA 382 ARG 0.005 0.000 ARGJA 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 918 time to evaluate : 7.143 Fit side-chains revert: symmetry clash REVERT: JA 85 ARG cc_start: 0.3981 (mtt-85) cc_final: 0.3774 (ttp-170) REVERT: JA 240 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7546 (mm) REVERT: JA 275 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.4980 (mtp180) REVERT: JA 345 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7293 (tp) REVERT: A 73 MET cc_start: 0.4613 (mpm) cc_final: 0.3047 (mtm) REVERT: A 389 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7068 (tp-100) REVERT: C 389 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7357 (tp-100) REVERT: C 402 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6866 (mtp) REVERT: E 184 MET cc_start: 0.8257 (mmm) cc_final: 0.7818 (tpp) REVERT: E 345 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7164 (tp) REVERT: G 36 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6339 (p0) REVERT: G 49 LYS cc_start: 0.6534 (mmmm) cc_final: 0.6226 (mmtm) REVERT: G 389 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7627 (tp40) REVERT: I 345 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7189 (tp) REVERT: I 402 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6948 (mtp) REVERT: K 49 LYS cc_start: 0.6512 (mmmm) cc_final: 0.6225 (mmtt) REVERT: K 85 ARG cc_start: 0.3967 (mtt180) cc_final: 0.3763 (ttp-170) REVERT: K 314 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7002 (tpt) REVERT: M 123 MET cc_start: 0.4495 (tpp) cc_final: 0.3962 (mpp) REVERT: M 389 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: O 345 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7225 (tp) REVERT: O 396 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7815 (tmtt) REVERT: O 402 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6908 (mtp) REVERT: Q 85 ARG cc_start: 0.4071 (mtt-85) cc_final: 0.3837 (ttp-170) REVERT: Q 184 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7578 (tpp) REVERT: Q 389 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6970 (mm-40) REVERT: S 53 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.6070 (tt0) REVERT: S 84 MET cc_start: 0.4658 (OUTLIER) cc_final: 0.4179 (mmm) REVERT: S 389 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7166 (tp-100) REVERT: V 292 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5034 (tpp) REVERT: V 345 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7274 (tp) REVERT: V 402 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6897 (mtt) REVERT: X 85 ARG cc_start: 0.4142 (mtt-85) cc_final: 0.3912 (ttp-170) REVERT: X 184 MET cc_start: 0.8249 (mmm) cc_final: 0.7690 (tpp) REVERT: X 345 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7146 (tp) REVERT: Z 275 ARG cc_start: 0.5480 (OUTLIER) cc_final: 0.4853 (mtp180) REVERT: BA 345 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7330 (tp) REVERT: BA 402 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6928 (mtp) REVERT: DA 184 MET cc_start: 0.8212 (mmm) cc_final: 0.7818 (tpp) REVERT: DA 240 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7576 (mm) REVERT: FA 123 MET cc_start: 0.4450 (tpp) cc_final: 0.3837 (mpp) REVERT: FA 389 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7081 (tp-100) REVERT: HA 345 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7290 (tp) REVERT: HA 389 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7242 (tp-100) REVERT: HA 402 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6847 (mtt) REVERT: LA 184 MET cc_start: 0.8288 (mmm) cc_final: 0.7738 (tpp) REVERT: LA 240 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7603 (mm) REVERT: NA 73 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.3904 (mmp) REVERT: NA 85 ARG cc_start: 0.3665 (mtt90) cc_final: 0.3374 (mpt-90) REVERT: NA 123 MET cc_start: 0.4424 (tpp) cc_final: 0.3787 (mpp) REVERT: NA 389 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7254 (tp-100) REVERT: PA 345 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7179 (tp) REVERT: PA 402 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6901 (mtp) REVERT: RA 184 MET cc_start: 0.8219 (mmm) cc_final: 0.7684 (tpp) REVERT: RA 275 ARG cc_start: 0.5457 (OUTLIER) cc_final: 0.4927 (mtp180) REVERT: RA 345 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7293 (tp) REVERT: RA 389 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6939 (mm-40) REVERT: TA 84 MET cc_start: 0.4524 (OUTLIER) cc_final: 0.4032 (mmm) REVERT: TA 85 ARG cc_start: 0.3758 (mtt90) cc_final: 0.3532 (ttt180) REVERT: TA 275 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.4875 (mtp180) REVERT: TA 389 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7190 (tp-100) REVERT: VA 345 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7152 (tp) REVERT: VA 389 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7416 (tp-100) REVERT: VA 402 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6818 (mtp) outliers start: 246 outliers final: 126 residues processed: 1071 average time/residue: 1.4240 time to fit residues: 2147.9091 Evaluate side-chains 1080 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 907 time to evaluate : 7.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain JA residue 156 VAL Chi-restraints excluded: chain JA residue 240 LEU Chi-restraints excluded: chain JA residue 255 LEU Chi-restraints excluded: chain JA residue 275 ARG Chi-restraints excluded: chain JA residue 345 ILE Chi-restraints excluded: chain JA residue 384 ILE Chi-restraints excluded: chain JA residue 386 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 424 LYS Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 314 MET Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 389 GLN Chi-restraints excluded: chain O residue 9 ASP Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 217 LEU Chi-restraints excluded: chain O residue 226 SER Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 396 LYS Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain O residue 424 LYS Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 184 MET Chi-restraints excluded: chain Q residue 232 LYS Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 389 GLN Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 84 MET Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 313 LEU Chi-restraints excluded: chain S residue 389 GLN Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 292 MET Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 384 ILE Chi-restraints excluded: chain V residue 386 VAL Chi-restraints excluded: chain V residue 402 MET Chi-restraints excluded: chain X residue 53 GLN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 232 LYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain Z residue 217 LEU Chi-restraints excluded: chain Z residue 275 ARG Chi-restraints excluded: chain BA residue 44 SER Chi-restraints excluded: chain BA residue 53 GLN Chi-restraints excluded: chain BA residue 63 ASP Chi-restraints excluded: chain BA residue 112 ILE Chi-restraints excluded: chain BA residue 217 LEU Chi-restraints excluded: chain BA residue 345 ILE Chi-restraints excluded: chain BA residue 386 VAL Chi-restraints excluded: chain BA residue 402 MET Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 93 LEU Chi-restraints excluded: chain DA residue 112 ILE Chi-restraints excluded: chain DA residue 156 VAL Chi-restraints excluded: chain DA residue 226 SER Chi-restraints excluded: chain DA residue 240 LEU Chi-restraints excluded: chain DA residue 291 THR Chi-restraints excluded: chain DA residue 384 ILE Chi-restraints excluded: chain DA residue 386 VAL Chi-restraints excluded: chain FA residue 53 GLN Chi-restraints excluded: chain FA residue 63 ASP Chi-restraints excluded: chain FA residue 93 LEU Chi-restraints excluded: chain FA residue 217 LEU Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain FA residue 386 VAL Chi-restraints excluded: chain FA residue 389 GLN Chi-restraints excluded: chain HA residue 9 ASP Chi-restraints excluded: chain HA residue 53 GLN Chi-restraints excluded: chain HA residue 63 ASP Chi-restraints excluded: chain HA residue 112 ILE Chi-restraints excluded: chain HA residue 345 ILE Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain HA residue 389 GLN Chi-restraints excluded: chain HA residue 402 MET Chi-restraints excluded: chain LA residue 53 GLN Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 146 ASP Chi-restraints excluded: chain LA residue 156 VAL Chi-restraints excluded: chain LA residue 240 LEU Chi-restraints excluded: chain LA residue 255 LEU Chi-restraints excluded: chain NA residue 53 GLN Chi-restraints excluded: chain NA residue 63 ASP Chi-restraints excluded: chain NA residue 73 MET Chi-restraints excluded: chain NA residue 93 LEU Chi-restraints excluded: chain NA residue 217 LEU Chi-restraints excluded: chain NA residue 345 ILE Chi-restraints excluded: chain NA residue 386 VAL Chi-restraints excluded: chain NA residue 389 GLN Chi-restraints excluded: chain PA residue 63 ASP Chi-restraints excluded: chain PA residue 112 ILE Chi-restraints excluded: chain PA residue 123 MET Chi-restraints excluded: chain PA residue 226 SER Chi-restraints excluded: chain PA residue 291 THR Chi-restraints excluded: chain PA residue 345 ILE Chi-restraints excluded: chain PA residue 350 VAL Chi-restraints excluded: chain PA residue 384 ILE Chi-restraints excluded: chain PA residue 386 VAL Chi-restraints excluded: chain PA residue 402 MET Chi-restraints excluded: chain RA residue 53 GLN Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 226 SER Chi-restraints excluded: chain RA residue 255 LEU Chi-restraints excluded: chain RA residue 275 ARG Chi-restraints excluded: chain RA residue 345 ILE Chi-restraints excluded: chain RA residue 384 ILE Chi-restraints excluded: chain RA residue 389 GLN Chi-restraints excluded: chain TA residue 63 ASP Chi-restraints excluded: chain TA residue 84 MET Chi-restraints excluded: chain TA residue 93 LEU Chi-restraints excluded: chain TA residue 217 LEU Chi-restraints excluded: chain TA residue 275 ARG Chi-restraints excluded: chain TA residue 386 VAL Chi-restraints excluded: chain TA residue 389 GLN Chi-restraints excluded: chain TA residue 402 MET Chi-restraints excluded: chain VA residue 9 ASP Chi-restraints excluded: chain VA residue 53 GLN Chi-restraints excluded: chain VA residue 63 ASP Chi-restraints excluded: chain VA residue 112 ILE Chi-restraints excluded: chain VA residue 345 ILE Chi-restraints excluded: chain VA residue 350 VAL Chi-restraints excluded: chain VA residue 386 VAL Chi-restraints excluded: chain VA residue 389 GLN Chi-restraints excluded: chain VA residue 402 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 335 optimal weight: 10.0000 chunk 898 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 585 optimal weight: 7.9990 chunk 246 optimal weight: 0.9980 chunk 998 optimal weight: 0.9990 chunk 828 optimal weight: 0.9980 chunk 462 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 524 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: JA 209 ASN A 53 GLN A 444 GLN C 53 GLN C 186 ASN C 444 GLN G 186 ASN G 389 GLN G 444 GLN I 186 ASN I 444 GLN M 186 ASN M 444 GLN O 209 ASN O 444 GLN S 444 GLN V 186 ASN V 444 GLN Z 444 GLN BA 186 ASN BA 444 GLN DA 209 ASN FA 444 GLN HA 186 ASN NA 186 ASN NA 444 GLN PA 444 GLN TA 186 ASN TA 444 GLN VA 209 ASN VA 444 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 84864 Z= 0.147 Angle : 0.506 11.419 115344 Z= 0.256 Chirality : 0.042 0.141 13008 Planarity : 0.004 0.041 14808 Dihedral : 6.605 58.833 12538 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.28 % Allowed : 18.68 % Favored : 78.04 % 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: -1.08 (0.08), residues: 10752 helix: 0.43 (0.09), residues: 3288 sheet: -0.52 (0.11), residues: 2112 loop : -1.53 (0.08), residues: 5352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 258 HIS 0.007 0.001 HISHA 79 PHE 0.016 0.001 PHE V 183 TYR 0.014 0.001 TYR V 382 ARG 0.006 0.000 ARGHA 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 935 time to evaluate : 8.021 Fit side-chains revert: symmetry clash REVERT: JA 275 ARG cc_start: 0.5502 (OUTLIER) cc_final: 0.4993 (mtp180) REVERT: JA 345 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7236 (tp) REVERT: JA 389 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7123 (tp-100) REVERT: A 73 MET cc_start: 0.4421 (mpm) cc_final: 0.2815 (mtm) REVERT: A 84 MET cc_start: 0.4633 (OUTLIER) cc_final: 0.4308 (mmm) REVERT: A 345 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7169 (tp) REVERT: A 389 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6939 (tp-100) REVERT: C 389 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7323 (tp-100) REVERT: C 402 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6806 (mtp) REVERT: E 184 MET cc_start: 0.8220 (mmm) cc_final: 0.7786 (tpp) REVERT: E 345 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7098 (tp) REVERT: G 36 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6301 (p0) REVERT: G 84 MET cc_start: 0.4851 (OUTLIER) cc_final: 0.4478 (mmm) REVERT: I 345 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7069 (tp) REVERT: I 389 GLN cc_start: 0.7507 (tm-30) cc_final: 0.6925 (tp-100) REVERT: I 402 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6809 (mtp) REVERT: K 20 ARG cc_start: 0.7073 (mtm-85) cc_final: 0.6815 (ttm170) REVERT: M 36 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.5981 (p0) REVERT: M 123 MET cc_start: 0.4557 (tpp) cc_final: 0.4106 (mpp) REVERT: M 345 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7185 (tp) REVERT: O 345 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7138 (tp) REVERT: O 396 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7838 (tmtt) REVERT: Q 85 ARG cc_start: 0.4041 (mtt-85) cc_final: 0.3801 (ttp-170) REVERT: Q 292 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6421 (mmt) REVERT: Q 345 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7143 (tp) REVERT: Q 389 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6848 (mm-40) REVERT: S 36 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6347 (p0) REVERT: S 84 MET cc_start: 0.4896 (OUTLIER) cc_final: 0.4447 (mmm) REVERT: S 389 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7071 (tp-100) REVERT: V 345 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7251 (tp) REVERT: V 402 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6818 (mtp) REVERT: X 184 MET cc_start: 0.8266 (mmm) cc_final: 0.7708 (tpp) REVERT: X 275 ARG cc_start: 0.5417 (OUTLIER) cc_final: 0.4920 (mtp180) REVERT: X 345 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7108 (tp) REVERT: Z 36 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6406 (p0) REVERT: Z 389 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7076 (tp-100) REVERT: BA 345 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7176 (tp) REVERT: BA 402 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6752 (mtp) REVERT: DA 184 MET cc_start: 0.8210 (mmm) cc_final: 0.7770 (tpp) REVERT: DA 345 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7275 (tp) REVERT: FA 36 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6396 (p0) REVERT: FA 123 MET cc_start: 0.4552 (tpp) cc_final: 0.3962 (mpp) REVERT: HA 345 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7277 (tp) REVERT: HA 389 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7198 (tp-100) REVERT: LA 184 MET cc_start: 0.8304 (mmm) cc_final: 0.7745 (tpp) REVERT: LA 240 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7604 (mm) REVERT: LA 275 ARG cc_start: 0.5488 (mtm110) cc_final: 0.4978 (mtp180) REVERT: LA 389 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6965 (mm-40) REVERT: LA 444 GLN cc_start: 0.6520 (OUTLIER) cc_final: 0.6185 (tt0) REVERT: NA 36 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6407 (p0) REVERT: NA 84 MET cc_start: 0.4562 (OUTLIER) cc_final: 0.4150 (mmm) REVERT: NA 123 MET cc_start: 0.4579 (tpp) cc_final: 0.3906 (mpp) REVERT: NA 345 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7201 (tp) REVERT: NA 389 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7131 (tp-100) REVERT: PA 33 THR cc_start: 0.7234 (m) cc_final: 0.6854 (p) REVERT: PA 345 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7048 (tp) REVERT: PA 402 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6804 (mtp) REVERT: RA 184 MET cc_start: 0.8208 (mmm) cc_final: 0.7659 (tpp) REVERT: RA 275 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.4905 (mtp180) REVERT: RA 345 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7117 (tp) REVERT: RA 389 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6830 (mm-40) REVERT: RA 396 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8041 (tmtt) REVERT: TA 36 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6566 (p0) REVERT: TA 84 MET cc_start: 0.4571 (OUTLIER) cc_final: 0.4189 (mmm) REVERT: TA 275 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.4913 (mtp180) REVERT: TA 389 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7092 (tp-100) REVERT: VA 345 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7036 (tp) REVERT: VA 389 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7270 (tp-100) outliers start: 240 outliers final: 79 residues processed: 1079 average time/residue: 1.4456 time to fit residues: 2202.4157 Evaluate side-chains 1051 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 920 time to evaluate : 7.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain JA residue 156 VAL Chi-restraints excluded: chain JA residue 275 ARG Chi-restraints excluded: chain JA residue 345 ILE Chi-restraints excluded: chain JA residue 389 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain M residue 36 ASP Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 255 LEU Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 396 LYS Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 292 MET Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 389 GLN Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain S residue 84 MET Chi-restraints excluded: chain S residue 386 VAL Chi-restraints excluded: chain S residue 389 GLN Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 384 ILE Chi-restraints excluded: chain V residue 386 VAL Chi-restraints excluded: chain V residue 402 MET Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 275 ARG Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain Z residue 36 ASP Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 386 VAL Chi-restraints excluded: chain BA residue 63 ASP Chi-restraints excluded: chain BA residue 345 ILE Chi-restraints excluded: chain BA residue 386 VAL Chi-restraints excluded: chain BA residue 402 MET Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 93 LEU Chi-restraints excluded: chain DA residue 156 VAL Chi-restraints excluded: chain DA residue 226 SER Chi-restraints excluded: chain DA residue 291 THR Chi-restraints excluded: chain DA residue 345 ILE Chi-restraints excluded: chain FA residue 36 ASP Chi-restraints excluded: chain FA residue 53 GLN Chi-restraints excluded: chain FA residue 63 ASP Chi-restraints excluded: chain FA residue 93 LEU Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain FA residue 386 VAL Chi-restraints excluded: chain HA residue 16 LYS Chi-restraints excluded: chain HA residue 63 ASP Chi-restraints excluded: chain HA residue 345 ILE Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain LA residue 53 GLN Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 146 ASP Chi-restraints excluded: chain LA residue 156 VAL Chi-restraints excluded: chain LA residue 240 LEU Chi-restraints excluded: chain LA residue 389 GLN Chi-restraints excluded: chain LA residue 444 GLN Chi-restraints excluded: chain NA residue 36 ASP Chi-restraints excluded: chain NA residue 63 ASP Chi-restraints excluded: chain NA residue 84 MET Chi-restraints excluded: chain NA residue 93 LEU Chi-restraints excluded: chain NA residue 345 ILE Chi-restraints excluded: chain NA residue 386 VAL Chi-restraints excluded: chain NA residue 389 GLN Chi-restraints excluded: chain PA residue 63 ASP Chi-restraints excluded: chain PA residue 226 SER Chi-restraints excluded: chain PA residue 291 THR Chi-restraints excluded: chain PA residue 345 ILE Chi-restraints excluded: chain PA residue 384 ILE Chi-restraints excluded: chain PA residue 386 VAL Chi-restraints excluded: chain PA residue 402 MET Chi-restraints excluded: chain RA residue 53 GLN Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 156 VAL Chi-restraints excluded: chain RA residue 226 SER Chi-restraints excluded: chain RA residue 275 ARG Chi-restraints excluded: chain RA residue 345 ILE Chi-restraints excluded: chain RA residue 389 GLN Chi-restraints excluded: chain RA residue 396 LYS Chi-restraints excluded: chain TA residue 36 ASP Chi-restraints excluded: chain TA residue 63 ASP Chi-restraints excluded: chain TA residue 84 MET Chi-restraints excluded: chain TA residue 93 LEU Chi-restraints excluded: chain TA residue 275 ARG Chi-restraints excluded: chain TA residue 386 VAL Chi-restraints excluded: chain TA residue 389 GLN Chi-restraints excluded: chain TA residue 402 MET Chi-restraints excluded: chain VA residue 63 ASP Chi-restraints excluded: chain VA residue 226 SER Chi-restraints excluded: chain VA residue 345 ILE Chi-restraints excluded: chain VA residue 386 VAL Chi-restraints excluded: chain VA residue 389 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 962 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 568 optimal weight: 9.9990 chunk 729 optimal weight: 10.0000 chunk 564 optimal weight: 0.8980 chunk 840 optimal weight: 7.9990 chunk 557 optimal weight: 5.9990 chunk 994 optimal weight: 20.0000 chunk 622 optimal weight: 4.9990 chunk 606 optimal weight: 5.9990 chunk 459 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN C 53 GLN C 186 ASN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN G 389 GLN I 186 ASN M 186 ASN M 389 GLN O 429 HIS V 186 ASN V 444 GLN ** X 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 186 ASN ** DA 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 53 GLN HA 186 ASN ** LA 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 186 ASN PA 389 GLN TA 186 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 84864 Z= 0.301 Angle : 0.634 14.269 115344 Z= 0.321 Chirality : 0.047 0.326 13008 Planarity : 0.005 0.063 14808 Dihedral : 7.067 59.657 12534 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.16 % Allowed : 19.25 % Favored : 77.59 % 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: -1.25 (0.08), residues: 10752 helix: 0.25 (0.09), residues: 3336 sheet: -0.59 (0.11), residues: 2136 loop : -1.65 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRPFA 394 HIS 0.009 0.002 HISFA 164 PHE 0.019 0.002 PHE V 183 TYR 0.017 0.002 TYR X 150 ARG 0.009 0.001 ARGLA 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 918 time to evaluate : 8.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: JA 85 ARG cc_start: 0.4002 (mtt-85) cc_final: 0.3782 (ttp-170) REVERT: JA 240 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7545 (mm) REVERT: JA 345 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7203 (tp) REVERT: JA 389 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7143 (tp-100) REVERT: A 84 MET cc_start: 0.4326 (OUTLIER) cc_final: 0.3925 (mmm) REVERT: A 85 ARG cc_start: 0.3642 (mtt-85) cc_final: 0.3308 (ttp-170) REVERT: A 389 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7105 (tp-100) REVERT: C 389 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7368 (tp-100) REVERT: C 402 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6786 (mtp) REVERT: E 184 MET cc_start: 0.8274 (mmm) cc_final: 0.7809 (tpp) REVERT: E 240 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7504 (mm) REVERT: E 345 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7225 (tp) REVERT: E 389 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7298 (tp-100) REVERT: G 36 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6350 (p0) REVERT: G 84 MET cc_start: 0.4682 (OUTLIER) cc_final: 0.4130 (mmm) REVERT: G 389 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7094 (tp-100) REVERT: I 345 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7277 (tp) REVERT: K 184 MET cc_start: 0.8007 (mmm) cc_final: 0.7548 (tpp) REVERT: K 314 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7979 (tpp) REVERT: K 345 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7198 (tp) REVERT: M 49 LYS cc_start: 0.6471 (mmmm) cc_final: 0.6166 (mmtm) REVERT: M 389 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: O 345 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7156 (tp) REVERT: O 396 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7815 (tmtt) REVERT: O 402 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6942 (mtp) REVERT: Q 85 ARG cc_start: 0.4091 (mtt-85) cc_final: 0.3835 (ttp-170) REVERT: Q 345 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7261 (tp) REVERT: Q 389 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6892 (mm-40) REVERT: S 84 MET cc_start: 0.4581 (OUTLIER) cc_final: 0.4033 (mmm) REVERT: S 389 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7103 (tp-100) REVERT: V 84 MET cc_start: 0.4400 (mmm) cc_final: 0.3995 (mmt) REVERT: V 345 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7339 (tp) REVERT: V 402 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6954 (mtt) REVERT: X 85 ARG cc_start: 0.4111 (mtt-85) cc_final: 0.3873 (ttp-170) REVERT: X 345 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7212 (tp) REVERT: Z 389 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7290 (tp-100) REVERT: BA 345 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7344 (tp) REVERT: BA 402 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6810 (mtp) REVERT: DA 184 MET cc_start: 0.8241 (mmm) cc_final: 0.7775 (tpp) REVERT: DA 240 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7598 (mm) REVERT: DA 345 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7157 (tp) REVERT: DA 389 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7073 (tp-100) REVERT: HA 345 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7312 (tp) REVERT: HA 389 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7260 (tp-100) REVERT: HA 402 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6925 (mtt) REVERT: LA 184 MET cc_start: 0.8316 (mmm) cc_final: 0.7888 (tpp) REVERT: LA 240 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7596 (mm) REVERT: LA 389 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6937 (mm-40) REVERT: LA 444 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6208 (tt0) REVERT: NA 73 MET cc_start: 0.4550 (OUTLIER) cc_final: 0.3955 (mmp) REVERT: NA 84 MET cc_start: 0.4463 (OUTLIER) cc_final: 0.3933 (mmm) REVERT: NA 389 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7284 (tp-100) REVERT: PA 84 MET cc_start: 0.4399 (mmt) cc_final: 0.4196 (tpt) REVERT: PA 345 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7127 (tp) REVERT: PA 389 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7507 (tp-100) REVERT: PA 396 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7733 (tmtt) REVERT: PA 402 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6928 (mtp) REVERT: RA 184 MET cc_start: 0.8241 (mmm) cc_final: 0.7831 (tpp) REVERT: RA 345 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7273 (tp) REVERT: RA 389 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6879 (mm-40) REVERT: TA 84 MET cc_start: 0.4659 (OUTLIER) cc_final: 0.4080 (mmm) REVERT: TA 275 ARG cc_start: 0.5573 (OUTLIER) cc_final: 0.4916 (mtp180) REVERT: TA 389 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7200 (tp-100) REVERT: VA 345 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7047 (tp) REVERT: VA 389 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7425 (tp-100) REVERT: VA 402 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6852 (mtp) outliers start: 228 outliers final: 110 residues processed: 1047 average time/residue: 1.4323 time to fit residues: 2116.0339 Evaluate side-chains 1070 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 908 time to evaluate : 7.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain JA residue 156 VAL Chi-restraints excluded: chain JA residue 226 SER Chi-restraints excluded: chain JA residue 240 LEU Chi-restraints excluded: chain JA residue 255 LEU Chi-restraints excluded: chain JA residue 275 ARG Chi-restraints excluded: chain JA residue 345 ILE Chi-restraints excluded: chain JA residue 389 GLN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 424 LYS Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 314 MET Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 389 GLN Chi-restraints excluded: chain O residue 53 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 226 SER Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 396 LYS Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain O residue 424 LYS Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 389 GLN Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain S residue 63 ASP Chi-restraints excluded: chain S residue 84 MET Chi-restraints excluded: chain S residue 313 LEU Chi-restraints excluded: chain S residue 386 VAL Chi-restraints excluded: chain S residue 389 GLN Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 384 ILE Chi-restraints excluded: chain V residue 386 VAL Chi-restraints excluded: chain V residue 402 MET Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 386 VAL Chi-restraints excluded: chain BA residue 44 SER Chi-restraints excluded: chain BA residue 63 ASP Chi-restraints excluded: chain BA residue 112 ILE Chi-restraints excluded: chain BA residue 345 ILE Chi-restraints excluded: chain BA residue 386 VAL Chi-restraints excluded: chain BA residue 402 MET Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 93 LEU Chi-restraints excluded: chain DA residue 156 VAL Chi-restraints excluded: chain DA residue 226 SER Chi-restraints excluded: chain DA residue 240 LEU Chi-restraints excluded: chain DA residue 291 THR Chi-restraints excluded: chain DA residue 345 ILE Chi-restraints excluded: chain DA residue 384 ILE Chi-restraints excluded: chain DA residue 389 GLN Chi-restraints excluded: chain FA residue 53 GLN Chi-restraints excluded: chain FA residue 63 ASP Chi-restraints excluded: chain FA residue 93 LEU Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain FA residue 386 VAL Chi-restraints excluded: chain HA residue 63 ASP Chi-restraints excluded: chain HA residue 226 SER Chi-restraints excluded: chain HA residue 345 ILE Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain HA residue 389 GLN Chi-restraints excluded: chain HA residue 402 MET Chi-restraints excluded: chain LA residue 53 GLN Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 146 ASP Chi-restraints excluded: chain LA residue 156 VAL Chi-restraints excluded: chain LA residue 240 LEU Chi-restraints excluded: chain LA residue 384 ILE Chi-restraints excluded: chain LA residue 389 GLN Chi-restraints excluded: chain LA residue 444 GLN Chi-restraints excluded: chain NA residue 63 ASP Chi-restraints excluded: chain NA residue 73 MET Chi-restraints excluded: chain NA residue 84 MET Chi-restraints excluded: chain NA residue 93 LEU Chi-restraints excluded: chain NA residue 156 VAL Chi-restraints excluded: chain NA residue 386 VAL Chi-restraints excluded: chain NA residue 389 GLN Chi-restraints excluded: chain NA residue 424 LYS Chi-restraints excluded: chain PA residue 63 ASP Chi-restraints excluded: chain PA residue 226 SER Chi-restraints excluded: chain PA residue 291 THR Chi-restraints excluded: chain PA residue 345 ILE Chi-restraints excluded: chain PA residue 384 ILE Chi-restraints excluded: chain PA residue 386 VAL Chi-restraints excluded: chain PA residue 389 GLN Chi-restraints excluded: chain PA residue 396 LYS Chi-restraints excluded: chain PA residue 402 MET Chi-restraints excluded: chain RA residue 53 GLN Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 156 VAL Chi-restraints excluded: chain RA residue 226 SER Chi-restraints excluded: chain RA residue 255 LEU Chi-restraints excluded: chain RA residue 300 THR Chi-restraints excluded: chain RA residue 345 ILE Chi-restraints excluded: chain RA residue 384 ILE Chi-restraints excluded: chain RA residue 389 GLN Chi-restraints excluded: chain TA residue 63 ASP Chi-restraints excluded: chain TA residue 84 MET Chi-restraints excluded: chain TA residue 275 ARG Chi-restraints excluded: chain TA residue 313 LEU Chi-restraints excluded: chain TA residue 386 VAL Chi-restraints excluded: chain TA residue 389 GLN Chi-restraints excluded: chain TA residue 402 MET Chi-restraints excluded: chain VA residue 63 ASP Chi-restraints excluded: chain VA residue 112 ILE Chi-restraints excluded: chain VA residue 226 SER Chi-restraints excluded: chain VA residue 345 ILE Chi-restraints excluded: chain VA residue 386 VAL Chi-restraints excluded: chain VA residue 389 GLN Chi-restraints excluded: chain VA residue 402 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 615 optimal weight: 8.9990 chunk 397 optimal weight: 4.9990 chunk 594 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 632 optimal weight: 5.9990 chunk 677 optimal weight: 0.9980 chunk 491 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 781 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN C 186 ASN C 444 GLN G 186 ASN G 444 GLN I 186 ASN I 389 GLN I 444 GLN M 186 ASN M 444 GLN S 53 GLN S 444 GLN V 186 ASN V 444 GLN Z 444 GLN BA 186 ASN BA 444 GLN DA 209 ASN FA 444 GLN HA 186 ASN NA 186 ASN NA 444 GLN PA 389 GLN PA 444 GLN TA 186 ASN TA 444 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 84864 Z= 0.256 Angle : 0.608 14.706 115344 Z= 0.306 Chirality : 0.045 0.195 13008 Planarity : 0.005 0.049 14808 Dihedral : 6.879 59.723 12534 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.88 % Allowed : 19.60 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.08), residues: 10752 helix: 0.23 (0.09), residues: 3336 sheet: -0.61 (0.11), residues: 2136 loop : -1.66 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPFA 394 HIS 0.009 0.002 HISFA 164 PHE 0.020 0.002 PHE V 183 TYR 0.015 0.002 TYR M 382 ARG 0.009 0.000 ARGLA 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 921 time to evaluate : 7.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: JA 85 ARG cc_start: 0.3967 (mtt-85) cc_final: 0.3750 (ttp-170) REVERT: JA 240 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7538 (mm) REVERT: JA 345 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7255 (tp) REVERT: JA 389 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7158 (tp-100) REVERT: A 84 MET cc_start: 0.4411 (OUTLIER) cc_final: 0.4034 (mmm) REVERT: A 85 ARG cc_start: 0.3624 (mtt-85) cc_final: 0.3279 (ttp-170) REVERT: A 345 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7069 (tp) REVERT: A 389 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7076 (tp-100) REVERT: C 314 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8005 (ttt) REVERT: C 389 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7365 (tp-100) REVERT: C 402 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6836 (mtp) REVERT: E 184 MET cc_start: 0.8267 (mmm) cc_final: 0.7833 (tpp) REVERT: E 345 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7194 (tp) REVERT: E 389 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7353 (tp-100) REVERT: G 36 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6323 (p0) REVERT: G 84 MET cc_start: 0.4670 (OUTLIER) cc_final: 0.4127 (mmm) REVERT: I 345 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7247 (tp) REVERT: I 389 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.6483 (tm130) REVERT: I 402 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6949 (mtp) REVERT: K 184 MET cc_start: 0.8025 (mmm) cc_final: 0.7570 (tpp) REVERT: K 240 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7545 (mm) REVERT: K 314 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7015 (tpt) REVERT: K 345 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7203 (tp) REVERT: K 389 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7081 (tp-100) REVERT: M 49 LYS cc_start: 0.6473 (mmmm) cc_final: 0.6170 (mmtm) REVERT: M 345 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7113 (tp) REVERT: O 345 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7123 (tp) REVERT: O 396 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7814 (tmtt) REVERT: Q 85 ARG cc_start: 0.4097 (mtt-85) cc_final: 0.3816 (ttp-170) REVERT: Q 292 MET cc_start: 0.6643 (mpp) cc_final: 0.6368 (mmt) REVERT: Q 345 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7233 (tp) REVERT: Q 389 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6928 (mm-40) REVERT: S 84 MET cc_start: 0.4607 (OUTLIER) cc_final: 0.4165 (mmm) REVERT: S 389 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7103 (tp-100) REVERT: V 84 MET cc_start: 0.4474 (mmm) cc_final: 0.3657 (mmt) REVERT: V 345 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7196 (tp) REVERT: V 402 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6915 (mtt) REVERT: X 184 MET cc_start: 0.8260 (mmm) cc_final: 0.7709 (tpp) REVERT: X 345 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7240 (tp) REVERT: Z 389 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7263 (tp-100) REVERT: BA 345 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7245 (tp) REVERT: BA 402 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6807 (mtp) REVERT: DA 184 MET cc_start: 0.8241 (mmm) cc_final: 0.7774 (tpp) REVERT: DA 240 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7574 (mm) REVERT: DA 345 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7179 (tp) REVERT: DA 389 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7093 (tp-100) REVERT: HA 345 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7299 (tp) REVERT: HA 389 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7246 (tp-100) REVERT: HA 402 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6893 (mtt) REVERT: LA 184 MET cc_start: 0.8303 (mmm) cc_final: 0.7881 (tpp) REVERT: LA 240 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7584 (mm) REVERT: LA 389 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6990 (mm-40) REVERT: LA 444 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.6148 (tt0) REVERT: NA 73 MET cc_start: 0.4547 (OUTLIER) cc_final: 0.3881 (mmp) REVERT: NA 84 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.3899 (mmm) REVERT: NA 275 ARG cc_start: 0.5462 (OUTLIER) cc_final: 0.4841 (mtp180) REVERT: NA 389 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7247 (tp-100) REVERT: PA 345 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7084 (tp) REVERT: PA 389 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7436 (tp-100) REVERT: PA 396 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7714 (tmtt) REVERT: PA 402 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6893 (mtp) REVERT: RA 116 ILE cc_start: 0.3591 (OUTLIER) cc_final: 0.3365 (mm) REVERT: RA 184 MET cc_start: 0.8233 (mmm) cc_final: 0.7818 (tpp) REVERT: RA 275 ARG cc_start: 0.5464 (OUTLIER) cc_final: 0.4934 (mtp180) REVERT: RA 345 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7242 (tp) REVERT: RA 389 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6925 (mm-40) REVERT: TA 84 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.4119 (mmm) REVERT: TA 275 ARG cc_start: 0.5543 (OUTLIER) cc_final: 0.4881 (mtp180) REVERT: TA 389 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7178 (tp-100) REVERT: VA 345 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7045 (tp) REVERT: VA 389 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7443 (tp-100) REVERT: VA 402 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6814 (mtp) outliers start: 201 outliers final: 113 residues processed: 1040 average time/residue: 1.4802 time to fit residues: 2169.8084 Evaluate side-chains 1085 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 913 time to evaluate : 7.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain JA residue 156 VAL Chi-restraints excluded: chain JA residue 226 SER Chi-restraints excluded: chain JA residue 240 LEU Chi-restraints excluded: chain JA residue 255 LEU Chi-restraints excluded: chain JA residue 275 ARG Chi-restraints excluded: chain JA residue 345 ILE Chi-restraints excluded: chain JA residue 389 GLN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 314 MET Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain O residue 53 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 226 SER Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 396 LYS Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 300 THR Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 389 GLN Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain S residue 63 ASP Chi-restraints excluded: chain S residue 84 MET Chi-restraints excluded: chain S residue 386 VAL Chi-restraints excluded: chain S residue 389 GLN Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 384 ILE Chi-restraints excluded: chain V residue 386 VAL Chi-restraints excluded: chain V residue 402 MET Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 386 VAL Chi-restraints excluded: chain BA residue 44 SER Chi-restraints excluded: chain BA residue 63 ASP Chi-restraints excluded: chain BA residue 93 LEU Chi-restraints excluded: chain BA residue 345 ILE Chi-restraints excluded: chain BA residue 386 VAL Chi-restraints excluded: chain BA residue 402 MET Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 93 LEU Chi-restraints excluded: chain DA residue 112 ILE Chi-restraints excluded: chain DA residue 156 VAL Chi-restraints excluded: chain DA residue 226 SER Chi-restraints excluded: chain DA residue 240 LEU Chi-restraints excluded: chain DA residue 291 THR Chi-restraints excluded: chain DA residue 300 THR Chi-restraints excluded: chain DA residue 345 ILE Chi-restraints excluded: chain DA residue 384 ILE Chi-restraints excluded: chain DA residue 389 GLN Chi-restraints excluded: chain FA residue 53 GLN Chi-restraints excluded: chain FA residue 63 ASP Chi-restraints excluded: chain FA residue 93 LEU Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain FA residue 386 VAL Chi-restraints excluded: chain HA residue 63 ASP Chi-restraints excluded: chain HA residue 345 ILE Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain HA residue 389 GLN Chi-restraints excluded: chain HA residue 402 MET Chi-restraints excluded: chain LA residue 53 GLN Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 146 ASP Chi-restraints excluded: chain LA residue 156 VAL Chi-restraints excluded: chain LA residue 240 LEU Chi-restraints excluded: chain LA residue 384 ILE Chi-restraints excluded: chain LA residue 389 GLN Chi-restraints excluded: chain LA residue 444 GLN Chi-restraints excluded: chain NA residue 53 GLN Chi-restraints excluded: chain NA residue 63 ASP Chi-restraints excluded: chain NA residue 73 MET Chi-restraints excluded: chain NA residue 84 MET Chi-restraints excluded: chain NA residue 93 LEU Chi-restraints excluded: chain NA residue 156 VAL Chi-restraints excluded: chain NA residue 275 ARG Chi-restraints excluded: chain NA residue 386 VAL Chi-restraints excluded: chain NA residue 389 GLN Chi-restraints excluded: chain PA residue 63 ASP Chi-restraints excluded: chain PA residue 112 ILE Chi-restraints excluded: chain PA residue 123 MET Chi-restraints excluded: chain PA residue 226 SER Chi-restraints excluded: chain PA residue 291 THR Chi-restraints excluded: chain PA residue 345 ILE Chi-restraints excluded: chain PA residue 384 ILE Chi-restraints excluded: chain PA residue 386 VAL Chi-restraints excluded: chain PA residue 389 GLN Chi-restraints excluded: chain PA residue 396 LYS Chi-restraints excluded: chain PA residue 402 MET Chi-restraints excluded: chain RA residue 53 GLN Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 116 ILE Chi-restraints excluded: chain RA residue 156 VAL Chi-restraints excluded: chain RA residue 226 SER Chi-restraints excluded: chain RA residue 255 LEU Chi-restraints excluded: chain RA residue 275 ARG Chi-restraints excluded: chain RA residue 300 THR Chi-restraints excluded: chain RA residue 345 ILE Chi-restraints excluded: chain RA residue 384 ILE Chi-restraints excluded: chain RA residue 389 GLN Chi-restraints excluded: chain TA residue 63 ASP Chi-restraints excluded: chain TA residue 84 MET Chi-restraints excluded: chain TA residue 275 ARG Chi-restraints excluded: chain TA residue 386 VAL Chi-restraints excluded: chain TA residue 389 GLN Chi-restraints excluded: chain TA residue 402 MET Chi-restraints excluded: chain VA residue 63 ASP Chi-restraints excluded: chain VA residue 112 ILE Chi-restraints excluded: chain VA residue 226 SER Chi-restraints excluded: chain VA residue 345 ILE Chi-restraints excluded: chain VA residue 386 VAL Chi-restraints excluded: chain VA residue 389 GLN Chi-restraints excluded: chain VA residue 402 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 904 optimal weight: 4.9990 chunk 952 optimal weight: 0.0170 chunk 869 optimal weight: 1.9990 chunk 926 optimal weight: 7.9990 chunk 557 optimal weight: 3.9990 chunk 403 optimal weight: 9.9990 chunk 727 optimal weight: 8.9990 chunk 284 optimal weight: 20.0000 chunk 837 optimal weight: 1.9990 chunk 876 optimal weight: 9.9990 chunk 923 optimal weight: 3.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN C 186 ASN C 444 GLN G 186 ASN G 389 GLN I 186 ASN I 389 GLN I 444 GLN M 186 ASN M 389 GLN M 444 GLN S 53 GLN S 444 GLN V 186 ASN V 444 GLN BA 186 ASN BA 444 GLN DA 209 ASN HA 186 ASN NA 186 ASN NA 444 GLN PA 389 GLN PA 444 GLN TA 186 ASN TA 444 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 84864 Z= 0.202 Angle : 0.567 14.513 115344 Z= 0.285 Chirality : 0.044 0.242 13008 Planarity : 0.004 0.065 14808 Dihedral : 6.564 57.640 12534 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.01 % Allowed : 19.59 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.08), residues: 10752 helix: 0.32 (0.09), residues: 3336 sheet: -0.57 (0.11), residues: 2136 loop : -1.59 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 258 HIS 0.009 0.001 HISFA 164 PHE 0.019 0.002 PHE V 183 TYR 0.014 0.002 TYR M 382 ARG 0.008 0.000 ARGLA 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 922 time to evaluate : 7.310 Fit side-chains revert: symmetry clash REVERT: JA 275 ARG cc_start: 0.5556 (OUTLIER) cc_final: 0.5000 (mtp180) REVERT: JA 345 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7264 (tp) REVERT: JA 389 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7134 (tp-100) REVERT: A 73 MET cc_start: 0.4544 (mpm) cc_final: 0.2792 (mtm) REVERT: A 84 MET cc_start: 0.4402 (OUTLIER) cc_final: 0.3946 (mmm) REVERT: A 85 ARG cc_start: 0.3713 (mtt-85) cc_final: 0.3346 (ttp-170) REVERT: A 345 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7056 (tp) REVERT: A 389 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7004 (tp-100) REVERT: C 314 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8003 (ttt) REVERT: C 389 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7358 (tp-100) REVERT: C 402 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6805 (mtp) REVERT: E 184 MET cc_start: 0.8266 (mmm) cc_final: 0.7829 (tpp) REVERT: E 275 ARG cc_start: 0.5421 (mtm110) cc_final: 0.4934 (mtp180) REVERT: E 345 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7182 (tp) REVERT: E 389 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7329 (tp-100) REVERT: G 36 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6331 (p0) REVERT: G 49 LYS cc_start: 0.6481 (mmmm) cc_final: 0.6190 (mmtm) REVERT: G 84 MET cc_start: 0.4701 (OUTLIER) cc_final: 0.4162 (mmm) REVERT: G 389 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7066 (tp-100) REVERT: I 345 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7253 (tp) REVERT: I 389 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.6363 (tm130) REVERT: I 402 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6984 (mtp) REVERT: K 184 MET cc_start: 0.8080 (mmm) cc_final: 0.7601 (tpp) REVERT: K 240 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7538 (mm) REVERT: K 345 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7246 (tp) REVERT: K 389 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7018 (tp-100) REVERT: M 49 LYS cc_start: 0.6497 (mmmm) cc_final: 0.6192 (mmtm) REVERT: M 123 MET cc_start: 0.4535 (tpp) cc_final: 0.3854 (mpp) REVERT: M 345 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7104 (tp) REVERT: M 389 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: O 345 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7131 (tp) REVERT: O 396 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7856 (tmtt) REVERT: Q 85 ARG cc_start: 0.4061 (mtt-85) cc_final: 0.3792 (ttp-170) REVERT: Q 292 MET cc_start: 0.6646 (mpp) cc_final: 0.6270 (mmt) REVERT: Q 345 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7254 (tp) REVERT: Q 389 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.6887 (mm-40) REVERT: S 72 MET cc_start: 0.3678 (mmt) cc_final: 0.3466 (mmt) REVERT: S 84 MET cc_start: 0.4579 (OUTLIER) cc_final: 0.4049 (mmm) REVERT: S 345 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7032 (tp) REVERT: S 389 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7145 (tp-100) REVERT: V 84 MET cc_start: 0.4397 (mmm) cc_final: 0.3677 (mmt) REVERT: V 345 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7182 (tp) REVERT: V 402 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6932 (mtp) REVERT: X 184 MET cc_start: 0.8262 (mmm) cc_final: 0.7560 (tpp) REVERT: X 275 ARG cc_start: 0.5448 (OUTLIER) cc_final: 0.4914 (mtp180) REVERT: X 345 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7175 (tp) REVERT: X 389 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6998 (tp-100) REVERT: X 441 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6911 (mt0) REVERT: Z 123 MET cc_start: 0.4633 (tpp) cc_final: 0.4016 (mpp) REVERT: Z 389 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7197 (tp-100) REVERT: BA 345 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7229 (tp) REVERT: BA 402 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6848 (mtp) REVERT: DA 184 MET cc_start: 0.8206 (mmm) cc_final: 0.7775 (tpp) REVERT: DA 345 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7126 (tp) REVERT: DA 389 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7150 (tp-100) REVERT: FA 123 MET cc_start: 0.4552 (tpp) cc_final: 0.3847 (mpp) REVERT: FA 345 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7041 (tp) REVERT: FA 389 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7080 (tp-100) REVERT: HA 345 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7217 (tp) REVERT: HA 389 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7226 (tp-100) REVERT: HA 402 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6893 (mtt) REVERT: LA 184 MET cc_start: 0.8308 (mmm) cc_final: 0.7884 (tpp) REVERT: LA 240 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7577 (mm) REVERT: LA 389 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6967 (mm-40) REVERT: LA 444 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.6150 (tt0) REVERT: NA 84 MET cc_start: 0.4581 (OUTLIER) cc_final: 0.4020 (mmm) REVERT: NA 123 MET cc_start: 0.4488 (tpp) cc_final: 0.3852 (mpp) REVERT: NA 275 ARG cc_start: 0.5436 (OUTLIER) cc_final: 0.4829 (mtp180) REVERT: NA 389 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7191 (tp-100) REVERT: PA 345 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7124 (tp) REVERT: PA 389 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7325 (tp-100) REVERT: PA 396 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7742 (tmtt) REVERT: PA 402 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6850 (mtp) REVERT: RA 116 ILE cc_start: 0.3711 (OUTLIER) cc_final: 0.3466 (mm) REVERT: RA 184 MET cc_start: 0.8234 (mmm) cc_final: 0.7814 (tpp) REVERT: RA 275 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.4918 (mtp180) REVERT: RA 345 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7228 (tp) REVERT: RA 389 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6913 (mm-40) REVERT: TA 84 MET cc_start: 0.4733 (OUTLIER) cc_final: 0.4237 (mmm) REVERT: TA 275 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.4904 (mtp180) REVERT: TA 389 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7159 (tp-100) REVERT: VA 345 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7082 (tp) REVERT: VA 389 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7375 (tp-100) REVERT: VA 402 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6828 (mtp) outliers start: 213 outliers final: 118 residues processed: 1044 average time/residue: 1.4485 time to fit residues: 2131.6590 Evaluate side-chains 1096 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 914 time to evaluate : 7.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain JA residue 156 VAL Chi-restraints excluded: chain JA residue 226 SER Chi-restraints excluded: chain JA residue 232 LYS Chi-restraints excluded: chain JA residue 255 LEU Chi-restraints excluded: chain JA residue 275 ARG Chi-restraints excluded: chain JA residue 345 ILE Chi-restraints excluded: chain JA residue 384 ILE Chi-restraints excluded: chain JA residue 389 GLN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 424 LYS Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 389 GLN Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 226 SER Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 396 LYS Chi-restraints excluded: chain O residue 424 LYS Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 389 GLN Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain S residue 63 ASP Chi-restraints excluded: chain S residue 84 MET Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain S residue 386 VAL Chi-restraints excluded: chain S residue 389 GLN Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 384 ILE Chi-restraints excluded: chain V residue 386 VAL Chi-restraints excluded: chain V residue 402 MET Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 275 ARG Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 389 GLN Chi-restraints excluded: chain X residue 441 GLN Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 386 VAL Chi-restraints excluded: chain BA residue 63 ASP Chi-restraints excluded: chain BA residue 112 ILE Chi-restraints excluded: chain BA residue 345 ILE Chi-restraints excluded: chain BA residue 386 VAL Chi-restraints excluded: chain BA residue 402 MET Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 93 LEU Chi-restraints excluded: chain DA residue 112 ILE Chi-restraints excluded: chain DA residue 156 VAL Chi-restraints excluded: chain DA residue 226 SER Chi-restraints excluded: chain DA residue 291 THR Chi-restraints excluded: chain DA residue 345 ILE Chi-restraints excluded: chain DA residue 389 GLN Chi-restraints excluded: chain FA residue 53 GLN Chi-restraints excluded: chain FA residue 63 ASP Chi-restraints excluded: chain FA residue 93 LEU Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain FA residue 313 LEU Chi-restraints excluded: chain FA residue 345 ILE Chi-restraints excluded: chain FA residue 386 VAL Chi-restraints excluded: chain FA residue 389 GLN Chi-restraints excluded: chain HA residue 63 ASP Chi-restraints excluded: chain HA residue 226 SER Chi-restraints excluded: chain HA residue 345 ILE Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain HA residue 389 GLN Chi-restraints excluded: chain HA residue 402 MET Chi-restraints excluded: chain LA residue 53 GLN Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 146 ASP Chi-restraints excluded: chain LA residue 156 VAL Chi-restraints excluded: chain LA residue 226 SER Chi-restraints excluded: chain LA residue 240 LEU Chi-restraints excluded: chain LA residue 384 ILE Chi-restraints excluded: chain LA residue 389 GLN Chi-restraints excluded: chain LA residue 444 GLN Chi-restraints excluded: chain NA residue 53 GLN Chi-restraints excluded: chain NA residue 63 ASP Chi-restraints excluded: chain NA residue 84 MET Chi-restraints excluded: chain NA residue 93 LEU Chi-restraints excluded: chain NA residue 156 VAL Chi-restraints excluded: chain NA residue 275 ARG Chi-restraints excluded: chain NA residue 386 VAL Chi-restraints excluded: chain NA residue 389 GLN Chi-restraints excluded: chain PA residue 63 ASP Chi-restraints excluded: chain PA residue 112 ILE Chi-restraints excluded: chain PA residue 123 MET Chi-restraints excluded: chain PA residue 226 SER Chi-restraints excluded: chain PA residue 291 THR Chi-restraints excluded: chain PA residue 345 ILE Chi-restraints excluded: chain PA residue 384 ILE Chi-restraints excluded: chain PA residue 386 VAL Chi-restraints excluded: chain PA residue 389 GLN Chi-restraints excluded: chain PA residue 396 LYS Chi-restraints excluded: chain PA residue 402 MET Chi-restraints excluded: chain RA residue 53 GLN Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 116 ILE Chi-restraints excluded: chain RA residue 156 VAL Chi-restraints excluded: chain RA residue 226 SER Chi-restraints excluded: chain RA residue 232 LYS Chi-restraints excluded: chain RA residue 255 LEU Chi-restraints excluded: chain RA residue 275 ARG Chi-restraints excluded: chain RA residue 300 THR Chi-restraints excluded: chain RA residue 345 ILE Chi-restraints excluded: chain RA residue 384 ILE Chi-restraints excluded: chain RA residue 389 GLN Chi-restraints excluded: chain TA residue 63 ASP Chi-restraints excluded: chain TA residue 84 MET Chi-restraints excluded: chain TA residue 275 ARG Chi-restraints excluded: chain TA residue 386 VAL Chi-restraints excluded: chain TA residue 389 GLN Chi-restraints excluded: chain TA residue 402 MET Chi-restraints excluded: chain VA residue 63 ASP Chi-restraints excluded: chain VA residue 112 ILE Chi-restraints excluded: chain VA residue 226 SER Chi-restraints excluded: chain VA residue 345 ILE Chi-restraints excluded: chain VA residue 386 VAL Chi-restraints excluded: chain VA residue 389 GLN Chi-restraints excluded: chain VA residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 608 optimal weight: 0.0770 chunk 980 optimal weight: 4.9990 chunk 598 optimal weight: 5.9990 chunk 464 optimal weight: 6.9990 chunk 681 optimal weight: 0.5980 chunk 1028 optimal weight: 20.0000 chunk 946 optimal weight: 30.0000 chunk 818 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 632 optimal weight: 5.9990 chunk 502 optimal weight: 0.9990 overall best weight: 2.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN C 186 ASN G 186 ASN G 389 GLN I 186 ASN I 444 GLN M 186 ASN M 389 GLN S 53 GLN V 186 ASN BA 186 ASN BA 444 GLN HA 186 ASN NA 186 ASN ** NA 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 186 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 84864 Z= 0.222 Angle : 0.712 59.118 115344 Z= 0.388 Chirality : 0.046 0.857 13008 Planarity : 0.005 0.142 14808 Dihedral : 6.562 57.613 12534 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.79 % Allowed : 19.85 % Favored : 77.36 % Cbeta Deviations : 0.04 % 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: -1.17 (0.08), residues: 10752 helix: 0.32 (0.09), residues: 3336 sheet: -0.56 (0.11), residues: 2136 loop : -1.59 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 258 HIS 0.008 0.001 HISFA 164 PHE 0.019 0.002 PHE V 183 TYR 0.013 0.002 TYRBA 382 ARG 0.008 0.000 ARGLA 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21504 Ramachandran restraints generated. 10752 Oldfield, 0 Emsley, 10752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 912 time to evaluate : 7.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: JA 275 ARG cc_start: 0.5556 (OUTLIER) cc_final: 0.5001 (mtp180) REVERT: JA 345 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7264 (tp) REVERT: JA 389 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7136 (tp-100) REVERT: A 73 MET cc_start: 0.4567 (mpm) cc_final: 0.2793 (mtm) REVERT: A 84 MET cc_start: 0.4398 (OUTLIER) cc_final: 0.3944 (mmm) REVERT: A 85 ARG cc_start: 0.3711 (mtt-85) cc_final: 0.3350 (ttp-170) REVERT: A 345 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7057 (tp) REVERT: A 389 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7006 (tp-100) REVERT: C 314 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8003 (ttt) REVERT: C 389 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7359 (tp-100) REVERT: C 402 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6804 (mtp) REVERT: E 184 MET cc_start: 0.8266 (mmm) cc_final: 0.7828 (tpp) REVERT: E 345 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7182 (tp) REVERT: E 389 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7329 (tp-100) REVERT: G 36 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6329 (p0) REVERT: G 49 LYS cc_start: 0.6488 (mmmm) cc_final: 0.6191 (mmtm) REVERT: G 84 MET cc_start: 0.4700 (OUTLIER) cc_final: 0.4166 (mmm) REVERT: I 345 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7228 (tp) REVERT: I 396 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7866 (tmtt) REVERT: I 402 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6988 (mtp) REVERT: K 184 MET cc_start: 0.8098 (mmm) cc_final: 0.7626 (tpp) REVERT: K 240 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7539 (mm) REVERT: K 314 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.6979 (tpt) REVERT: K 345 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7245 (tp) REVERT: K 389 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7018 (tp-100) REVERT: M 49 LYS cc_start: 0.6499 (mmmm) cc_final: 0.6191 (mmtm) REVERT: M 123 MET cc_start: 0.4538 (tpp) cc_final: 0.3856 (mpp) REVERT: M 345 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7079 (tp) REVERT: O 345 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7122 (tp) REVERT: O 396 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7851 (tmtt) REVERT: Q 85 ARG cc_start: 0.4062 (mtt-85) cc_final: 0.3792 (ttp-170) REVERT: Q 292 MET cc_start: 0.6646 (mpp) cc_final: 0.6277 (mmt) REVERT: Q 345 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7256 (tp) REVERT: Q 389 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6888 (mm-40) REVERT: S 72 MET cc_start: 0.3678 (mmt) cc_final: 0.3473 (mmt) REVERT: S 84 MET cc_start: 0.4579 (OUTLIER) cc_final: 0.4048 (mmm) REVERT: S 345 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7032 (tp) REVERT: S 389 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7146 (tp-100) REVERT: V 84 MET cc_start: 0.4418 (mmm) cc_final: 0.3710 (mmt) REVERT: V 345 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7182 (tp) REVERT: V 402 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6932 (mtp) REVERT: X 184 MET cc_start: 0.8261 (mmm) cc_final: 0.7558 (tpp) REVERT: X 275 ARG cc_start: 0.5449 (OUTLIER) cc_final: 0.4914 (mtp180) REVERT: X 345 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7172 (tp) REVERT: X 389 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7005 (tp-100) REVERT: X 441 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6922 (mt0) REVERT: Z 123 MET cc_start: 0.4633 (tpp) cc_final: 0.4016 (mpp) REVERT: Z 389 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7205 (tp-100) REVERT: BA 345 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7228 (tp) REVERT: BA 402 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6849 (mtp) REVERT: DA 184 MET cc_start: 0.8206 (mmm) cc_final: 0.7775 (tpp) REVERT: DA 345 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7127 (tp) REVERT: DA 389 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7149 (tp-100) REVERT: FA 123 MET cc_start: 0.4554 (tpp) cc_final: 0.3848 (mpp) REVERT: FA 345 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7040 (tp) REVERT: FA 389 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7080 (tp-100) REVERT: HA 345 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7219 (tp) REVERT: HA 389 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7226 (tp-100) REVERT: HA 402 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6892 (mtt) REVERT: LA 184 MET cc_start: 0.8307 (mmm) cc_final: 0.7883 (tpp) REVERT: LA 240 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7577 (mm) REVERT: LA 389 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6970 (mm-40) REVERT: LA 444 GLN cc_start: 0.6491 (OUTLIER) cc_final: 0.6151 (tt0) REVERT: NA 84 MET cc_start: 0.4615 (OUTLIER) cc_final: 0.4066 (mmm) REVERT: NA 123 MET cc_start: 0.4488 (tpp) cc_final: 0.3852 (mpp) REVERT: NA 275 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.4828 (mtp180) REVERT: NA 345 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7079 (tp) REVERT: NA 389 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7217 (tp-100) REVERT: PA 345 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7130 (tp) REVERT: PA 389 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7626 (tp40) REVERT: PA 396 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7733 (tmtt) REVERT: PA 402 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6854 (mtp) REVERT: RA 116 ILE cc_start: 0.3711 (OUTLIER) cc_final: 0.3468 (mm) REVERT: RA 184 MET cc_start: 0.8235 (mmm) cc_final: 0.7813 (tpp) REVERT: RA 275 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.4918 (mtp180) REVERT: RA 345 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7217 (tp) REVERT: RA 389 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6911 (mm-40) REVERT: TA 84 MET cc_start: 0.4722 (OUTLIER) cc_final: 0.4237 (mmm) REVERT: TA 275 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.4904 (mtp180) REVERT: TA 389 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7160 (tp-100) REVERT: VA 345 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7082 (tp) REVERT: VA 389 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7375 (tp-100) REVERT: VA 402 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6828 (mtp) outliers start: 193 outliers final: 120 residues processed: 1029 average time/residue: 1.4202 time to fit residues: 2064.2808 Evaluate side-chains 1093 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 909 time to evaluate : 7.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 63 ASP Chi-restraints excluded: chain JA residue 112 ILE Chi-restraints excluded: chain JA residue 156 VAL Chi-restraints excluded: chain JA residue 226 SER Chi-restraints excluded: chain JA residue 232 LYS Chi-restraints excluded: chain JA residue 275 ARG Chi-restraints excluded: chain JA residue 345 ILE Chi-restraints excluded: chain JA residue 384 ILE Chi-restraints excluded: chain JA residue 389 GLN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 396 LYS Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 424 LYS Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 314 MET Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 226 SER Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 396 LYS Chi-restraints excluded: chain O residue 424 LYS Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 389 GLN Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain S residue 63 ASP Chi-restraints excluded: chain S residue 84 MET Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain S residue 386 VAL Chi-restraints excluded: chain S residue 389 GLN Chi-restraints excluded: chain V residue 53 GLN Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 384 ILE Chi-restraints excluded: chain V residue 386 VAL Chi-restraints excluded: chain V residue 402 MET Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 275 ARG Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 389 GLN Chi-restraints excluded: chain X residue 441 GLN Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 386 VAL Chi-restraints excluded: chain BA residue 63 ASP Chi-restraints excluded: chain BA residue 112 ILE Chi-restraints excluded: chain BA residue 345 ILE Chi-restraints excluded: chain BA residue 386 VAL Chi-restraints excluded: chain BA residue 402 MET Chi-restraints excluded: chain DA residue 63 ASP Chi-restraints excluded: chain DA residue 93 LEU Chi-restraints excluded: chain DA residue 112 ILE Chi-restraints excluded: chain DA residue 156 VAL Chi-restraints excluded: chain DA residue 226 SER Chi-restraints excluded: chain DA residue 291 THR Chi-restraints excluded: chain DA residue 300 THR Chi-restraints excluded: chain DA residue 345 ILE Chi-restraints excluded: chain DA residue 389 GLN Chi-restraints excluded: chain FA residue 53 GLN Chi-restraints excluded: chain FA residue 63 ASP Chi-restraints excluded: chain FA residue 93 LEU Chi-restraints excluded: chain FA residue 291 THR Chi-restraints excluded: chain FA residue 313 LEU Chi-restraints excluded: chain FA residue 345 ILE Chi-restraints excluded: chain FA residue 386 VAL Chi-restraints excluded: chain FA residue 389 GLN Chi-restraints excluded: chain HA residue 63 ASP Chi-restraints excluded: chain HA residue 226 SER Chi-restraints excluded: chain HA residue 345 ILE Chi-restraints excluded: chain HA residue 386 VAL Chi-restraints excluded: chain HA residue 389 GLN Chi-restraints excluded: chain HA residue 402 MET Chi-restraints excluded: chain LA residue 53 GLN Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 146 ASP Chi-restraints excluded: chain LA residue 156 VAL Chi-restraints excluded: chain LA residue 226 SER Chi-restraints excluded: chain LA residue 240 LEU Chi-restraints excluded: chain LA residue 384 ILE Chi-restraints excluded: chain LA residue 389 GLN Chi-restraints excluded: chain LA residue 444 GLN Chi-restraints excluded: chain NA residue 53 GLN Chi-restraints excluded: chain NA residue 63 ASP Chi-restraints excluded: chain NA residue 84 MET Chi-restraints excluded: chain NA residue 93 LEU Chi-restraints excluded: chain NA residue 156 VAL Chi-restraints excluded: chain NA residue 275 ARG Chi-restraints excluded: chain NA residue 345 ILE Chi-restraints excluded: chain NA residue 386 VAL Chi-restraints excluded: chain NA residue 389 GLN Chi-restraints excluded: chain PA residue 63 ASP Chi-restraints excluded: chain PA residue 112 ILE Chi-restraints excluded: chain PA residue 123 MET Chi-restraints excluded: chain PA residue 226 SER Chi-restraints excluded: chain PA residue 291 THR Chi-restraints excluded: chain PA residue 345 ILE Chi-restraints excluded: chain PA residue 384 ILE Chi-restraints excluded: chain PA residue 386 VAL Chi-restraints excluded: chain PA residue 389 GLN Chi-restraints excluded: chain PA residue 396 LYS Chi-restraints excluded: chain PA residue 402 MET Chi-restraints excluded: chain RA residue 53 GLN Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain RA residue 112 ILE Chi-restraints excluded: chain RA residue 116 ILE Chi-restraints excluded: chain RA residue 156 VAL Chi-restraints excluded: chain RA residue 226 SER Chi-restraints excluded: chain RA residue 232 LYS Chi-restraints excluded: chain RA residue 255 LEU Chi-restraints excluded: chain RA residue 275 ARG Chi-restraints excluded: chain RA residue 300 THR Chi-restraints excluded: chain RA residue 345 ILE Chi-restraints excluded: chain RA residue 384 ILE Chi-restraints excluded: chain RA residue 389 GLN Chi-restraints excluded: chain TA residue 63 ASP Chi-restraints excluded: chain TA residue 84 MET Chi-restraints excluded: chain TA residue 275 ARG Chi-restraints excluded: chain TA residue 386 VAL Chi-restraints excluded: chain TA residue 389 GLN Chi-restraints excluded: chain TA residue 402 MET Chi-restraints excluded: chain VA residue 63 ASP Chi-restraints excluded: chain VA residue 112 ILE Chi-restraints excluded: chain VA residue 226 SER Chi-restraints excluded: chain VA residue 300 THR Chi-restraints excluded: chain VA residue 345 ILE Chi-restraints excluded: chain VA residue 386 VAL Chi-restraints excluded: chain VA residue 389 GLN Chi-restraints excluded: chain VA residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 650 optimal weight: 3.9990 chunk 872 optimal weight: 0.0050 chunk 250 optimal weight: 0.9990 chunk 754 optimal weight: 9.9990 chunk 120 optimal weight: 0.0370 chunk 227 optimal weight: 6.9990 chunk 820 optimal weight: 5.9990 chunk 343 optimal weight: 0.9980 chunk 842 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 overall best weight: 1.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN C 186 ASN G 186 ASN G 389 GLN I 186 ASN I 444 GLN M 186 ASN M 389 GLN S 53 GLN V 186 ASN BA 186 ASN BA 444 GLN HA 186 ASN NA 186 ASN PA 389 GLN TA 186 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.198453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.159602 restraints weight = 562550.953| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 7.95 r_work: 0.3369 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 84864 Z= 0.165 Angle : 0.546 14.538 115344 Z= 0.274 Chirality : 0.043 0.284 13008 Planarity : 0.004 0.041 14808 Dihedral : 6.405 55.649 12534 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.63 % Allowed : 20.02 % Favored : 77.35 % 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: -1.10 (0.08), residues: 10752 helix: 0.35 (0.09), residues: 3336 sheet: -0.51 (0.11), residues: 2136 loop : -1.54 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPJA 258 HIS 0.009 0.001 HIS Z 79 PHE 0.022 0.002 PHE I 391 TYR 0.013 0.001 TYR S 382 ARG 0.008 0.000 ARGLA 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30050.86 seconds wall clock time: 528 minutes 9.00 seconds (31689.00 seconds total)