Starting phenix.real_space_refine on Fri Feb 23 11:46:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxj_11522/02_2024/6zxj_11522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxj_11522/02_2024/6zxj_11522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxj_11522/02_2024/6zxj_11522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxj_11522/02_2024/6zxj_11522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxj_11522/02_2024/6zxj_11522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxj_11522/02_2024/6zxj_11522.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 24017 2.51 5 N 6635 2.21 5 O 7554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B ASP 512": "OD1" <-> "OD2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 546": "OD1" <-> "OD2" Residue "B PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 512": "OD1" <-> "OD2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C ASP 546": "OD1" <-> "OD2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 512": "OD1" <-> "OD2" Residue "D ASP 520": "OD1" <-> "OD2" Residue "D PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 535": "OE1" <-> "OE2" Residue "D ASP 546": "OD1" <-> "OD2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 568": "OE1" <-> "OE2" Residue "D ASP 634": "OD1" <-> "OD2" Residue "D TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 235": "OD1" <-> "OD2" Residue "E PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 497": "OD1" <-> "OD2" Residue "E ASP 512": "OD1" <-> "OD2" Residue "E ASP 520": "OD1" <-> "OD2" Residue "E PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 535": "OE1" <-> "OE2" Residue "E PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 579": "OD1" <-> "OD2" Residue "E ASP 593": "OD1" <-> "OD2" Residue "E TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 235": "OD1" <-> "OD2" Residue "F PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 486": "OE1" <-> "OE2" Residue "F ASP 512": "OD1" <-> "OD2" Residue "F PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 535": "OE1" <-> "OE2" Residue "F ASP 546": "OD1" <-> "OD2" Residue "F PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 235": "OD1" <-> "OD2" Residue "G PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 512": "OD1" <-> "OD2" Residue "G PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 535": "OE1" <-> "OE2" Residue "G ASP 546": "OD1" <-> "OD2" Residue "G PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 568": "OE1" <-> "OE2" Residue "G TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H ASP 136": "OD1" <-> "OD2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "H TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 257": "OE1" <-> "OE2" Residue "H ASP 328": "OD1" <-> "OD2" Residue "H GLU 372": "OE1" <-> "OE2" Residue "H ASP 415": "OD1" <-> "OD2" Residue "H TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 561": "OE1" <-> "OE2" Residue "H PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 613": "OD1" <-> "OD2" Residue "H TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 647": "OD1" <-> "OD2" Residue "H ARG 664": "NH1" <-> "NH2" Residue "H TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 706": "OD1" <-> "OD2" Residue "I TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 200": "OD1" <-> "OD2" Residue "I PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 215": "OE1" <-> "OE2" Residue "I PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 261": "OD1" <-> "OD2" Residue "I ARG 267": "NH1" <-> "NH2" Residue "I TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 415": "OD1" <-> "OD2" Residue "I PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38244 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3963 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3966 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3962 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3962 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "E" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3966 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "F" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3962 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3966 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "H" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5618 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 681} Chain breaks: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "I" Number of atoms: 4879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 4879 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 275} Link IDs: {'PTRANS': 18, 'TRANS': 691} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 987 Unresolved non-hydrogen angles: 1238 Unresolved non-hydrogen dihedrals: 807 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 18, 'TRP:plan': 1, 'ASP:plan': 26, 'PHE:plan': 10, 'GLU:plan': 37, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 558 Time building chain proxies: 18.53, per 1000 atoms: 0.48 Number of scatterers: 38244 At special positions: 0 Unit cell: (182.97, 179.76, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 7554 8.00 N 6635 7.00 C 24017 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: 16.84 Conformation dependent library (CDL) restraints added in 7.8 seconds 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9748 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 73 sheets defined 32.1% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.528A pdb=" N HIS A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 213' Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.556A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.903A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.847A pdb=" N THR A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.519A pdb=" N PHE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.618A pdb=" N LEU A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.546A pdb=" N ASP A 579 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 634 through 637 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.674A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.923A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 477 through 487 Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 512 through 517 removed outlier: 3.784A pdb=" N THR B 517 " --> pdb=" O PRO B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.655A pdb=" N LEU B 569 " --> pdb=" O GLN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 581 removed outlier: 4.478A pdb=" N ASP B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 634 through 637 removed outlier: 3.512A pdb=" N LYS B 637 " --> pdb=" O ASP B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.778A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.558A pdb=" N VAL C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.992A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 477 through 487 Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 512 through 517 removed outlier: 3.868A pdb=" N THR C 517 " --> pdb=" O PRO C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 531 Processing helix chain 'C' and resid 555 through 570 removed outlier: 3.666A pdb=" N LEU C 569 " --> pdb=" O GLN C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 581 removed outlier: 4.557A pdb=" N ASP C 579 " --> pdb=" O THR C 576 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 581 " --> pdb=" O LEU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 615 Processing helix chain 'C' and resid 634 through 637 Processing helix chain 'C' and resid 704 through 706 No H-bonds generated for 'chain 'C' and resid 704 through 706' Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.558A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.517A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.763A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 512 through 517 removed outlier: 3.853A pdb=" N THR D 517 " --> pdb=" O PRO D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 Processing helix chain 'D' and resid 555 through 570 removed outlier: 3.575A pdb=" N LEU D 569 " --> pdb=" O GLN D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 581 removed outlier: 4.447A pdb=" N ASP D 579 " --> pdb=" O THR D 576 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 615 Processing helix chain 'D' and resid 634 through 637 Processing helix chain 'D' and resid 704 through 706 No H-bonds generated for 'chain 'D' and resid 704 through 706' Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 213 removed outlier: 3.898A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.916A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 480 through 487 Processing helix chain 'E' and resid 512 through 517 removed outlier: 3.809A pdb=" N THR E 517 " --> pdb=" O PRO E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 531 removed outlier: 3.589A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 568 Processing helix chain 'E' and resid 576 through 581 removed outlier: 4.455A pdb=" N ASP E 579 " --> pdb=" O THR E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 615 Processing helix chain 'E' and resid 634 through 637 removed outlier: 3.501A pdb=" N LYS E 637 " --> pdb=" O ASP E 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 634 through 637' Processing helix chain 'E' and resid 704 through 706 No H-bonds generated for 'chain 'E' and resid 704 through 706' Processing helix chain 'E' and resid 732 through 734 No H-bonds generated for 'chain 'E' and resid 732 through 734' Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 213 removed outlier: 3.881A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.587A pdb=" N VAL F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.925A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 477 through 487 Proline residue: F 482 - end of helix Processing helix chain 'F' and resid 512 through 517 removed outlier: 3.753A pdb=" N THR F 517 " --> pdb=" O PRO F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 531 removed outlier: 3.513A pdb=" N PHE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 550 No H-bonds generated for 'chain 'F' and resid 548 through 550' Processing helix chain 'F' and resid 555 through 568 Processing helix chain 'F' and resid 576 through 581 removed outlier: 4.486A pdb=" N ASP F 579 " --> pdb=" O THR F 576 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 581 " --> pdb=" O LEU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 615 Processing helix chain 'F' and resid 634 through 637 Processing helix chain 'F' and resid 704 through 706 No H-bonds generated for 'chain 'F' and resid 704 through 706' Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 213 removed outlier: 3.892A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS G 213 " --> pdb=" O ASN G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.940A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 480 through 487 Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.833A pdb=" N THR G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 removed outlier: 3.649A pdb=" N GLY G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 570 removed outlier: 3.676A pdb=" N LEU G 569 " --> pdb=" O GLN G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 576 through 581 removed outlier: 4.629A pdb=" N ASP G 579 " --> pdb=" O THR G 576 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 615 Processing helix chain 'G' and resid 634 through 637 removed outlier: 3.529A pdb=" N LYS G 637 " --> pdb=" O ASP G 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 634 through 637' Processing helix chain 'G' and resid 704 through 706 No H-bonds generated for 'chain 'G' and resid 704 through 706' Processing helix chain 'G' and resid 732 through 734 No H-bonds generated for 'chain 'G' and resid 732 through 734' Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 69 through 77 removed outlier: 4.347A pdb=" N MET H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 99 through 103 removed outlier: 3.599A pdb=" N LYS H 103 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 159 removed outlier: 4.125A pdb=" N ASN H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'H' and resid 168 through 179 removed outlier: 3.897A pdb=" N VAL H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.539A pdb=" N LYS H 195 " --> pdb=" O THR H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 Processing helix chain 'H' and resid 210 through 226 Processing helix chain 'H' and resid 229 through 237 Processing helix chain 'H' and resid 237 through 248 Processing helix chain 'H' and resid 250 through 261 removed outlier: 3.690A pdb=" N LEU H 254 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU H 256 " --> pdb=" O ILE H 252 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU H 257 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 278 removed outlier: 3.536A pdb=" N GLN H 276 " --> pdb=" O GLU H 272 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR H 278 " --> pdb=" O ILE H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 284 Processing helix chain 'H' and resid 286 through 298 removed outlier: 3.601A pdb=" N GLN H 297 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE H 298 " --> pdb=" O LYS H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.620A pdb=" N ILE H 307 " --> pdb=" O LYS H 303 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 321 removed outlier: 4.085A pdb=" N GLU H 317 " --> pdb=" O GLN H 313 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 327 removed outlier: 5.562A pdb=" N ASP H 325 " --> pdb=" O ILE H 322 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER H 326 " --> pdb=" O GLN H 323 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER H 327 " --> pdb=" O ILE H 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 322 through 327' Processing helix chain 'H' and resid 331 through 342 Processing helix chain 'H' and resid 343 through 345 No H-bonds generated for 'chain 'H' and resid 343 through 345' Processing helix chain 'H' and resid 371 through 381 removed outlier: 4.017A pdb=" N PHE H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU H 381 " --> pdb=" O LYS H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 Processing helix chain 'H' and resid 405 through 423 Processing helix chain 'H' and resid 442 through 446 Processing helix chain 'H' and resid 447 through 452 removed outlier: 3.612A pdb=" N ALA H 452 " --> pdb=" O ALA H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 474 removed outlier: 3.516A pdb=" N GLU H 470 " --> pdb=" O GLY H 466 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN H 474 " --> pdb=" O GLU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 575 removed outlier: 3.796A pdb=" N ILE H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS H 558 " --> pdb=" O LYS H 554 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS H 572 " --> pdb=" O GLN H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 591 through 608 removed outlier: 3.532A pdb=" N ILE H 595 " --> pdb=" O TYR H 591 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR H 600 " --> pdb=" O VAL H 596 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU H 601 " --> pdb=" O GLU H 597 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 624 Processing helix chain 'H' and resid 635 through 639 Processing helix chain 'H' and resid 640 through 647 removed outlier: 3.586A pdb=" N THR H 644 " --> pdb=" O ALA H 640 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS H 645 " --> pdb=" O GLU H 641 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN H 646 " --> pdb=" O GLN H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 679 through 701 removed outlier: 3.760A pdb=" N GLY H 683 " --> pdb=" O ASN H 679 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS H 690 " --> pdb=" O HIS H 686 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA H 691 " --> pdb=" O GLU H 687 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU H 700 " --> pdb=" O ALA H 696 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP H 701 " --> pdb=" O GLY H 697 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 721 removed outlier: 3.980A pdb=" N ASP H 716 " --> pdb=" O LYS H 712 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE H 717 " --> pdb=" O LYS H 713 " (cutoff:3.500A) Processing helix chain 'H' and resid 728 through 731 Processing helix chain 'H' and resid 732 through 745 Processing helix chain 'H' and resid 748 through 759 removed outlier: 3.533A pdb=" N ARG H 752 " --> pdb=" O ASP H 748 " (cutoff:3.500A) Processing helix chain 'H' and resid 759 through 770 removed outlier: 3.630A pdb=" N GLN H 764 " --> pdb=" O PRO H 760 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 44 removed outlier: 3.947A pdb=" N LYS I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 38 " --> pdb=" O GLU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 65 removed outlier: 3.751A pdb=" N LYS I 56 " --> pdb=" O GLU I 52 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.836A pdb=" N LEU I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.138A pdb=" N ALA I 96 " --> pdb=" O ILE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 158 removed outlier: 3.633A pdb=" N ASN I 146 " --> pdb=" O GLU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 163 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.587A pdb=" N ASN I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 193 through 197 removed outlier: 3.595A pdb=" N GLU I 196 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 209 removed outlier: 3.599A pdb=" N LEU I 206 " --> pdb=" O SER I 202 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU I 207 " --> pdb=" O VAL I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 removed outlier: 3.544A pdb=" N GLN I 214 " --> pdb=" O SER I 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 237 removed outlier: 4.269A pdb=" N ASP I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 251 Processing helix chain 'I' and resid 252 through 261 Processing helix chain 'I' and resid 263 through 285 removed outlier: 4.547A pdb=" N HIS I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP I 281 " --> pdb=" O HIS I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 298 Processing helix chain 'I' and resid 303 through 312 removed outlier: 3.900A pdb=" N SER I 312 " --> pdb=" O ILE I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 321 removed outlier: 4.136A pdb=" N GLU I 317 " --> pdb=" O GLN I 313 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 327 removed outlier: 3.849A pdb=" N SER I 327 " --> pdb=" O ILE I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 338 Processing helix chain 'I' and resid 372 through 383 removed outlier: 3.863A pdb=" N LEU I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 381 " --> pdb=" O LYS I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 396 Processing helix chain 'I' and resid 405 through 421 Processing helix chain 'I' and resid 444 through 446 No H-bonds generated for 'chain 'I' and resid 444 through 446' Processing helix chain 'I' and resid 447 through 452 removed outlier: 3.677A pdb=" N ALA I 452 " --> pdb=" O ALA I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 473 Processing helix chain 'I' and resid 551 through 574 removed outlier: 3.507A pdb=" N ILE I 555 " --> pdb=" O PRO I 551 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS I 572 " --> pdb=" O GLN I 568 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU I 574 " --> pdb=" O TRP I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 591 through 610 removed outlier: 3.924A pdb=" N TYR I 600 " --> pdb=" O VAL I 596 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU I 601 " --> pdb=" O GLU I 597 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 624 Processing helix chain 'I' and resid 635 through 640 removed outlier: 4.831A pdb=" N ALA I 640 " --> pdb=" O LEU I 636 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 646 Processing helix chain 'I' and resid 648 through 652 Processing helix chain 'I' and resid 679 through 699 removed outlier: 3.599A pdb=" N GLY I 683 " --> pdb=" O ASN I 679 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS I 690 " --> pdb=" O HIS I 686 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 691 " --> pdb=" O GLU I 687 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 721 removed outlier: 4.224A pdb=" N LYS I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS I 713 " --> pdb=" O THR I 709 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP I 716 " --> pdb=" O LYS I 712 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE I 717 " --> pdb=" O LYS I 713 " (cutoff:3.500A) Processing helix chain 'I' and resid 722 through 725 removed outlier: 3.717A pdb=" N LEU I 725 " --> pdb=" O GLY I 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 722 through 725' Processing helix chain 'I' and resid 728 through 731 Processing helix chain 'I' and resid 732 through 745 Processing helix chain 'I' and resid 748 through 759 removed outlier: 3.549A pdb=" N ARG I 752 " --> pdb=" O ASP I 748 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL I 755 " --> pdb=" O GLU I 751 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN I 756 " --> pdb=" O ARG I 752 " (cutoff:3.500A) Processing helix chain 'I' and resid 759 through 772 removed outlier: 4.078A pdb=" N GLN I 764 " --> pdb=" O PRO I 760 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE I 765 " --> pdb=" O LYS I 761 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS I 771 " --> pdb=" O ASN I 767 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE I 772 " --> pdb=" O ASP I 768 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 394 removed outlier: 5.139A pdb=" N THR A 390 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 385 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 392 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 381 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 328 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 394 removed outlier: 5.139A pdb=" N THR A 390 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 385 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 392 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 381 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 328 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.135A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.647A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 598 Processing sheet with id=AA8, first strand: chain 'A' and resid 626 through 629 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.630A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 695 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 696 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 728 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 698 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.593A pdb=" N PHE B 202 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 389 through 394 removed outlier: 5.094A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 389 through 394 removed outlier: 5.094A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 458 through 462 removed outlier: 4.241A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 501 through 506 Processing sheet with id=AB6, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AB7, first strand: chain 'B' and resid 596 through 598 Processing sheet with id=AB8, first strand: chain 'B' and resid 628 through 629 Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.673A pdb=" N GLY B 641 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL B 696 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 728 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL B 698 " --> pdb=" O ILE B 726 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 192 through 197 Processing sheet with id=AC2, first strand: chain 'C' and resid 358 through 360 removed outlier: 6.870A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 389 through 394 removed outlier: 5.121A pdb=" N THR C 390 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 385 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 392 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR C 381 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU C 267 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR C 295 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP C 265 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ARG C 297 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N HIS C 263 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 458 through 462 removed outlier: 4.099A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.636A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AC7, first strand: chain 'C' and resid 596 through 598 removed outlier: 6.556A pdb=" N HIS C 597 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.646A pdb=" N GLY C 641 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL C 696 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 728 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 698 " --> pdb=" O ILE C 726 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 192 through 197 removed outlier: 3.556A pdb=" N PHE D 202 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 389 through 394 removed outlier: 5.085A pdb=" N THR D 390 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 392 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 381 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU D 267 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR D 295 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP D 265 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ARG D 297 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N HIS D 263 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 389 through 394 removed outlier: 5.085A pdb=" N THR D 390 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 392 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 381 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU D 267 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR D 295 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP D 265 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ARG D 297 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N HIS D 263 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 364 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 419 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 458 through 462 removed outlier: 4.131A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.725A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AD7, first strand: chain 'D' and resid 596 through 598 Processing sheet with id=AD8, first strand: chain 'D' and resid 628 through 629 Processing sheet with id=AD9, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.505A pdb=" N GLY D 641 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA D 700 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU D 725 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 192 through 197 Processing sheet with id=AE2, first strand: chain 'E' and resid 389 through 394 removed outlier: 5.015A pdb=" N THR E 390 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 385 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA E 392 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR E 381 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 389 through 394 removed outlier: 5.015A pdb=" N THR E 390 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 385 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA E 392 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR E 381 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 364 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 419 " --> pdb=" O ILE E 364 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 458 through 462 removed outlier: 4.087A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.677A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AE7, first strand: chain 'E' and resid 596 through 598 Processing sheet with id=AE8, first strand: chain 'E' and resid 626 through 629 removed outlier: 3.501A pdb=" N LEU E 627 " --> pdb=" O ILE E 676 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 654 through 655 removed outlier: 3.614A pdb=" N GLY E 641 " --> pdb=" O VAL E 701 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL E 696 " --> pdb=" O SER E 728 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 728 " --> pdb=" O VAL E 696 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL E 698 " --> pdb=" O ILE E 726 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 192 through 197 Processing sheet with id=AF2, first strand: chain 'F' and resid 389 through 394 removed outlier: 5.034A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR F 381 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN F 328 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU F 267 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR F 295 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP F 265 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ARG F 297 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N HIS F 263 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE F 269 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN F 361 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU F 271 " --> pdb=" O ARG F 359 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 359 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 389 through 394 removed outlier: 5.034A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR F 381 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN F 328 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU F 267 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR F 295 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP F 265 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ARG F 297 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N HIS F 263 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE F 269 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN F 361 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU F 271 " --> pdb=" O ARG F 359 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 359 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 458 through 462 removed outlier: 4.127A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.632A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AF7, first strand: chain 'F' and resid 596 through 598 Processing sheet with id=AF8, first strand: chain 'F' and resid 628 through 629 Processing sheet with id=AF9, first strand: chain 'F' and resid 654 through 655 removed outlier: 3.784A pdb=" N GLY F 641 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL F 696 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER F 728 " --> pdb=" O VAL F 696 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL F 698 " --> pdb=" O ILE F 726 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AG2, first strand: chain 'G' and resid 389 through 394 removed outlier: 5.054A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 389 through 394 removed outlier: 5.054A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 458 through 462 removed outlier: 4.267A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.628A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AG7, first strand: chain 'G' and resid 596 through 598 Processing sheet with id=AG8, first strand: chain 'G' and resid 628 through 629 Processing sheet with id=AG9, first strand: chain 'G' and resid 654 through 655 removed outlier: 3.572A pdb=" N GLY G 641 " --> pdb=" O VAL G 701 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS G 695 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL G 696 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER G 728 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL G 698 " --> pdb=" O ILE G 726 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 81 through 82 Processing sheet with id=AH2, first strand: chain 'H' and resid 436 through 441 removed outlier: 3.627A pdb=" N GLU H 439 " --> pdb=" O TRP H 501 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 436 through 441 removed outlier: 3.627A pdb=" N GLU H 439 " --> pdb=" O TRP H 501 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 485 through 486 Processing sheet with id=AH5, first strand: chain 'H' and resid 630 through 632 Processing sheet with id=AH6, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.567A pdb=" N ILE I 131 " --> pdb=" O TYR I 82 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 103 through 105 Processing sheet with id=AH8, first strand: chain 'I' and resid 436 through 442 removed outlier: 3.935A pdb=" N LEU I 437 " --> pdb=" O ILE I 503 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU I 499 " --> pdb=" O MET I 441 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG I 498 " --> pdb=" O ILE I 543 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE I 545 " --> pdb=" O ARG I 498 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS I 500 " --> pdb=" O ILE I 545 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA I 547 " --> pdb=" O LYS I 500 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG I 502 " --> pdb=" O ALA I 547 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL I 549 " --> pdb=" O ARG I 502 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLN I 504 " --> pdb=" O VAL I 549 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS I 540 " --> pdb=" O LYS I 536 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS I 536 " --> pdb=" O LYS I 540 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR I 542 " --> pdb=" O ILE I 534 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE I 534 " --> pdb=" O TYR I 542 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG I 544 " --> pdb=" O VAL I 532 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL I 532 " --> pdb=" O ARG I 544 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP I 546 " --> pdb=" O LYS I 530 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY I 526 " --> pdb=" O VAL I 550 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 485 through 487 Processing sheet with id=AI1, first strand: chain 'I' and resid 583 through 586 1510 hydrogen bonds defined for protein. 4164 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: 17.12 Time building geometry restraints manager: 17.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6726 1.28 - 1.41: 9230 1.41 - 1.55: 22820 1.55 - 1.68: 33 1.68 - 1.81: 76 Bond restraints: 38885 Sorted by residual: bond pdb=" CB THR C 517 " pdb=" CG2 THR C 517 " ideal model delta sigma weight residual 1.521 1.402 0.119 3.30e-02 9.18e+02 1.31e+01 bond pdb=" N VAL I 119 " pdb=" CA VAL I 119 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" CB ILE B 183 " pdb=" CG2 ILE B 183 " ideal model delta sigma weight residual 1.521 1.410 0.111 3.30e-02 9.18e+02 1.14e+01 bond pdb=" N VAL I 44 " pdb=" CA VAL I 44 " ideal model delta sigma weight residual 1.465 1.511 -0.046 1.38e-02 5.25e+03 1.13e+01 bond pdb=" CG1 ILE D 726 " pdb=" CD1 ILE D 726 " ideal model delta sigma weight residual 1.513 1.383 0.130 3.90e-02 6.57e+02 1.11e+01 ... (remaining 38880 not shown) Histogram of bond angle deviations from ideal: 94.17 - 102.19: 141 102.19 - 110.22: 10316 110.22 - 118.24: 19821 118.24 - 126.26: 22224 126.26 - 134.29: 420 Bond angle restraints: 52922 Sorted by residual: angle pdb=" N VAL I 44 " pdb=" CA VAL I 44 " pdb=" C VAL I 44 " ideal model delta sigma weight residual 106.55 118.78 -12.23 1.45e+00 4.76e-01 7.11e+01 angle pdb=" C ASN D 198 " pdb=" N LYS D 199 " pdb=" CA LYS D 199 " ideal model delta sigma weight residual 122.49 111.60 10.89 1.55e+00 4.16e-01 4.94e+01 angle pdb=" N LYS E 197 " pdb=" CA LYS E 197 " pdb=" C LYS E 197 " ideal model delta sigma weight residual 109.24 99.24 10.00 1.63e+00 3.76e-01 3.76e+01 angle pdb=" C VAL I 44 " pdb=" N LYS I 45 " pdb=" CA LYS I 45 " ideal model delta sigma weight residual 121.24 112.82 8.42 1.44e+00 4.82e-01 3.42e+01 angle pdb=" N GLU D 614 " pdb=" CA GLU D 614 " pdb=" CB GLU D 614 " ideal model delta sigma weight residual 110.22 118.88 -8.66 1.54e+00 4.22e-01 3.16e+01 ... (remaining 52917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 21983 18.06 - 36.13: 1358 36.13 - 54.19: 210 54.19 - 72.25: 40 72.25 - 90.31: 10 Dihedral angle restraints: 23601 sinusoidal: 8597 harmonic: 15004 Sorted by residual: dihedral pdb=" CA GLN H 165 " pdb=" C GLN H 165 " pdb=" N PRO H 166 " pdb=" CA PRO H 166 " ideal model delta harmonic sigma weight residual 0.00 37.35 -37.35 0 5.00e+00 4.00e-02 5.58e+01 dihedral pdb=" C VAL I 44 " pdb=" N VAL I 44 " pdb=" CA VAL I 44 " pdb=" CB VAL I 44 " ideal model delta harmonic sigma weight residual -122.00 -135.58 13.58 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" N VAL I 44 " pdb=" C VAL I 44 " pdb=" CA VAL I 44 " pdb=" CB VAL I 44 " ideal model delta harmonic sigma weight residual 123.40 135.48 -12.08 0 2.50e+00 1.60e-01 2.33e+01 ... (remaining 23598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4835 0.083 - 0.165: 1157 0.165 - 0.248: 178 0.248 - 0.330: 18 0.330 - 0.413: 2 Chirality restraints: 6190 Sorted by residual: chirality pdb=" CA VAL I 44 " pdb=" N VAL I 44 " pdb=" C VAL I 44 " pdb=" CB VAL I 44 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA LYS B 199 " pdb=" N LYS B 199 " pdb=" C LYS B 199 " pdb=" CB LYS B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA LYS C 199 " pdb=" N LYS C 199 " pdb=" C LYS C 199 " pdb=" CB LYS C 199 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 6187 not shown) Planarity restraints: 6947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 384 " -0.110 5.00e-02 4.00e+02 1.63e-01 4.24e+01 pdb=" N PRO I 385 " 0.281 5.00e-02 4.00e+02 pdb=" CA PRO I 385 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO I 385 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 513 " -0.033 2.00e-02 2.50e+03 3.90e-02 3.04e+01 pdb=" CG TYR I 513 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR I 513 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR I 513 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR I 513 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR I 513 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR I 513 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR I 513 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 44 " 0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C VAL I 44 " -0.074 2.00e-02 2.50e+03 pdb=" O VAL I 44 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS I 45 " 0.025 2.00e-02 2.50e+03 ... (remaining 6944 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 688 2.62 - 3.19: 38207 3.19 - 3.76: 55776 3.76 - 4.33: 76886 4.33 - 4.90: 123712 Nonbonded interactions: 295269 Sorted by model distance: nonbonded pdb=" OE1 GLU H 374 " pdb=" NZ LYS H 378 " model vdw 2.048 2.520 nonbonded pdb=" OD1 ASP A 599 " pdb=" N ARG A 600 " model vdw 2.090 2.520 nonbonded pdb=" O ASN F 209 " pdb=" NZ LYS F 213 " model vdw 2.107 2.520 nonbonded pdb=" OD1 ASP B 185 " pdb=" N SER B 186 " model vdw 2.118 2.520 nonbonded pdb=" OD2 ASP B 195 " pdb=" OH TYR H 236 " model vdw 2.120 2.440 ... (remaining 295264 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 175 through 722 or (resid 723 and (name N or name CA or na \ me C or name O or name CB )) or resid 724 through 734)) selection = (chain 'B' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 722 or (resid 723 and (name N \ or name CA or name C or name O or name CB )) or resid 724 through 734)) selection = (chain 'C' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 734)) selection = (chain 'D' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 734)) selection = (chain 'E' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 722 or (resid 723 and (name N \ or name CA or name C or name O or name CB )) or resid 724 through 734)) selection = (chain 'F' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 734)) selection = (chain 'G' and (resid 175 through 670 or (resid 671 and (name N or name CA or na \ me C or name O or name CB )) or resid 672 through 722 or (resid 723 and (name N \ or name CA or name C or name O or name CB )) or resid 724 through 734)) } ncs_group { reference = (chain 'H' and (resid 52 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 72 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )) or resid 74 through 79 or (r \ esid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thr \ ough 86 or (resid 87 through 90 and (name N or name CA or name C or name O or na \ me CB )) or resid 91 through 94 or (resid 95 through 96 and (name N or name CA o \ r name C or name O or name CB )) or resid 97 or (resid 98 through 101 and (name \ N or name CA or name C or name O or name CB )) or resid 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 or (resid 105 th \ rough 106 and (name N or name CA or name C or name O or name CB )) or resid 107 \ through 122 or (resid 123 and (name N or name CA or name C or name O or name CB \ )) or resid 124 or (resid 125 through 126 and (name N or name CA or name C or na \ me O or name CB )) or resid 127 through 163 or (resid 164 through 165 and (name \ N or name CA or name C or name O or name CB )) or resid 166 through 192 or (resi \ d 193 and (name N or name CA or name C or name O or name CB )) or resid 194 or ( \ resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ through 249 or (resid 250 through 251 and (name N or name CA or name C or name O \ or name CB )) or resid 252 through 272 or (resid 273 and (name N or name CA or \ name C or name O or name CB )) or resid 274 through 283 or (resid 284 through 28 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 289 or (resi \ d 290 and (name N or name CA or name C or name O or name CB )) or resid 291 thro \ ugh 294 or (resid 295 through 297 and (name N or name CA or name C or name O or \ name CB )) or resid 298 or (resid 299 through 336 and (name N or name CA or name \ C or name O or name CB )) or resid 337 through 338 or (resid 343 through 384 an \ d (name N or name CA or name C or name O or name CB )) or resid 385 through 387 \ or (resid 388 through 389 and (name N or name CA or name C or name O or name CB \ )) or resid 390 or (resid 391 and (name N or name CA or name C or name O or name \ CB )) or resid 392 or (resid 393 and (name N or name CA or name C or name O or \ name CB )) or resid 394 through 397 or resid 401 through 403 or (resid 404 and ( \ name N or name CA or name C or name O or name CB )) or resid 405 through 425 or \ (resid 426 through 427 and (name N or name CA or name C or name O or name CB )) \ or resid 428 or (resid 429 and (name N or name CA or name C or name O or name CB \ )) or resid 433 or (resid 434 through 435 and (name N or name CA or name C or n \ ame O or name CB )) or resid 436 through 445 or (resid 446 through 450 and (name \ N or name CA or name C or name O or name CB )) or (resid 451 through 453 and (n \ ame N or name CA or name C or name O or name CB )) or resid 454 through 456 or ( \ resid 457 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 478 or (resid 479 through 480 and (name N or name CA or name \ C or name O or name CB )) or resid 481 through 482 or (resid 483 through 487 an \ d (name N or name CA or name C or name O or name CB )) or resid 488 or (resid 48 \ 9 through 490 and (name N or name CA or name C or name O or name CB )) or resid \ 491 through 507 or (resid 508 through 511 and (name N or name CA or name C or na \ me O or name CB )) or resid 512 through 519 or (resid 520 and (name N or name CA \ or name C or name O or name CB )) or resid 521 through 523 or (resid 524 throug \ h 525 and (name N or name CA or name C or name O or name CB )) or resid 526 or ( \ resid 527 through 528 and (name N or name CA or name C or name O or name CB )) o \ r resid 529 through 557 or (resid 558 and (name N or name CA or name C or name O \ or name CB )) or resid 559 through 564 or (resid 565 and (name N or name CA or \ name C or name O or name CB )) or resid 566 or (resid 567 through 569 and (name \ N or name CA or name C or name O or name CB )) or resid 570 or (resid 571 throug \ h 574 and (name N or name CA or name C or name O or name CB )) or resid 575 thro \ ugh 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) o \ r resid 579 through 601 or (resid 602 through 604 and (name N or name CA or name \ C or name O or name CB )) or resid 605 or (resid 606 through 614 and (name N or \ name CA or name C or name O or name CB )) or resid 615 or (resid 616 through 61 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 618 through \ 622 or (resid 623 through 624 and (name N or name CA or name C or name O or name \ CB )) or resid 625 through 630 or (resid 631 through 636 and (name N or name CA \ or name C or name O or name CB )) or resid 637 or (resid 638 through 656 and (n \ ame N or name CA or name C or name O or name CB )) or resid 657 or (resid 658 th \ rough 663 and (name N or name CA or name C or name O or name CB )) or resid 664 \ or (resid 665 through 669 and (name N or name CA or name C or name O or name CB \ )) or resid 670 or (resid 671 through 673 and (name N or name CA or name C or na \ me O or name CB )) or resid 674 or (resid 675 through 682 and (name N or name CA \ or name C or name O or name CB )) or resid 683 through 684 or (resid 685 throug \ h 688 and (name N or name CA or name C or name O or name CB )) or resid 689 or ( \ resid 690 through 696 and (name N or name CA or name C or name O or name CB )) o \ r resid 697 or (resid 698 through 710 and (name N or name CA or name C or name O \ or name CB )) or resid 711 through 714 or (resid 715 through 721 and (name N or \ name CA or name C or name O or name CB )) or resid 722 or (resid 723 through 72 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 729 or (resi \ d 730 through 746 and (name N or name CA or name C or name O or name CB )) or re \ sid 747 through 748 or (resid 749 through 759 and (name N or name CA or name C o \ r name O or name CB )) or resid 760 or (resid 761 through 763 and (name N or nam \ e CA or name C or name O or name CB )) or resid 764 through 765 or (resid 766 th \ rough 767 and (name N or name CA or name C or name O or name CB )) or resid 768 \ through 773)) selection = (chain 'I' and (resid 52 through 87 or (resid 88 through 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 277 or (resid 278 throu \ gh 279 and (name N or name CA or name C or name O or name CB )) or resid 280 thr \ ough 539 or (resid 540 and (name N or name CA or name C or name O or name CB )) \ or resid 541 through 551 or (resid 552 and (name N or name CA or name C or name \ O or name CB )) or resid 553 through 753 or (resid 754 through 759 and (name N o \ r name CA or name C or name O or name CB )) or resid 760 through 773)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 10.200 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 103.870 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.016 0.190 38885 Z= 1.028 Angle : 1.305 18.456 52922 Z= 0.723 Chirality : 0.072 0.413 6190 Planarity : 0.008 0.163 6947 Dihedral : 12.146 90.314 13853 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.33 % Favored : 91.08 % Rotamer: Outliers : 0.26 % Allowed : 0.85 % Favored : 98.89 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.10), residues: 5043 helix: -2.17 (0.13), residues: 1152 sheet: -1.18 (0.14), residues: 1183 loop : -2.45 (0.10), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP H 570 HIS 0.020 0.004 HIS B 253 PHE 0.043 0.004 PHE D 202 TYR 0.061 0.004 TYR H 591 ARG 0.013 0.001 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 847 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7563 (ptp-170) cc_final: 0.7180 (ptm160) REVERT: A 180 ASN cc_start: 0.8715 (t0) cc_final: 0.8514 (t0) REVERT: A 389 GLN cc_start: 0.7424 (mp10) cc_final: 0.6780 (mp10) REVERT: A 415 ASN cc_start: 0.8721 (m110) cc_final: 0.8442 (m110) REVERT: A 472 ASP cc_start: 0.8068 (t0) cc_final: 0.7755 (t0) REVERT: A 497 ASP cc_start: 0.7884 (p0) cc_final: 0.7500 (p0) REVERT: B 291 LYS cc_start: 0.8307 (mptt) cc_final: 0.8039 (mmtt) REVERT: B 335 ASP cc_start: 0.8265 (t0) cc_final: 0.7694 (t0) REVERT: B 353 ASN cc_start: 0.8028 (t0) cc_final: 0.7758 (t0) REVERT: B 560 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7345 (tm-30) REVERT: B 570 ASN cc_start: 0.9038 (m-40) cc_final: 0.8787 (m-40) REVERT: B 594 LYS cc_start: 0.8228 (ttmt) cc_final: 0.8023 (ttpt) REVERT: B 614 GLU cc_start: 0.8723 (mp0) cc_final: 0.8255 (mp0) REVERT: B 638 ILE cc_start: 0.8683 (pt) cc_final: 0.8238 (pt) REVERT: B 703 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7923 (mmtm) REVERT: B 722 LYS cc_start: 0.8785 (tptm) cc_final: 0.8532 (tppt) REVERT: C 389 GLN cc_start: 0.7901 (mp10) cc_final: 0.7510 (mp10) REVERT: C 434 MET cc_start: 0.7457 (ppp) cc_final: 0.7107 (ppp) REVERT: C 441 GLU cc_start: 0.8746 (mp0) cc_final: 0.8396 (mp0) REVERT: C 446 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7538 (mmtm) REVERT: C 449 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7530 (ttm-80) REVERT: C 451 ASP cc_start: 0.7968 (m-30) cc_final: 0.7560 (m-30) REVERT: C 560 GLN cc_start: 0.8032 (tp40) cc_final: 0.7502 (tp40) REVERT: C 593 ASP cc_start: 0.8308 (t0) cc_final: 0.8055 (t0) REVERT: C 599 ASP cc_start: 0.8883 (t70) cc_final: 0.8642 (t70) REVERT: C 608 ASP cc_start: 0.8348 (m-30) cc_final: 0.7649 (t0) REVERT: C 613 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8526 (ptpp) REVERT: C 627 LEU cc_start: 0.8378 (mm) cc_final: 0.8172 (mm) REVERT: C 705 ASN cc_start: 0.9044 (m110) cc_final: 0.8594 (m-40) REVERT: D 250 GLU cc_start: 0.7767 (pm20) cc_final: 0.7368 (mp0) REVERT: D 346 TRP cc_start: 0.8615 (m-10) cc_final: 0.8390 (m-10) REVERT: D 359 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7831 (mtp180) REVERT: D 389 GLN cc_start: 0.7730 (mp10) cc_final: 0.7282 (mp10) REVERT: D 434 MET cc_start: 0.7889 (ppp) cc_final: 0.7580 (ppp) REVERT: D 442 LEU cc_start: 0.8438 (tt) cc_final: 0.8119 (tt) REVERT: D 446 LYS cc_start: 0.7865 (mmtm) cc_final: 0.7597 (mmmt) REVERT: D 447 GLN cc_start: 0.8683 (pp30) cc_final: 0.8327 (pp30) REVERT: D 448 LEU cc_start: 0.8594 (mp) cc_final: 0.8229 (mt) REVERT: D 509 ASN cc_start: 0.8742 (t0) cc_final: 0.8230 (t0) REVERT: D 633 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8299 (tppt) REVERT: D 703 LYS cc_start: 0.8384 (mptt) cc_final: 0.8042 (mptt) REVERT: D 727 PHE cc_start: 0.8290 (t80) cc_final: 0.7219 (t80) REVERT: E 328 ASN cc_start: 0.8476 (m-40) cc_final: 0.8230 (m110) REVERT: E 444 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8470 (ptpp) REVERT: E 446 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8085 (ttmm) REVERT: E 447 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7488 (tp-100) REVERT: E 470 ARG cc_start: 0.7831 (ptm-80) cc_final: 0.7374 (ptm-80) REVERT: E 472 ASP cc_start: 0.8422 (t0) cc_final: 0.8142 (t0) REVERT: E 599 ASP cc_start: 0.8640 (t70) cc_final: 0.7910 (p0) REVERT: E 600 ARG cc_start: 0.7721 (tpt90) cc_final: 0.6683 (tpm170) REVERT: E 602 ASN cc_start: 0.8935 (m-40) cc_final: 0.8692 (m110) REVERT: E 613 LYS cc_start: 0.8916 (ptpp) cc_final: 0.8653 (ptpp) REVERT: F 361 ASN cc_start: 0.8789 (t0) cc_final: 0.8537 (t0) REVERT: F 385 LEU cc_start: 0.8946 (tt) cc_final: 0.8653 (tt) REVERT: F 387 LYS cc_start: 0.9234 (mmpt) cc_final: 0.8752 (ptmm) REVERT: F 389 GLN cc_start: 0.7699 (mp10) cc_final: 0.7433 (mp10) REVERT: F 434 MET cc_start: 0.7880 (ppp) cc_final: 0.7666 (ppp) REVERT: F 438 GLN cc_start: 0.8889 (mt0) cc_final: 0.8495 (mp10) REVERT: F 444 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8666 (ptpt) REVERT: F 447 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7031 (mm110) REVERT: F 470 ARG cc_start: 0.7681 (ptp-110) cc_final: 0.7446 (ptp-110) REVERT: F 472 ASP cc_start: 0.8331 (t0) cc_final: 0.7879 (t0) REVERT: F 479 GLU cc_start: 0.7833 (mp0) cc_final: 0.7520 (mp0) REVERT: F 557 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7575 (mm-40) REVERT: F 560 GLN cc_start: 0.8734 (tp40) cc_final: 0.7614 (tm-30) REVERT: F 602 ASN cc_start: 0.8974 (m110) cc_final: 0.8774 (m-40) REVERT: G 265 ASP cc_start: 0.7716 (t0) cc_final: 0.7390 (t0) REVERT: G 387 LYS cc_start: 0.8917 (mmpt) cc_final: 0.8660 (tppt) REVERT: G 472 ASP cc_start: 0.8310 (t70) cc_final: 0.7961 (t0) REVERT: G 486 GLU cc_start: 0.8079 (tp30) cc_final: 0.7530 (tp30) REVERT: G 496 LYS cc_start: 0.9024 (tptt) cc_final: 0.8798 (tppt) REVERT: G 563 LYS cc_start: 0.8604 (mppt) cc_final: 0.8276 (mmtm) REVERT: G 569 LEU cc_start: 0.9395 (mt) cc_final: 0.9096 (mp) REVERT: G 593 ASP cc_start: 0.8468 (t0) cc_final: 0.8174 (t0) REVERT: G 705 ASN cc_start: 0.8820 (m-40) cc_final: 0.8601 (m-40) REVERT: H 138 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.8893 (m) REVERT: H 158 ASP cc_start: 0.7836 (t70) cc_final: 0.7308 (t70) REVERT: H 187 ASP cc_start: 0.8648 (m-30) cc_final: 0.8098 (m-30) REVERT: H 215 GLU cc_start: 0.8092 (pt0) cc_final: 0.7890 (pt0) REVERT: H 226 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7879 (tm-30) REVERT: H 268 TYR cc_start: 0.8951 (t80) cc_final: 0.8710 (t80) REVERT: H 533 GLN cc_start: 0.7512 (pm20) cc_final: 0.6843 (pm20) REVERT: H 548 LYS cc_start: 0.7250 (tppt) cc_final: 0.6957 (tptp) REVERT: H 589 ASN cc_start: 0.8972 (m-40) cc_final: 0.8707 (m110) REVERT: H 604 ASN cc_start: 0.8561 (m-40) cc_final: 0.8248 (m-40) REVERT: H 620 ASN cc_start: 0.8734 (m110) cc_final: 0.8454 (m-40) REVERT: H 678 ARG cc_start: 0.6619 (mpt180) cc_final: 0.6368 (mpt180) REVERT: H 765 PHE cc_start: 0.8377 (t80) cc_final: 0.8139 (t80) REVERT: I 118 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7438 (p90) REVERT: I 162 LYS cc_start: 0.8754 (mmtp) cc_final: 0.8511 (mmmt) REVERT: I 472 LYS cc_start: 0.8761 (ptpp) cc_final: 0.8365 (ptpp) REVERT: I 533 GLN cc_start: 0.8449 (pt0) cc_final: 0.8227 (pt0) REVERT: I 537 GLN cc_start: 0.6630 (tm-30) cc_final: 0.6393 (tm-30) REVERT: I 542 TYR cc_start: 0.7976 (m-80) cc_final: 0.7624 (m-80) REVERT: I 544 ARG cc_start: 0.7763 (tpp80) cc_final: 0.7397 (tpp80) REVERT: I 764 GLN cc_start: 0.8940 (mp10) cc_final: 0.8733 (mp10) outliers start: 10 outliers final: 3 residues processed: 850 average time/residue: 0.5321 time to fit residues: 714.9811 Evaluate side-chains 716 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 711 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 700 LEU Chi-restraints excluded: chain I residue 118 TYR Chi-restraints excluded: chain I residue 138 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 426 optimal weight: 4.9990 chunk 382 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 258 optimal weight: 0.0370 chunk 204 optimal weight: 20.0000 chunk 395 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 chunk 294 optimal weight: 0.8980 chunk 458 optimal weight: 3.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 GLN D 422 ASN D 541 GLN E 565 GLN F 198 ASN ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 GLN F 560 GLN G 198 ASN ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN H 228 GLN H 567 ASN ** H 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 GLN ** H 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38885 Z= 0.213 Angle : 0.717 10.406 52922 Z= 0.375 Chirality : 0.048 0.200 6190 Planarity : 0.005 0.086 6947 Dihedral : 4.894 38.185 5431 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 1.60 % Allowed : 10.07 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.58 (0.11), residues: 5043 helix: -0.52 (0.14), residues: 1285 sheet: -0.70 (0.14), residues: 1186 loop : -1.46 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 570 HIS 0.007 0.001 HIS I 280 PHE 0.033 0.002 PHE E 202 TYR 0.032 0.001 TYR I 513 ARG 0.010 0.001 ARG H 502 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 843 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7682 (ptp-170) cc_final: 0.7337 (ptm160) REVERT: A 180 ASN cc_start: 0.8667 (t0) cc_final: 0.8389 (t0) REVERT: A 224 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 389 GLN cc_start: 0.7392 (mp10) cc_final: 0.6784 (mp10) REVERT: A 415 ASN cc_start: 0.8668 (m110) cc_final: 0.8424 (m-40) REVERT: A 434 MET cc_start: 0.7233 (ppp) cc_final: 0.6314 (ppp) REVERT: A 453 ASP cc_start: 0.8573 (p0) cc_final: 0.8209 (p0) REVERT: A 555 ASP cc_start: 0.7393 (t0) cc_final: 0.6973 (t0) REVERT: A 703 LYS cc_start: 0.8356 (mmtm) cc_final: 0.8024 (mmtm) REVERT: B 190 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7070 (mm-30) REVERT: B 335 ASP cc_start: 0.8197 (t0) cc_final: 0.7654 (t0) REVERT: B 353 ASN cc_start: 0.8144 (t0) cc_final: 0.7889 (t0) REVERT: B 434 MET cc_start: 0.8340 (ppp) cc_final: 0.8053 (ppp) REVERT: B 469 VAL cc_start: 0.9218 (m) cc_final: 0.8867 (m) REVERT: B 515 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 525 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 546 ASP cc_start: 0.8201 (t70) cc_final: 0.7963 (t0) REVERT: B 560 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7084 (tm-30) REVERT: B 594 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8133 (ttpt) REVERT: B 613 LYS cc_start: 0.9338 (mttt) cc_final: 0.9099 (ptpp) REVERT: B 614 GLU cc_start: 0.8637 (mp0) cc_final: 0.8416 (mp0) REVERT: B 635 ILE cc_start: 0.7972 (mm) cc_final: 0.7752 (mm) REVERT: C 178 ARG cc_start: 0.8101 (mtm180) cc_final: 0.7749 (mtt180) REVERT: C 326 ASN cc_start: 0.8778 (p0) cc_final: 0.8304 (p0) REVERT: C 385 LEU cc_start: 0.8625 (tt) cc_final: 0.7877 (tt) REVERT: C 387 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8459 (tptt) REVERT: C 389 GLN cc_start: 0.7944 (mp10) cc_final: 0.7279 (mp10) REVERT: C 434 MET cc_start: 0.8085 (ppp) cc_final: 0.7856 (ppp) REVERT: C 451 ASP cc_start: 0.7969 (m-30) cc_final: 0.7660 (m-30) REVERT: C 479 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7333 (tt0) REVERT: C 496 LYS cc_start: 0.9311 (ttmm) cc_final: 0.8923 (tppt) REVERT: C 497 ASP cc_start: 0.7820 (p0) cc_final: 0.7537 (p0) REVERT: C 499 ASN cc_start: 0.8558 (m-40) cc_final: 0.8052 (m-40) REVERT: C 555 ASP cc_start: 0.7442 (t70) cc_final: 0.7128 (t70) REVERT: C 582 LYS cc_start: 0.8948 (mmtm) cc_final: 0.8680 (mmmm) REVERT: C 587 MET cc_start: 0.8418 (mtt) cc_final: 0.8203 (mtt) REVERT: C 593 ASP cc_start: 0.8043 (t0) cc_final: 0.7777 (t0) REVERT: C 599 ASP cc_start: 0.8881 (t70) cc_final: 0.8564 (t70) REVERT: C 613 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8534 (ptpp) REVERT: C 703 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7771 (mmtp) REVERT: D 202 PHE cc_start: 0.8707 (p90) cc_final: 0.8496 (p90) REVERT: D 250 GLU cc_start: 0.7436 (pm20) cc_final: 0.7171 (mp0) REVERT: D 346 TRP cc_start: 0.8223 (m-10) cc_final: 0.7978 (m-10) REVERT: D 359 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8139 (mtp180) REVERT: D 389 GLN cc_start: 0.7658 (mp10) cc_final: 0.7221 (mp10) REVERT: D 434 MET cc_start: 0.8067 (ppp) cc_final: 0.7559 (ppp) REVERT: D 438 GLN cc_start: 0.8351 (mp10) cc_final: 0.7847 (mp10) REVERT: D 446 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7652 (mmmt) REVERT: D 447 GLN cc_start: 0.8640 (pp30) cc_final: 0.8432 (pp30) REVERT: D 448 LEU cc_start: 0.8554 (mp) cc_final: 0.8139 (mp) REVERT: D 472 ASP cc_start: 0.7897 (t0) cc_final: 0.7608 (t0) REVERT: D 509 ASN cc_start: 0.8666 (t0) cc_final: 0.8328 (t0) REVERT: D 555 ASP cc_start: 0.7249 (t0) cc_final: 0.6759 (t0) REVERT: D 557 GLN cc_start: 0.7764 (mp10) cc_final: 0.7516 (mp10) REVERT: D 633 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8008 (tptp) REVERT: D 643 ILE cc_start: 0.8887 (mm) cc_final: 0.8613 (pt) REVERT: D 703 LYS cc_start: 0.8444 (mptt) cc_final: 0.8073 (mptt) REVERT: D 727 PHE cc_start: 0.8383 (t80) cc_final: 0.7638 (t80) REVERT: E 359 ARG cc_start: 0.7054 (ptp90) cc_final: 0.6741 (mmt90) REVERT: E 446 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8412 (ttmt) REVERT: E 447 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7588 (tp-100) REVERT: E 472 ASP cc_start: 0.8234 (t0) cc_final: 0.7729 (t0) REVERT: E 496 LYS cc_start: 0.8858 (tppt) cc_final: 0.8593 (tppt) REVERT: E 580 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8910 (mmmt) REVERT: E 599 ASP cc_start: 0.8564 (t70) cc_final: 0.8038 (p0) REVERT: E 600 ARG cc_start: 0.7721 (tpt90) cc_final: 0.6662 (tpm170) REVERT: E 602 ASN cc_start: 0.8871 (m-40) cc_final: 0.8200 (m110) REVERT: E 633 LYS cc_start: 0.8971 (pptt) cc_final: 0.8235 (tptp) REVERT: E 638 ILE cc_start: 0.7665 (pt) cc_final: 0.7458 (pt) REVERT: F 195 ASP cc_start: 0.8107 (t0) cc_final: 0.7844 (t0) REVERT: F 387 LYS cc_start: 0.9314 (mmpt) cc_final: 0.8791 (ptmm) REVERT: F 434 MET cc_start: 0.7959 (ppp) cc_final: 0.7703 (ppp) REVERT: F 479 GLU cc_start: 0.8103 (mp0) cc_final: 0.7858 (mp0) REVERT: F 525 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7697 (mm-30) REVERT: F 596 PHE cc_start: 0.9042 (m-10) cc_final: 0.8818 (m-10) REVERT: F 602 ASN cc_start: 0.8859 (m110) cc_final: 0.8568 (m110) REVERT: F 633 LYS cc_start: 0.9015 (tppt) cc_final: 0.8410 (tppt) REVERT: F 634 ASP cc_start: 0.9353 (p0) cc_final: 0.8996 (p0) REVERT: F 636 ARG cc_start: 0.8332 (ptp90) cc_final: 0.7659 (ptp90) REVERT: F 637 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8382 (mttp) REVERT: G 265 ASP cc_start: 0.7773 (t0) cc_final: 0.7317 (t0) REVERT: G 291 LYS cc_start: 0.8323 (mmmm) cc_final: 0.8052 (mmmt) REVERT: G 434 MET cc_start: 0.7011 (tmm) cc_final: 0.6766 (tmm) REVERT: G 472 ASP cc_start: 0.7660 (t70) cc_final: 0.7226 (t0) REVERT: G 486 GLU cc_start: 0.8042 (tp30) cc_final: 0.7619 (tp30) REVERT: G 496 LYS cc_start: 0.8941 (tptt) cc_final: 0.8691 (tppt) REVERT: G 593 ASP cc_start: 0.8332 (t0) cc_final: 0.7957 (t0) REVERT: G 703 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7585 (mtmm) REVERT: G 705 ASN cc_start: 0.8840 (m-40) cc_final: 0.8572 (m110) REVERT: H 118 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6083 (p90) REVERT: H 123 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8017 (mp0) REVERT: H 158 ASP cc_start: 0.7691 (t70) cc_final: 0.7195 (t70) REVERT: H 187 ASP cc_start: 0.8548 (m-30) cc_final: 0.8045 (m-30) REVERT: H 215 GLU cc_start: 0.8073 (pt0) cc_final: 0.7836 (pt0) REVERT: H 246 LYS cc_start: 0.8521 (tmmt) cc_final: 0.8261 (tmmt) REVERT: H 268 TYR cc_start: 0.8918 (t80) cc_final: 0.8652 (t80) REVERT: H 273 LYS cc_start: 0.8866 (tmtt) cc_final: 0.8569 (ptpp) REVERT: H 488 ILE cc_start: 0.7290 (tt) cc_final: 0.7011 (tt) REVERT: H 548 LYS cc_start: 0.7503 (tppt) cc_final: 0.7216 (tptp) REVERT: H 604 ASN cc_start: 0.8474 (m-40) cc_final: 0.8231 (m-40) REVERT: H 742 ARG cc_start: 0.8963 (tmm-80) cc_final: 0.8681 (ttp80) REVERT: H 772 PHE cc_start: 0.8471 (m-80) cc_final: 0.8005 (m-80) REVERT: I 61 LYS cc_start: 0.8961 (tppt) cc_final: 0.8667 (tppt) REVERT: I 118 TYR cc_start: 0.8477 (p90) cc_final: 0.7734 (p90) REVERT: I 162 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8449 (mmmt) REVERT: I 167 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.6408 (t80) REVERT: I 182 ASP cc_start: 0.7835 (t0) cc_final: 0.7577 (t70) REVERT: I 262 GLN cc_start: 0.8806 (mm110) cc_final: 0.8494 (mt0) REVERT: I 263 ARG cc_start: 0.9069 (mmm160) cc_final: 0.8673 (mmp80) REVERT: I 472 LYS cc_start: 0.8651 (ptpp) cc_final: 0.8301 (ptpp) REVERT: I 475 PHE cc_start: 0.8074 (t80) cc_final: 0.7722 (t80) REVERT: I 531 ASP cc_start: 0.7688 (t70) cc_final: 0.7409 (t70) REVERT: I 533 GLN cc_start: 0.8476 (pt0) cc_final: 0.8049 (pt0) REVERT: I 537 GLN cc_start: 0.6862 (tm-30) cc_final: 0.6172 (tm-30) REVERT: I 542 TYR cc_start: 0.7912 (m-80) cc_final: 0.7558 (m-80) outliers start: 62 outliers final: 37 residues processed: 872 average time/residue: 0.5147 time to fit residues: 714.7700 Evaluate side-chains 792 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 752 time to evaluate : 4.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 565 GLN Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 563 LYS Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 700 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 405 ASN Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 461 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 254 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 381 optimal weight: 0.0870 chunk 312 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 459 optimal weight: 50.0000 chunk 496 optimal weight: 40.0000 chunk 409 optimal weight: 6.9990 chunk 455 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 368 optimal weight: 7.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN C 438 GLN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN F 326 ASN ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 ASN H 567 ASN ** H 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 424 HIS I 496 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 38885 Z= 0.476 Angle : 0.707 8.905 52922 Z= 0.372 Chirality : 0.048 0.191 6190 Planarity : 0.005 0.064 6947 Dihedral : 4.887 34.851 5428 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.47 % Favored : 94.47 % Rotamer: Outliers : 3.23 % Allowed : 13.16 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.12), residues: 5043 helix: -0.16 (0.15), residues: 1294 sheet: -0.29 (0.14), residues: 1160 loop : -1.30 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 570 HIS 0.015 0.002 HIS I 424 PHE 0.031 0.002 PHE A 202 TYR 0.022 0.002 TYR H 591 ARG 0.006 0.001 ARG G 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 771 time to evaluate : 4.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7944 (ptp-170) cc_final: 0.7401 (ptm160) REVERT: A 180 ASN cc_start: 0.8753 (t0) cc_final: 0.8420 (t0) REVERT: A 224 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8169 (mm-30) REVERT: A 363 ASN cc_start: 0.8978 (m-40) cc_final: 0.8744 (m-40) REVERT: A 389 GLN cc_start: 0.7526 (mp10) cc_final: 0.6902 (mp10) REVERT: A 415 ASN cc_start: 0.8722 (m110) cc_final: 0.8421 (m110) REVERT: A 434 MET cc_start: 0.7524 (ppp) cc_final: 0.6559 (ppp) REVERT: A 436 TYR cc_start: 0.8076 (t80) cc_final: 0.7805 (t80) REVERT: A 446 LYS cc_start: 0.8692 (mmpt) cc_final: 0.8449 (mmpt) REVERT: A 453 ASP cc_start: 0.8732 (p0) cc_final: 0.8303 (p0) REVERT: A 486 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7568 (mm-30) REVERT: A 525 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 555 ASP cc_start: 0.7477 (t0) cc_final: 0.7128 (t0) REVERT: A 637 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8934 (ttpt) REVERT: B 224 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 291 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7561 (mmtm) REVERT: B 292 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8027 (p0) REVERT: B 335 ASP cc_start: 0.8197 (t0) cc_final: 0.7727 (t0) REVERT: B 353 ASN cc_start: 0.8190 (t0) cc_final: 0.7920 (t0) REVERT: B 434 MET cc_start: 0.8588 (ppp) cc_final: 0.8319 (ppp) REVERT: B 446 LYS cc_start: 0.7760 (mmpt) cc_final: 0.7515 (mmtt) REVERT: B 515 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 525 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7350 (mt-10) REVERT: B 546 ASP cc_start: 0.8273 (t70) cc_final: 0.8000 (t0) REVERT: B 551 ASP cc_start: 0.7670 (m-30) cc_final: 0.7177 (p0) REVERT: B 560 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 595 ARG cc_start: 0.8480 (ptt-90) cc_final: 0.8062 (ptt90) REVERT: B 603 ILE cc_start: 0.9499 (tp) cc_final: 0.9197 (mp) REVERT: B 613 LYS cc_start: 0.9332 (mttt) cc_final: 0.8987 (ptpt) REVERT: B 637 LYS cc_start: 0.9106 (ptmt) cc_final: 0.8821 (pttt) REVERT: B 703 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7810 (mmtp) REVERT: C 291 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8508 (mtpt) REVERT: C 346 TRP cc_start: 0.8157 (m-10) cc_final: 0.7826 (m-10) REVERT: C 385 LEU cc_start: 0.8572 (tt) cc_final: 0.7829 (tt) REVERT: C 389 GLN cc_start: 0.7927 (mp10) cc_final: 0.7252 (mp10) REVERT: C 434 MET cc_start: 0.8196 (ppp) cc_final: 0.7913 (ppp) REVERT: C 545 LYS cc_start: 0.8181 (mppt) cc_final: 0.7969 (mmtm) REVERT: C 555 ASP cc_start: 0.7633 (t70) cc_final: 0.7362 (t70) REVERT: C 582 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8730 (mmmm) REVERT: C 593 ASP cc_start: 0.8330 (t0) cc_final: 0.7925 (t0) REVERT: C 596 PHE cc_start: 0.8816 (m-80) cc_final: 0.8587 (m-80) REVERT: C 599 ASP cc_start: 0.8881 (t70) cc_final: 0.8567 (t70) REVERT: C 613 LYS cc_start: 0.8773 (ptpp) cc_final: 0.8513 (ptpp) REVERT: C 703 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7842 (mmtp) REVERT: D 389 GLN cc_start: 0.7778 (mp10) cc_final: 0.7327 (mp10) REVERT: D 434 MET cc_start: 0.8098 (ppp) cc_final: 0.7401 (ppp) REVERT: D 444 LYS cc_start: 0.8959 (tppt) cc_final: 0.8727 (tppt) REVERT: D 447 GLN cc_start: 0.8650 (pp30) cc_final: 0.8395 (pp30) REVERT: D 515 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7453 (mm-30) REVERT: D 555 ASP cc_start: 0.7616 (t0) cc_final: 0.7234 (t0) REVERT: D 557 GLN cc_start: 0.7787 (mp10) cc_final: 0.7558 (mp10) REVERT: D 633 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8040 (tptp) REVERT: D 643 ILE cc_start: 0.8812 (mm) cc_final: 0.8505 (pt) REVERT: D 703 LYS cc_start: 0.8522 (mptt) cc_final: 0.8074 (mptt) REVERT: D 727 PHE cc_start: 0.8440 (t80) cc_final: 0.8042 (t80) REVERT: E 197 LYS cc_start: 0.7665 (tptp) cc_final: 0.7457 (tmtt) REVERT: E 213 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8488 (mmtm) REVERT: E 359 ARG cc_start: 0.7331 (ptp90) cc_final: 0.7125 (mtt-85) REVERT: E 438 GLN cc_start: 0.8891 (mt0) cc_final: 0.8626 (mt0) REVERT: E 446 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8562 (ttmt) REVERT: E 447 GLN cc_start: 0.7944 (tp-100) cc_final: 0.7518 (tp40) REVERT: E 472 ASP cc_start: 0.8228 (t0) cc_final: 0.7826 (t0) REVERT: E 496 LYS cc_start: 0.8874 (tppt) cc_final: 0.8590 (tppt) REVERT: E 561 ASN cc_start: 0.7693 (t0) cc_final: 0.7412 (t0) REVERT: E 599 ASP cc_start: 0.8619 (t70) cc_final: 0.8026 (p0) REVERT: E 600 ARG cc_start: 0.7733 (tpt90) cc_final: 0.6817 (tpm170) REVERT: E 602 ASN cc_start: 0.8975 (m-40) cc_final: 0.8237 (m110) REVERT: E 613 LYS cc_start: 0.8770 (pttm) cc_final: 0.8545 (pttm) REVERT: E 633 LYS cc_start: 0.8956 (pptt) cc_final: 0.8235 (tptp) REVERT: E 638 ILE cc_start: 0.7742 (pt) cc_final: 0.7540 (pt) REVERT: F 195 ASP cc_start: 0.8158 (t0) cc_final: 0.7850 (t0) REVERT: F 434 MET cc_start: 0.7977 (ppp) cc_final: 0.7758 (ppp) REVERT: F 446 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7508 (mmmt) REVERT: F 447 GLN cc_start: 0.7477 (mm-40) cc_final: 0.6943 (mp10) REVERT: F 449 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8372 (mtm110) REVERT: F 479 GLU cc_start: 0.8082 (mp0) cc_final: 0.7711 (mp0) REVERT: F 579 ASP cc_start: 0.8397 (p0) cc_final: 0.8101 (t0) REVERT: F 599 ASP cc_start: 0.8132 (t0) cc_final: 0.7913 (t0) REVERT: F 602 ASN cc_start: 0.8793 (m110) cc_final: 0.8405 (m110) REVERT: F 633 LYS cc_start: 0.9013 (tppt) cc_final: 0.8343 (tppt) REVERT: F 634 ASP cc_start: 0.9352 (p0) cc_final: 0.8853 (p0) REVERT: F 637 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8339 (mttp) REVERT: G 265 ASP cc_start: 0.7885 (t0) cc_final: 0.7442 (t0) REVERT: G 387 LYS cc_start: 0.8921 (tppt) cc_final: 0.8624 (tppt) REVERT: G 434 MET cc_start: 0.7005 (tmm) cc_final: 0.6715 (tmm) REVERT: G 472 ASP cc_start: 0.7960 (t70) cc_final: 0.7393 (t70) REVERT: G 479 GLU cc_start: 0.8111 (mp0) cc_final: 0.7867 (mp0) REVERT: G 486 GLU cc_start: 0.8120 (tp30) cc_final: 0.7704 (tp30) REVERT: G 496 LYS cc_start: 0.9093 (tptt) cc_final: 0.8837 (tppt) REVERT: G 521 MET cc_start: 0.8443 (tpp) cc_final: 0.7528 (mpp) REVERT: G 563 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8588 (mmtm) REVERT: G 569 LEU cc_start: 0.9250 (mt) cc_final: 0.8848 (mt) REVERT: G 593 ASP cc_start: 0.8393 (t0) cc_final: 0.8059 (t0) REVERT: G 636 ARG cc_start: 0.8217 (ptp90) cc_final: 0.7881 (ptp90) REVERT: G 705 ASN cc_start: 0.8907 (m-40) cc_final: 0.8673 (m-40) REVERT: H 118 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6174 (p90) REVERT: H 187 ASP cc_start: 0.8526 (m-30) cc_final: 0.8048 (m-30) REVERT: H 189 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8548 (mp) REVERT: H 215 GLU cc_start: 0.8082 (pt0) cc_final: 0.7860 (pt0) REVERT: H 246 LYS cc_start: 0.8529 (tmmt) cc_final: 0.8235 (tmmt) REVERT: H 268 TYR cc_start: 0.8937 (t80) cc_final: 0.8704 (t80) REVERT: H 273 LYS cc_start: 0.8902 (tmtt) cc_final: 0.8540 (ptpp) REVERT: H 296 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8578 (mm) REVERT: H 488 ILE cc_start: 0.7665 (tt) cc_final: 0.7017 (tt) REVERT: H 548 LYS cc_start: 0.7519 (tppt) cc_final: 0.7235 (tptp) REVERT: H 604 ASN cc_start: 0.8459 (m-40) cc_final: 0.8219 (m-40) REVERT: H 772 PHE cc_start: 0.8440 (m-80) cc_final: 0.7987 (m-80) REVERT: I 61 LYS cc_start: 0.9017 (tppt) cc_final: 0.8773 (tppt) REVERT: I 118 TYR cc_start: 0.8707 (p90) cc_final: 0.7935 (p90) REVERT: I 162 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8418 (mmtt) REVERT: I 182 ASP cc_start: 0.7834 (t0) cc_final: 0.7623 (t70) REVERT: I 194 LEU cc_start: 0.8915 (mt) cc_final: 0.8694 (mp) REVERT: I 246 LYS cc_start: 0.8742 (tppt) cc_final: 0.8456 (tptp) REVERT: I 475 PHE cc_start: 0.8119 (t80) cc_final: 0.7850 (t80) REVERT: I 533 GLN cc_start: 0.8537 (pt0) cc_final: 0.8210 (pt0) REVERT: I 537 GLN cc_start: 0.6799 (tm-30) cc_final: 0.6538 (tm-30) REVERT: I 542 TYR cc_start: 0.7903 (m-80) cc_final: 0.7583 (m-80) outliers start: 125 outliers final: 88 residues processed: 838 average time/residue: 0.5348 time to fit residues: 716.7093 Evaluate side-chains 813 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 721 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 336 HIS Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 502 GLU Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 559 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 405 ASN Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 453 optimal weight: 0.9980 chunk 345 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 219 optimal weight: 8.9990 chunk 308 optimal weight: 8.9990 chunk 461 optimal weight: 40.0000 chunk 488 optimal weight: 30.0000 chunk 240 optimal weight: 1.9990 chunk 436 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 485 GLN E 565 GLN ** F 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN H 604 ASN ** H 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN I 424 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 38885 Z= 0.280 Angle : 0.623 8.978 52922 Z= 0.324 Chirality : 0.046 0.213 6190 Planarity : 0.004 0.054 6947 Dihedral : 4.607 31.714 5426 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 3.38 % Allowed : 15.38 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 5043 helix: 0.22 (0.15), residues: 1283 sheet: -0.11 (0.14), residues: 1172 loop : -1.10 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 570 HIS 0.017 0.001 HIS I 424 PHE 0.030 0.002 PHE I 247 TYR 0.022 0.001 TYR C 436 ARG 0.007 0.000 ARG G 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 791 time to evaluate : 4.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7948 (ptp-170) cc_final: 0.7433 (ptm160) REVERT: A 180 ASN cc_start: 0.8755 (t0) cc_final: 0.8487 (t0) REVERT: A 197 LYS cc_start: 0.7839 (tppt) cc_final: 0.7430 (tptt) REVERT: A 224 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8120 (mm-30) REVERT: A 363 ASN cc_start: 0.9030 (m-40) cc_final: 0.8374 (m-40) REVERT: A 389 GLN cc_start: 0.7514 (mp10) cc_final: 0.6883 (mp10) REVERT: A 434 MET cc_start: 0.7648 (ppp) cc_final: 0.6522 (ppp) REVERT: A 446 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8330 (mmmt) REVERT: A 453 ASP cc_start: 0.8775 (p0) cc_final: 0.8301 (p0) REVERT: A 525 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7463 (mm-30) REVERT: A 555 ASP cc_start: 0.7416 (t0) cc_final: 0.7153 (t70) REVERT: A 631 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8406 (mm) REVERT: A 636 ARG cc_start: 0.8470 (ptp90) cc_final: 0.8230 (ptp90) REVERT: A 637 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8947 (ttpt) REVERT: A 703 LYS cc_start: 0.8582 (mmtp) cc_final: 0.8329 (mmtm) REVERT: B 190 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7105 (mt-10) REVERT: B 224 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7508 (mm-30) REVERT: B 292 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7664 (p0) REVERT: B 335 ASP cc_start: 0.8162 (t0) cc_final: 0.7234 (t0) REVERT: B 353 ASN cc_start: 0.8211 (t0) cc_final: 0.7931 (t0) REVERT: B 361 ASN cc_start: 0.8672 (t0) cc_final: 0.8084 (t0) REVERT: B 434 MET cc_start: 0.8691 (ppp) cc_final: 0.8423 (ppp) REVERT: B 446 LYS cc_start: 0.7840 (mmpt) cc_final: 0.7539 (mmtt) REVERT: B 476 ASN cc_start: 0.8128 (t0) cc_final: 0.7824 (t0) REVERT: B 515 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 551 ASP cc_start: 0.7659 (m-30) cc_final: 0.7271 (p0) REVERT: B 595 ARG cc_start: 0.8533 (ptt-90) cc_final: 0.8107 (ptt90) REVERT: B 603 ILE cc_start: 0.9450 (tp) cc_final: 0.9199 (mp) REVERT: B 613 LYS cc_start: 0.9264 (mttt) cc_final: 0.8976 (mmtt) REVERT: B 637 LYS cc_start: 0.9067 (ptmt) cc_final: 0.8862 (ptmt) REVERT: B 703 LYS cc_start: 0.8198 (mmtm) cc_final: 0.7986 (mmtm) REVERT: C 385 LEU cc_start: 0.8596 (tt) cc_final: 0.7837 (tt) REVERT: C 387 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8393 (tptt) REVERT: C 389 GLN cc_start: 0.7946 (mp10) cc_final: 0.7269 (mp10) REVERT: C 434 MET cc_start: 0.8256 (ppp) cc_final: 0.7938 (ppp) REVERT: C 446 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7976 (mmtt) REVERT: C 496 LYS cc_start: 0.9310 (ttmm) cc_final: 0.9077 (tppt) REVERT: C 499 ASN cc_start: 0.8601 (m-40) cc_final: 0.8173 (m-40) REVERT: C 555 ASP cc_start: 0.7636 (t70) cc_final: 0.7346 (t70) REVERT: C 582 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8775 (mptt) REVERT: C 593 ASP cc_start: 0.8311 (t0) cc_final: 0.7866 (t0) REVERT: C 599 ASP cc_start: 0.8845 (t70) cc_final: 0.8537 (t70) REVERT: D 202 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8604 (p90) REVERT: D 389 GLN cc_start: 0.7781 (mp10) cc_final: 0.7327 (mp10) REVERT: D 434 MET cc_start: 0.8219 (ppp) cc_final: 0.7538 (ppp) REVERT: D 446 LYS cc_start: 0.7545 (mmmt) cc_final: 0.7155 (mmmt) REVERT: D 447 GLN cc_start: 0.8622 (pp30) cc_final: 0.8394 (pp30) REVERT: D 448 LEU cc_start: 0.8765 (mp) cc_final: 0.8281 (mp) REVERT: D 509 ASN cc_start: 0.8636 (t0) cc_final: 0.8158 (t0) REVERT: D 515 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7328 (mm-30) REVERT: D 555 ASP cc_start: 0.7566 (t0) cc_final: 0.6864 (t0) REVERT: D 557 GLN cc_start: 0.7761 (mp10) cc_final: 0.7533 (mp10) REVERT: D 633 LYS cc_start: 0.8596 (ttpt) cc_final: 0.7959 (tppt) REVERT: D 643 ILE cc_start: 0.8738 (mm) cc_final: 0.8460 (pt) REVERT: D 703 LYS cc_start: 0.8565 (mptt) cc_final: 0.8087 (mptt) REVERT: D 727 PHE cc_start: 0.8418 (t80) cc_final: 0.7730 (t80) REVERT: E 434 MET cc_start: 0.7698 (tmm) cc_final: 0.7470 (tmm) REVERT: E 438 GLN cc_start: 0.8921 (mt0) cc_final: 0.8564 (mt0) REVERT: E 446 LYS cc_start: 0.8775 (ttmt) cc_final: 0.8476 (ttmt) REVERT: E 447 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7515 (tp40) REVERT: E 472 ASP cc_start: 0.8125 (t0) cc_final: 0.7732 (t0) REVERT: E 565 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: E 578 LEU cc_start: 0.8417 (tp) cc_final: 0.8144 (tt) REVERT: E 587 MET cc_start: 0.7902 (mtt) cc_final: 0.7601 (mtt) REVERT: E 599 ASP cc_start: 0.8589 (t70) cc_final: 0.7876 (p0) REVERT: E 600 ARG cc_start: 0.7719 (tpt90) cc_final: 0.6754 (tpm170) REVERT: E 602 ASN cc_start: 0.8926 (m-40) cc_final: 0.8055 (m110) REVERT: E 613 LYS cc_start: 0.8804 (pttm) cc_final: 0.8582 (pttm) REVERT: F 195 ASP cc_start: 0.8150 (t0) cc_final: 0.7878 (t0) REVERT: F 361 ASN cc_start: 0.8705 (t0) cc_final: 0.8434 (m-40) REVERT: F 387 LYS cc_start: 0.9356 (mmmt) cc_final: 0.8940 (ptmm) REVERT: F 421 LEU cc_start: 0.8952 (tt) cc_final: 0.8693 (tt) REVERT: F 446 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7675 (mmmt) REVERT: F 447 GLN cc_start: 0.7467 (mm-40) cc_final: 0.6840 (mp10) REVERT: F 449 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8397 (mtm-85) REVERT: F 479 GLU cc_start: 0.8130 (mp0) cc_final: 0.7775 (mp0) REVERT: F 579 ASP cc_start: 0.8400 (p0) cc_final: 0.8067 (t0) REVERT: F 599 ASP cc_start: 0.8205 (t0) cc_final: 0.7967 (t0) REVERT: F 602 ASN cc_start: 0.8804 (m110) cc_final: 0.8492 (m110) REVERT: F 633 LYS cc_start: 0.8993 (tppt) cc_final: 0.8277 (tppt) REVERT: F 634 ASP cc_start: 0.9304 (p0) cc_final: 0.8869 (p0) REVERT: F 636 ARG cc_start: 0.8080 (ptp90) cc_final: 0.7469 (ptp90) REVERT: F 637 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8413 (mttp) REVERT: G 268 ASN cc_start: 0.8542 (p0) cc_final: 0.8283 (p0) REVERT: G 387 LYS cc_start: 0.8917 (tppt) cc_final: 0.8556 (tppt) REVERT: G 389 GLN cc_start: 0.8418 (mp10) cc_final: 0.8002 (mp10) REVERT: G 434 MET cc_start: 0.7189 (tmm) cc_final: 0.6956 (tmm) REVERT: G 470 ARG cc_start: 0.6910 (ttm-80) cc_final: 0.6405 (ttt90) REVERT: G 472 ASP cc_start: 0.7752 (t70) cc_final: 0.7185 (t70) REVERT: G 496 LYS cc_start: 0.9055 (tptt) cc_final: 0.8772 (tppt) REVERT: G 521 MET cc_start: 0.8505 (tpp) cc_final: 0.7692 (mpp) REVERT: G 593 ASP cc_start: 0.8251 (t0) cc_final: 0.7942 (t0) REVERT: G 703 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7774 (mtmm) REVERT: G 705 ASN cc_start: 0.8862 (m-40) cc_final: 0.8399 (p0) REVERT: H 118 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6363 (p90) REVERT: H 187 ASP cc_start: 0.8462 (m-30) cc_final: 0.7971 (m-30) REVERT: H 215 GLU cc_start: 0.8005 (pt0) cc_final: 0.7719 (pp20) REVERT: H 246 LYS cc_start: 0.8576 (tmmt) cc_final: 0.8278 (tmmt) REVERT: H 268 TYR cc_start: 0.9074 (t80) cc_final: 0.8845 (t80) REVERT: H 273 LYS cc_start: 0.8907 (tmtt) cc_final: 0.8521 (ptpp) REVERT: H 488 ILE cc_start: 0.7148 (tt) cc_final: 0.6890 (tt) REVERT: H 548 LYS cc_start: 0.7481 (tppt) cc_final: 0.7176 (tptp) REVERT: H 632 THR cc_start: 0.8889 (p) cc_final: 0.8512 (t) REVERT: H 764 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: H 765 PHE cc_start: 0.8463 (t80) cc_final: 0.8224 (t80) REVERT: I 61 LYS cc_start: 0.9047 (tppt) cc_final: 0.8825 (tppt) REVERT: I 118 TYR cc_start: 0.8772 (p90) cc_final: 0.8039 (p90) REVERT: I 162 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8312 (mmtt) REVERT: I 194 LEU cc_start: 0.8886 (mt) cc_final: 0.8685 (mp) REVERT: I 246 LYS cc_start: 0.8818 (tppt) cc_final: 0.8583 (tppt) REVERT: I 263 ARG cc_start: 0.8869 (mmm160) cc_final: 0.8462 (mmm160) REVERT: I 475 PHE cc_start: 0.8116 (t80) cc_final: 0.7887 (t80) REVERT: I 531 ASP cc_start: 0.7828 (t70) cc_final: 0.7513 (t70) REVERT: I 533 GLN cc_start: 0.8526 (pt0) cc_final: 0.8151 (pt0) REVERT: I 537 GLN cc_start: 0.6854 (tm-30) cc_final: 0.6584 (tm-30) REVERT: I 542 TYR cc_start: 0.7882 (m-80) cc_final: 0.7455 (m-80) REVERT: I 544 ARG cc_start: 0.7123 (tpp80) cc_final: 0.6876 (tpp80) outliers start: 131 outliers final: 91 residues processed: 866 average time/residue: 0.5326 time to fit residues: 739.8584 Evaluate side-chains 827 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 729 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 336 HIS Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 502 GLU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 556 GLN Chi-restraints excluded: chain E residue 565 GLN Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 406 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 363 optimal weight: 0.0570 chunk 201 optimal weight: 30.0000 chunk 416 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 249 optimal weight: 0.5980 chunk 438 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 437 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN H 588 HIS H 604 ASN ** H 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 424 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38885 Z= 0.178 Angle : 0.596 11.714 52922 Z= 0.308 Chirality : 0.046 0.276 6190 Planarity : 0.004 0.048 6947 Dihedral : 4.354 34.828 5425 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.12 % Allowed : 17.24 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.12), residues: 5043 helix: 0.46 (0.15), residues: 1280 sheet: 0.17 (0.15), residues: 1103 loop : -0.98 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 570 HIS 0.006 0.001 HIS I 424 PHE 0.025 0.001 PHE E 202 TYR 0.015 0.001 TYR I 236 ARG 0.005 0.000 ARG E 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 804 time to evaluate : 4.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7299 (ptm160) REVERT: A 180 ASN cc_start: 0.8745 (t0) cc_final: 0.8504 (t0) REVERT: A 197 LYS cc_start: 0.7910 (tppt) cc_final: 0.7478 (tptt) REVERT: A 204 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8613 (m) REVERT: A 224 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 346 TRP cc_start: 0.7793 (m-10) cc_final: 0.7572 (m-10) REVERT: A 389 GLN cc_start: 0.7576 (mp10) cc_final: 0.7009 (mp10) REVERT: A 434 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6649 (ppp) REVERT: A 446 LYS cc_start: 0.8641 (mmpt) cc_final: 0.8255 (mmmt) REVERT: A 453 ASP cc_start: 0.8778 (p0) cc_final: 0.8314 (p0) REVERT: A 525 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7444 (mm-30) REVERT: A 555 ASP cc_start: 0.7444 (t0) cc_final: 0.7233 (t70) REVERT: A 631 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8128 (tt) REVERT: A 636 ARG cc_start: 0.8519 (ptp90) cc_final: 0.8173 (ptp90) REVERT: A 637 LYS cc_start: 0.9138 (ttmt) cc_final: 0.8882 (ttpt) REVERT: A 703 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8380 (mmtp) REVERT: B 190 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7098 (mt-10) REVERT: B 224 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 335 ASP cc_start: 0.8164 (t0) cc_final: 0.7921 (t0) REVERT: B 353 ASN cc_start: 0.8199 (t0) cc_final: 0.7915 (t0) REVERT: B 361 ASN cc_start: 0.8600 (t0) cc_final: 0.8366 (m-40) REVERT: B 434 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8383 (ppp) REVERT: B 446 LYS cc_start: 0.8016 (mmpt) cc_final: 0.7645 (mmtt) REVERT: B 515 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7445 (mm-30) REVERT: B 525 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7317 (pt0) REVERT: B 546 ASP cc_start: 0.8101 (t70) cc_final: 0.7829 (t0) REVERT: B 551 ASP cc_start: 0.7644 (m-30) cc_final: 0.7237 (p0) REVERT: B 586 LYS cc_start: 0.8924 (mtmm) cc_final: 0.8705 (mtmm) REVERT: B 595 ARG cc_start: 0.8513 (ptt-90) cc_final: 0.8121 (ptt90) REVERT: B 603 ILE cc_start: 0.9421 (tp) cc_final: 0.9169 (mp) REVERT: B 703 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7968 (mmtm) REVERT: C 291 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8523 (mtpt) REVERT: C 385 LEU cc_start: 0.8656 (tt) cc_final: 0.7895 (tt) REVERT: C 387 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8350 (tptt) REVERT: C 389 GLN cc_start: 0.7936 (mp10) cc_final: 0.7215 (mp10) REVERT: C 434 MET cc_start: 0.8257 (ppp) cc_final: 0.7949 (ppp) REVERT: C 439 PHE cc_start: 0.8622 (t80) cc_final: 0.8420 (t80) REVERT: C 446 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8053 (mmtt) REVERT: C 499 ASN cc_start: 0.8627 (m-40) cc_final: 0.8158 (m-40) REVERT: C 555 ASP cc_start: 0.7576 (t70) cc_final: 0.7327 (t70) REVERT: C 593 ASP cc_start: 0.8224 (t0) cc_final: 0.7701 (t0) REVERT: C 599 ASP cc_start: 0.8868 (t70) cc_final: 0.8573 (t70) REVERT: C 608 ASP cc_start: 0.7937 (m-30) cc_final: 0.7467 (t0) REVERT: D 212 GLU cc_start: 0.8213 (tm-30) cc_final: 0.8008 (tm-30) REVERT: D 267 GLU cc_start: 0.8027 (mp0) cc_final: 0.7806 (mp0) REVERT: D 389 GLN cc_start: 0.7727 (mp10) cc_final: 0.7272 (mp10) REVERT: D 434 MET cc_start: 0.8217 (ppp) cc_final: 0.7531 (ppp) REVERT: D 446 LYS cc_start: 0.7521 (mmmt) cc_final: 0.7156 (mmmt) REVERT: D 447 GLN cc_start: 0.8593 (pp30) cc_final: 0.8387 (pp30) REVERT: D 448 LEU cc_start: 0.8725 (mp) cc_final: 0.8248 (mp) REVERT: D 472 ASP cc_start: 0.7733 (t0) cc_final: 0.7346 (t0) REVERT: D 515 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7347 (mm-30) REVERT: D 555 ASP cc_start: 0.7500 (t0) cc_final: 0.6958 (t0) REVERT: D 643 ILE cc_start: 0.8714 (mm) cc_final: 0.8449 (pt) REVERT: D 703 LYS cc_start: 0.8595 (mptt) cc_final: 0.8134 (mptt) REVERT: D 704 GLU cc_start: 0.7844 (pt0) cc_final: 0.7418 (pt0) REVERT: D 727 PHE cc_start: 0.8443 (t80) cc_final: 0.7751 (t80) REVERT: E 213 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8400 (mmtm) REVERT: E 291 LYS cc_start: 0.8379 (mmtm) cc_final: 0.8162 (mmtm) REVERT: E 359 ARG cc_start: 0.7364 (ptp90) cc_final: 0.6798 (mtt-85) REVERT: E 446 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8426 (mmmt) REVERT: E 447 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7537 (tp40) REVERT: E 472 ASP cc_start: 0.8024 (t0) cc_final: 0.7593 (t0) REVERT: E 565 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: E 578 LEU cc_start: 0.8380 (tp) cc_final: 0.8175 (tt) REVERT: E 600 ARG cc_start: 0.7672 (tpt90) cc_final: 0.7087 (tpm170) REVERT: E 602 ASN cc_start: 0.8876 (m-40) cc_final: 0.8333 (m110) REVERT: E 613 LYS cc_start: 0.8773 (pttm) cc_final: 0.8550 (pttm) REVERT: E 633 LYS cc_start: 0.8955 (pptt) cc_final: 0.8054 (tptp) REVERT: E 703 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8455 (mmtt) REVERT: F 195 ASP cc_start: 0.8100 (t0) cc_final: 0.7846 (t0) REVERT: F 197 LYS cc_start: 0.8707 (tptp) cc_final: 0.8328 (tptp) REVERT: F 387 LYS cc_start: 0.9367 (mmmt) cc_final: 0.8902 (ptmm) REVERT: F 389 GLN cc_start: 0.7858 (mp10) cc_final: 0.7547 (mp10) REVERT: F 421 LEU cc_start: 0.9065 (tt) cc_final: 0.8811 (tt) REVERT: F 434 MET cc_start: 0.7203 (ppp) cc_final: 0.6576 (ppp) REVERT: F 438 GLN cc_start: 0.8807 (mt0) cc_final: 0.8317 (mt0) REVERT: F 446 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7705 (mmmt) REVERT: F 447 GLN cc_start: 0.7385 (mm-40) cc_final: 0.6847 (mm110) REVERT: F 449 ARG cc_start: 0.8592 (mtm-85) cc_final: 0.8327 (mtm-85) REVERT: F 479 GLU cc_start: 0.8272 (mp0) cc_final: 0.7944 (mp0) REVERT: F 565 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8142 (mt0) REVERT: F 579 ASP cc_start: 0.8345 (p0) cc_final: 0.8046 (t0) REVERT: F 602 ASN cc_start: 0.8727 (m110) cc_final: 0.8391 (m110) REVERT: F 633 LYS cc_start: 0.9014 (tppt) cc_final: 0.8181 (tppt) REVERT: F 634 ASP cc_start: 0.9292 (p0) cc_final: 0.8648 (p0) REVERT: F 637 LYS cc_start: 0.9008 (mtpt) cc_final: 0.8327 (mttp) REVERT: G 235 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: G 267 GLU cc_start: 0.7601 (pp20) cc_final: 0.7206 (pp20) REVERT: G 268 ASN cc_start: 0.8542 (p0) cc_final: 0.8167 (p0) REVERT: G 387 LYS cc_start: 0.8931 (tppt) cc_final: 0.8545 (tppt) REVERT: G 389 GLN cc_start: 0.8425 (mp10) cc_final: 0.8041 (mp10) REVERT: G 441 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8868 (mt-10) REVERT: G 472 ASP cc_start: 0.7710 (t70) cc_final: 0.7084 (t70) REVERT: G 549 GLU cc_start: 0.8026 (mp0) cc_final: 0.7701 (tp30) REVERT: G 563 LYS cc_start: 0.8959 (mmtp) cc_final: 0.8704 (mmtm) REVERT: G 582 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8677 (mmmm) REVERT: G 593 ASP cc_start: 0.8114 (t0) cc_final: 0.7583 (t0) REVERT: G 703 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7820 (mtmm) REVERT: G 705 ASN cc_start: 0.8872 (m-40) cc_final: 0.8383 (p0) REVERT: H 118 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6307 (p90) REVERT: H 187 ASP cc_start: 0.8409 (m-30) cc_final: 0.7950 (m-30) REVERT: H 215 GLU cc_start: 0.7994 (pt0) cc_final: 0.7627 (pp20) REVERT: H 246 LYS cc_start: 0.8537 (tmmt) cc_final: 0.8323 (tmmt) REVERT: H 260 LYS cc_start: 0.9397 (mtmm) cc_final: 0.8968 (mtmt) REVERT: H 268 TYR cc_start: 0.9073 (t80) cc_final: 0.8838 (t80) REVERT: H 273 LYS cc_start: 0.8857 (tmtt) cc_final: 0.8469 (ptpp) REVERT: H 488 ILE cc_start: 0.7090 (tt) cc_final: 0.6841 (tt) REVERT: H 544 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.7273 (tpp-160) REVERT: H 548 LYS cc_start: 0.7465 (tppt) cc_final: 0.7169 (tptp) REVERT: H 604 ASN cc_start: 0.8509 (m-40) cc_final: 0.8304 (m-40) REVERT: H 632 THR cc_start: 0.8784 (p) cc_final: 0.8512 (t) REVERT: H 764 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: H 772 PHE cc_start: 0.8127 (m-80) cc_final: 0.7726 (m-80) REVERT: I 61 LYS cc_start: 0.8957 (tppt) cc_final: 0.8729 (tppt) REVERT: I 62 LEU cc_start: 0.8414 (tt) cc_final: 0.7780 (tp) REVERT: I 162 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8246 (mmtt) REVERT: I 246 LYS cc_start: 0.8858 (tppt) cc_final: 0.8611 (tppt) REVERT: I 263 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8414 (mmm160) REVERT: I 468 PHE cc_start: 0.8640 (t80) cc_final: 0.8216 (t80) REVERT: I 472 LYS cc_start: 0.8685 (ptpp) cc_final: 0.8165 (ptmt) REVERT: I 475 PHE cc_start: 0.8119 (t80) cc_final: 0.7914 (t80) REVERT: I 531 ASP cc_start: 0.7884 (t70) cc_final: 0.7425 (t70) REVERT: I 533 GLN cc_start: 0.8532 (pt0) cc_final: 0.7727 (pt0) REVERT: I 537 GLN cc_start: 0.6852 (tm-30) cc_final: 0.5902 (tm-30) REVERT: I 542 TYR cc_start: 0.7902 (m-80) cc_final: 0.6817 (m-80) REVERT: I 544 ARG cc_start: 0.6966 (tpp80) cc_final: 0.6744 (tpp80) REVERT: I 563 GLN cc_start: 0.8365 (tt0) cc_final: 0.7515 (mm-40) outliers start: 121 outliers final: 82 residues processed: 876 average time/residue: 0.5229 time to fit residues: 732.4371 Evaluate side-chains 840 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 749 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 336 HIS Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 556 GLN Chi-restraints excluded: chain E residue 565 GLN Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 563 GLN Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 424 HIS Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 164 optimal weight: 0.6980 chunk 439 optimal weight: 3.9990 chunk 96 optimal weight: 40.0000 chunk 286 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 488 optimal weight: 40.0000 chunk 405 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN ** F 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 GLN H 140 ASN H 567 ASN ** H 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 745 HIS I 424 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38885 Z= 0.187 Angle : 0.600 12.495 52922 Z= 0.308 Chirality : 0.045 0.238 6190 Planarity : 0.004 0.046 6947 Dihedral : 4.233 33.888 5425 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 3.69 % Allowed : 17.84 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 5043 helix: 0.71 (0.16), residues: 1231 sheet: 0.43 (0.15), residues: 1146 loop : -0.81 (0.12), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 570 HIS 0.017 0.001 HIS I 424 PHE 0.033 0.001 PHE I 247 TYR 0.017 0.001 TYR I 600 ARG 0.010 0.001 ARG G 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 788 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7890 (ptp-170) cc_final: 0.7250 (ptm160) REVERT: A 180 ASN cc_start: 0.8730 (t0) cc_final: 0.8495 (t0) REVERT: A 197 LYS cc_start: 0.7933 (tppt) cc_final: 0.7721 (tptt) REVERT: A 224 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 346 TRP cc_start: 0.7793 (m-10) cc_final: 0.7545 (m-10) REVERT: A 389 GLN cc_start: 0.7600 (mp10) cc_final: 0.7030 (mp10) REVERT: A 434 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6715 (ppp) REVERT: A 446 LYS cc_start: 0.8685 (mmpt) cc_final: 0.8310 (mmmt) REVERT: A 453 ASP cc_start: 0.8758 (p0) cc_final: 0.8277 (p0) REVERT: A 551 ASP cc_start: 0.7972 (m-30) cc_final: 0.7665 (p0) REVERT: A 631 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8156 (tt) REVERT: A 636 ARG cc_start: 0.8517 (ptp90) cc_final: 0.8094 (ptp90) REVERT: A 637 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8893 (ttpt) REVERT: A 703 LYS cc_start: 0.8684 (mmtp) cc_final: 0.8414 (mmtp) REVERT: B 190 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7068 (mt-10) REVERT: B 224 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 335 ASP cc_start: 0.8195 (t0) cc_final: 0.7887 (t0) REVERT: B 353 ASN cc_start: 0.8213 (t0) cc_final: 0.7917 (t0) REVERT: B 434 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8368 (ppp) REVERT: B 446 LYS cc_start: 0.7988 (mmpt) cc_final: 0.7542 (mmtt) REVERT: B 515 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 525 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7332 (pt0) REVERT: B 551 ASP cc_start: 0.7606 (m-30) cc_final: 0.7246 (p0) REVERT: B 586 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8697 (mtmm) REVERT: B 595 ARG cc_start: 0.8518 (ptt-90) cc_final: 0.8138 (ptt90) REVERT: B 603 ILE cc_start: 0.9400 (tp) cc_final: 0.9146 (mp) REVERT: B 636 ARG cc_start: 0.8289 (mpp80) cc_final: 0.8003 (mtm-85) REVERT: B 637 LYS cc_start: 0.9058 (ptmt) cc_final: 0.8801 (pttt) REVERT: B 703 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7994 (mmtm) REVERT: C 291 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8324 (mtpt) REVERT: C 385 LEU cc_start: 0.8680 (tt) cc_final: 0.7959 (tt) REVERT: C 387 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8387 (tptt) REVERT: C 389 GLN cc_start: 0.7943 (mp10) cc_final: 0.7234 (mp10) REVERT: C 434 MET cc_start: 0.8222 (ppp) cc_final: 0.7939 (ppp) REVERT: C 446 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7903 (mmtt) REVERT: C 497 ASP cc_start: 0.8094 (p0) cc_final: 0.7547 (p0) REVERT: C 499 ASN cc_start: 0.8610 (m-40) cc_final: 0.8281 (m-40) REVERT: C 593 ASP cc_start: 0.8203 (t0) cc_final: 0.7681 (t0) REVERT: C 599 ASP cc_start: 0.8831 (t70) cc_final: 0.8563 (t70) REVERT: C 608 ASP cc_start: 0.7885 (m-30) cc_final: 0.7419 (t0) REVERT: D 202 PHE cc_start: 0.8977 (p90) cc_final: 0.8749 (p90) REVERT: D 212 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8039 (tm-30) REVERT: D 267 GLU cc_start: 0.7987 (mp0) cc_final: 0.7769 (mp0) REVERT: D 389 GLN cc_start: 0.7739 (mp10) cc_final: 0.7241 (mp10) REVERT: D 434 MET cc_start: 0.8195 (ppp) cc_final: 0.7488 (ppp) REVERT: D 446 LYS cc_start: 0.7578 (mmmt) cc_final: 0.7135 (mmmt) REVERT: D 448 LEU cc_start: 0.8747 (mp) cc_final: 0.8240 (mp) REVERT: D 465 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7811 (mp0) REVERT: D 515 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7302 (mm-30) REVERT: D 643 ILE cc_start: 0.8586 (mm) cc_final: 0.8319 (pt) REVERT: D 703 LYS cc_start: 0.8626 (mptt) cc_final: 0.8197 (mptt) REVERT: D 704 GLU cc_start: 0.7833 (pt0) cc_final: 0.7403 (pt0) REVERT: D 727 PHE cc_start: 0.8477 (t80) cc_final: 0.7793 (t80) REVERT: E 446 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8339 (mmmt) REVERT: E 447 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7598 (tp40) REVERT: E 472 ASP cc_start: 0.8054 (t0) cc_final: 0.7597 (t0) REVERT: E 600 ARG cc_start: 0.7890 (tpt90) cc_final: 0.6964 (tpm170) REVERT: F 195 ASP cc_start: 0.8081 (t0) cc_final: 0.7868 (t0) REVERT: F 197 LYS cc_start: 0.8670 (tptp) cc_final: 0.8298 (tptp) REVERT: F 361 ASN cc_start: 0.8720 (t0) cc_final: 0.7586 (p0) REVERT: F 387 LYS cc_start: 0.9392 (mmmt) cc_final: 0.8946 (ptmm) REVERT: F 389 GLN cc_start: 0.7846 (mp10) cc_final: 0.7540 (mp10) REVERT: F 421 LEU cc_start: 0.9056 (tt) cc_final: 0.8782 (tt) REVERT: F 434 MET cc_start: 0.7454 (ppp) cc_final: 0.6812 (ppp) REVERT: F 449 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8298 (mtm-85) REVERT: F 479 GLU cc_start: 0.8363 (mp0) cc_final: 0.8033 (mp0) REVERT: F 565 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8166 (mt0) REVERT: F 579 ASP cc_start: 0.8330 (p0) cc_final: 0.8093 (t0) REVERT: F 602 ASN cc_start: 0.8729 (m110) cc_final: 0.8356 (m110) REVERT: F 633 LYS cc_start: 0.9027 (tppt) cc_final: 0.8152 (tppt) REVERT: F 634 ASP cc_start: 0.9278 (p0) cc_final: 0.8682 (p0) REVERT: F 637 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8347 (mttp) REVERT: G 235 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: G 267 GLU cc_start: 0.7574 (pp20) cc_final: 0.7175 (pp20) REVERT: G 268 ASN cc_start: 0.8520 (p0) cc_final: 0.8143 (p0) REVERT: G 387 LYS cc_start: 0.8945 (tppt) cc_final: 0.8549 (tppt) REVERT: G 389 GLN cc_start: 0.8455 (mp10) cc_final: 0.8070 (mp10) REVERT: G 441 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8878 (mt-10) REVERT: G 472 ASP cc_start: 0.7688 (t70) cc_final: 0.7076 (t70) REVERT: G 549 GLU cc_start: 0.8056 (mp0) cc_final: 0.7715 (tp30) REVERT: G 582 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8596 (mmmm) REVERT: G 593 ASP cc_start: 0.8073 (t0) cc_final: 0.7556 (t0) REVERT: G 703 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7827 (mtmm) REVERT: G 705 ASN cc_start: 0.8871 (m-40) cc_final: 0.8376 (p0) REVERT: H 187 ASP cc_start: 0.8391 (m-30) cc_final: 0.7933 (m-30) REVERT: H 215 GLU cc_start: 0.7992 (pt0) cc_final: 0.7698 (pp20) REVERT: H 257 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: H 260 LYS cc_start: 0.9369 (mtmm) cc_final: 0.8927 (mtmt) REVERT: H 268 TYR cc_start: 0.9075 (t80) cc_final: 0.8811 (t80) REVERT: H 273 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8572 (ptmt) REVERT: H 296 LEU cc_start: 0.8794 (mm) cc_final: 0.8575 (mm) REVERT: H 438 TYR cc_start: 0.8535 (m-80) cc_final: 0.8263 (m-80) REVERT: H 548 LYS cc_start: 0.7472 (tppt) cc_final: 0.7178 (tptp) REVERT: H 604 ASN cc_start: 0.8445 (m-40) cc_final: 0.8189 (m-40) REVERT: H 632 THR cc_start: 0.8730 (p) cc_final: 0.8453 (t) REVERT: H 764 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: H 772 PHE cc_start: 0.8116 (m-80) cc_final: 0.7560 (m-80) REVERT: I 61 LYS cc_start: 0.8960 (tppt) cc_final: 0.8724 (tppt) REVERT: I 162 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8218 (mmmt) REVERT: I 167 TYR cc_start: 0.6618 (OUTLIER) cc_final: 0.6187 (t80) REVERT: I 246 LYS cc_start: 0.8819 (tppt) cc_final: 0.8583 (tppt) REVERT: I 261 ASP cc_start: 0.8534 (t0) cc_final: 0.8323 (t0) REVERT: I 468 PHE cc_start: 0.8647 (t80) cc_final: 0.8183 (t80) REVERT: I 472 LYS cc_start: 0.8710 (ptpp) cc_final: 0.8168 (ptmt) REVERT: I 491 ARG cc_start: 0.7555 (ptp-170) cc_final: 0.7349 (ptp-170) REVERT: I 537 GLN cc_start: 0.6846 (tm-30) cc_final: 0.6526 (tm-30) REVERT: I 542 TYR cc_start: 0.7911 (m-80) cc_final: 0.7504 (m-80) outliers start: 143 outliers final: 101 residues processed: 869 average time/residue: 0.5277 time to fit residues: 738.1273 Evaluate side-chains 857 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 748 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 336 HIS Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 502 GLU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 556 GLN Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 556 GLN Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 563 GLN Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 622 LEU Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 471 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 278 optimal weight: 2.9990 chunk 356 optimal weight: 40.0000 chunk 276 optimal weight: 3.9990 chunk 411 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 486 optimal weight: 4.9990 chunk 304 optimal weight: 30.0000 chunk 296 optimal weight: 3.9990 chunk 224 optimal weight: 0.0370 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 565 GLN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 GLN F 557 GLN G 543 GLN H 248 ASN ** H 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN I 424 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 38885 Z= 0.308 Angle : 0.636 12.567 52922 Z= 0.329 Chirality : 0.046 0.247 6190 Planarity : 0.004 0.047 6947 Dihedral : 4.327 33.485 5425 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 4.10 % Allowed : 18.22 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 5043 helix: 0.32 (0.15), residues: 1338 sheet: 0.47 (0.15), residues: 1133 loop : -0.88 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 570 HIS 0.009 0.001 HIS H 745 PHE 0.023 0.002 PHE E 202 TYR 0.015 0.001 TYR I 82 ARG 0.006 0.001 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 781 time to evaluate : 4.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7917 (ptp-170) cc_final: 0.7346 (ptm160) REVERT: A 180 ASN cc_start: 0.8734 (t0) cc_final: 0.8496 (t0) REVERT: A 197 LYS cc_start: 0.8044 (tppt) cc_final: 0.7685 (tptp) REVERT: A 224 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8110 (mm-30) REVERT: A 346 TRP cc_start: 0.7787 (m-10) cc_final: 0.7584 (m-10) REVERT: A 389 GLN cc_start: 0.7677 (mp10) cc_final: 0.7066 (mp10) REVERT: A 434 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6787 (ppp) REVERT: A 446 LYS cc_start: 0.8700 (mmpt) cc_final: 0.8267 (mmmt) REVERT: A 453 ASP cc_start: 0.8772 (p0) cc_final: 0.8271 (p0) REVERT: A 555 ASP cc_start: 0.7321 (t70) cc_final: 0.6856 (t70) REVERT: A 599 ASP cc_start: 0.8008 (t0) cc_final: 0.7688 (t70) REVERT: A 636 ARG cc_start: 0.8420 (ptp90) cc_final: 0.8127 (ptp90) REVERT: A 637 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8901 (ttpt) REVERT: A 703 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8396 (mmtp) REVERT: B 190 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7078 (mt-10) REVERT: B 224 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 267 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7438 (tm-30) REVERT: B 335 ASP cc_start: 0.8174 (t0) cc_final: 0.7866 (p0) REVERT: B 353 ASN cc_start: 0.8191 (t0) cc_final: 0.7890 (t0) REVERT: B 434 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8352 (ppp) REVERT: B 446 LYS cc_start: 0.7935 (mmpt) cc_final: 0.7519 (mmtt) REVERT: B 515 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 546 ASP cc_start: 0.8114 (t70) cc_final: 0.7828 (t0) REVERT: B 551 ASP cc_start: 0.7595 (m-30) cc_final: 0.7246 (p0) REVERT: B 569 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8442 (mm) REVERT: B 586 LYS cc_start: 0.9093 (mtmm) cc_final: 0.8865 (mtmm) REVERT: B 595 ARG cc_start: 0.8543 (ptt-90) cc_final: 0.8134 (ptt90) REVERT: B 636 ARG cc_start: 0.8171 (mpp80) cc_final: 0.7894 (mtm-85) REVERT: B 703 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7772 (mmtm) REVERT: C 326 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8314 (p0) REVERT: C 387 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8396 (tptt) REVERT: C 434 MET cc_start: 0.8205 (ppp) cc_final: 0.7910 (ppp) REVERT: C 446 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7895 (mmtt) REVERT: C 497 ASP cc_start: 0.8096 (p0) cc_final: 0.7609 (p0) REVERT: C 499 ASN cc_start: 0.8591 (m-40) cc_final: 0.8115 (m-40) REVERT: C 593 ASP cc_start: 0.8189 (t0) cc_final: 0.7681 (t0) REVERT: C 599 ASP cc_start: 0.8890 (t70) cc_final: 0.8610 (t70) REVERT: C 608 ASP cc_start: 0.7930 (m-30) cc_final: 0.7408 (t70) REVERT: D 212 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8119 (tm-30) REVERT: D 389 GLN cc_start: 0.7771 (mp10) cc_final: 0.7373 (mp10) REVERT: D 434 MET cc_start: 0.8121 (ppp) cc_final: 0.7401 (ppp) REVERT: D 446 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7371 (mmmt) REVERT: D 472 ASP cc_start: 0.7746 (t0) cc_final: 0.7350 (t0) REVERT: D 496 LYS cc_start: 0.9107 (ttmm) cc_final: 0.8671 (tppt) REVERT: D 515 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7281 (mm-30) REVERT: D 565 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: D 643 ILE cc_start: 0.8548 (mm) cc_final: 0.8287 (pt) REVERT: D 703 LYS cc_start: 0.8661 (mptt) cc_final: 0.8250 (mptt) REVERT: D 727 PHE cc_start: 0.8506 (t80) cc_final: 0.7819 (t80) REVERT: E 446 LYS cc_start: 0.8720 (ttmt) cc_final: 0.8350 (mmtt) REVERT: E 447 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7591 (tp40) REVERT: E 472 ASP cc_start: 0.8106 (t0) cc_final: 0.7663 (t0) REVERT: E 600 ARG cc_start: 0.7859 (tpt90) cc_final: 0.6913 (tpm170) REVERT: E 631 ILE cc_start: 0.5769 (OUTLIER) cc_final: 0.5568 (mt) REVERT: F 195 ASP cc_start: 0.8087 (t0) cc_final: 0.7827 (t0) REVERT: F 197 LYS cc_start: 0.8710 (tptp) cc_final: 0.8344 (tptp) REVERT: F 361 ASN cc_start: 0.8768 (t0) cc_final: 0.7693 (p0) REVERT: F 389 GLN cc_start: 0.7904 (mp10) cc_final: 0.7644 (mp10) REVERT: F 421 LEU cc_start: 0.9052 (tt) cc_final: 0.8771 (tt) REVERT: F 434 MET cc_start: 0.7664 (ppp) cc_final: 0.6972 (ppp) REVERT: F 446 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7673 (mmpt) REVERT: F 447 GLN cc_start: 0.7460 (mm-40) cc_final: 0.6988 (mm110) REVERT: F 449 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8299 (mtm-85) REVERT: F 479 GLU cc_start: 0.8337 (mp0) cc_final: 0.7972 (mp0) REVERT: F 512 ASP cc_start: 0.7905 (t0) cc_final: 0.7595 (t0) REVERT: F 551 ASP cc_start: 0.7879 (m-30) cc_final: 0.7266 (t70) REVERT: F 556 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: F 565 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8133 (mt0) REVERT: F 579 ASP cc_start: 0.8325 (p0) cc_final: 0.8076 (t0) REVERT: F 602 ASN cc_start: 0.8714 (m110) cc_final: 0.8358 (m110) REVERT: F 633 LYS cc_start: 0.9026 (tppt) cc_final: 0.8128 (tppt) REVERT: F 634 ASP cc_start: 0.9284 (p0) cc_final: 0.8800 (p0) REVERT: F 637 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8370 (mttp) REVERT: G 235 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.7764 (m-30) REVERT: G 389 GLN cc_start: 0.8503 (mp10) cc_final: 0.8096 (mp10) REVERT: G 441 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8866 (mt-10) REVERT: G 470 ARG cc_start: 0.7600 (tpp80) cc_final: 0.7272 (tpp-160) REVERT: G 472 ASP cc_start: 0.7905 (t70) cc_final: 0.7245 (t0) REVERT: G 563 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8568 (mmtp) REVERT: G 582 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8657 (mmmm) REVERT: G 584 ASN cc_start: 0.8444 (m-40) cc_final: 0.8203 (m-40) REVERT: G 593 ASP cc_start: 0.8123 (t0) cc_final: 0.7731 (t0) REVERT: G 600 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7621 (tmm-80) REVERT: G 703 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7924 (mtmm) REVERT: G 705 ASN cc_start: 0.8926 (m-40) cc_final: 0.8650 (m110) REVERT: H 118 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6472 (p90) REVERT: H 215 GLU cc_start: 0.8027 (pt0) cc_final: 0.7758 (pp20) REVERT: H 248 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7520 (p0) REVERT: H 251 GLU cc_start: 0.7516 (pp20) cc_final: 0.7253 (tm-30) REVERT: H 260 LYS cc_start: 0.9351 (mtmm) cc_final: 0.8903 (mtmt) REVERT: H 268 TYR cc_start: 0.9098 (t80) cc_final: 0.8830 (t80) REVERT: H 273 LYS cc_start: 0.8855 (tttt) cc_final: 0.8470 (ptmt) REVERT: H 438 TYR cc_start: 0.8519 (m-80) cc_final: 0.8296 (m-80) REVERT: H 548 LYS cc_start: 0.7487 (tppt) cc_final: 0.7168 (tptp) REVERT: H 604 ASN cc_start: 0.8422 (m-40) cc_final: 0.8137 (m-40) REVERT: H 632 THR cc_start: 0.8776 (p) cc_final: 0.8493 (t) REVERT: H 742 ARG cc_start: 0.8981 (tmm-80) cc_final: 0.8615 (ttp80) REVERT: H 764 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: H 772 PHE cc_start: 0.8110 (m-80) cc_final: 0.7643 (m-80) REVERT: I 61 LYS cc_start: 0.9031 (tppt) cc_final: 0.8797 (tppt) REVERT: I 102 LYS cc_start: 0.6596 (mttt) cc_final: 0.5878 (mptt) REVERT: I 162 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8193 (mmmt) REVERT: I 246 LYS cc_start: 0.8803 (tppt) cc_final: 0.8537 (tppt) REVERT: I 468 PHE cc_start: 0.8643 (t80) cc_final: 0.8207 (t80) REVERT: I 472 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8198 (ptmt) REVERT: I 542 TYR cc_start: 0.7866 (m-80) cc_final: 0.7444 (m-10) outliers start: 159 outliers final: 121 residues processed: 871 average time/residue: 0.5116 time to fit residues: 713.6147 Evaluate side-chains 868 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 735 time to evaluate : 4.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 565 GLN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 336 HIS Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 502 GLU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 631 ILE Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 556 GLN Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 248 ASN Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 563 GLN Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 622 LEU Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 301 optimal weight: 0.0470 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 331 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 45 optimal weight: 30.0000 chunk 382 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 248 ASN H 250 GLN ** H 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN I 424 HIS I 533 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38885 Z= 0.181 Angle : 0.634 12.717 52922 Z= 0.323 Chirality : 0.046 0.338 6190 Planarity : 0.004 0.045 6947 Dihedral : 4.208 32.461 5425 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 3.46 % Allowed : 19.75 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 5043 helix: 0.46 (0.15), residues: 1320 sheet: 0.44 (0.15), residues: 1156 loop : -0.79 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 570 HIS 0.008 0.001 HIS H 745 PHE 0.021 0.001 PHE E 202 TYR 0.019 0.001 TYR F 542 ARG 0.008 0.001 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 779 time to evaluate : 4.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7316 (ptm160) REVERT: A 180 ASN cc_start: 0.8728 (t0) cc_final: 0.8511 (t0) REVERT: A 224 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8048 (mm-30) REVERT: A 389 GLN cc_start: 0.7668 (mp10) cc_final: 0.7077 (mp10) REVERT: A 434 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6815 (ppp) REVERT: A 446 LYS cc_start: 0.8725 (mmpt) cc_final: 0.8524 (mmtt) REVERT: A 453 ASP cc_start: 0.8724 (p0) cc_final: 0.8261 (p0) REVERT: A 486 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 555 ASP cc_start: 0.7108 (t70) cc_final: 0.6719 (t70) REVERT: A 599 ASP cc_start: 0.7932 (t0) cc_final: 0.7584 (t70) REVERT: A 636 ARG cc_start: 0.8440 (ptp90) cc_final: 0.8173 (ptp90) REVERT: A 637 LYS cc_start: 0.9146 (ttmt) cc_final: 0.8876 (ttpt) REVERT: A 703 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8359 (mmtp) REVERT: B 190 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7105 (mt-10) REVERT: B 224 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7606 (mm-30) REVERT: B 267 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7336 (tp30) REVERT: B 335 ASP cc_start: 0.8165 (t0) cc_final: 0.7885 (p0) REVERT: B 353 ASN cc_start: 0.8209 (t0) cc_final: 0.7936 (t0) REVERT: B 434 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8357 (ppp) REVERT: B 446 LYS cc_start: 0.8001 (mmpt) cc_final: 0.7554 (mmtt) REVERT: B 479 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6908 (mm-30) REVERT: B 546 ASP cc_start: 0.8095 (t70) cc_final: 0.7779 (t0) REVERT: B 551 ASP cc_start: 0.7590 (m-30) cc_final: 0.7191 (p0) REVERT: B 569 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8383 (mm) REVERT: B 586 LYS cc_start: 0.9081 (mtmm) cc_final: 0.8820 (mtmm) REVERT: B 595 ARG cc_start: 0.8548 (ptt-90) cc_final: 0.8130 (ptt90) REVERT: B 603 ILE cc_start: 0.9407 (tp) cc_final: 0.9118 (mp) REVERT: B 636 ARG cc_start: 0.8163 (mpp80) cc_final: 0.7872 (mtm-85) REVERT: B 703 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7791 (mmtm) REVERT: C 291 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8580 (mtpt) REVERT: C 326 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8477 (p0) REVERT: C 387 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8317 (tptt) REVERT: C 434 MET cc_start: 0.8280 (ppp) cc_final: 0.7963 (ppp) REVERT: C 446 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7957 (mmtt) REVERT: C 497 ASP cc_start: 0.8086 (p0) cc_final: 0.7556 (p0) REVERT: C 499 ASN cc_start: 0.8579 (m-40) cc_final: 0.8089 (m-40) REVERT: C 593 ASP cc_start: 0.8153 (t0) cc_final: 0.7668 (t0) REVERT: C 599 ASP cc_start: 0.8860 (t70) cc_final: 0.8630 (t70) REVERT: D 202 PHE cc_start: 0.8985 (p90) cc_final: 0.8761 (p90) REVERT: D 212 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8085 (tm-30) REVERT: D 389 GLN cc_start: 0.7780 (mp10) cc_final: 0.7274 (mp10) REVERT: D 434 MET cc_start: 0.8147 (ppp) cc_final: 0.7383 (ppp) REVERT: D 446 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7290 (mmmt) REVERT: D 465 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7781 (mp0) REVERT: D 472 ASP cc_start: 0.7706 (t0) cc_final: 0.7292 (t0) REVERT: D 496 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8740 (tppt) REVERT: D 515 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7179 (mm-30) REVERT: D 600 ARG cc_start: 0.8397 (ttp80) cc_final: 0.7610 (ptm-80) REVERT: D 643 ILE cc_start: 0.8518 (mm) cc_final: 0.8288 (pt) REVERT: D 703 LYS cc_start: 0.8661 (mptt) cc_final: 0.8344 (mptt) REVERT: D 727 PHE cc_start: 0.8525 (t80) cc_final: 0.7880 (t80) REVERT: E 185 ASP cc_start: 0.8242 (p0) cc_final: 0.8023 (p0) REVERT: E 446 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8312 (mmtt) REVERT: E 447 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7610 (tp40) REVERT: E 472 ASP cc_start: 0.8042 (t0) cc_final: 0.7602 (t0) REVERT: E 525 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7357 (mp0) REVERT: E 600 ARG cc_start: 0.7846 (tpt90) cc_final: 0.6894 (tpm170) REVERT: F 197 LYS cc_start: 0.8676 (tptp) cc_final: 0.8308 (tptp) REVERT: F 361 ASN cc_start: 0.8774 (t0) cc_final: 0.7728 (p0) REVERT: F 387 LYS cc_start: 0.9323 (mmmt) cc_final: 0.9014 (ptmm) REVERT: F 389 GLN cc_start: 0.7907 (mp10) cc_final: 0.7593 (mp10) REVERT: F 421 LEU cc_start: 0.9053 (tt) cc_final: 0.8783 (tt) REVERT: F 434 MET cc_start: 0.7655 (ppp) cc_final: 0.6955 (ppp) REVERT: F 446 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7670 (mmpt) REVERT: F 447 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6726 (mp10) REVERT: F 449 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8296 (mtm-85) REVERT: F 479 GLU cc_start: 0.8392 (mp0) cc_final: 0.8083 (mp0) REVERT: F 565 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8167 (mt0) REVERT: F 579 ASP cc_start: 0.8300 (p0) cc_final: 0.8076 (t0) REVERT: F 602 ASN cc_start: 0.8549 (m110) cc_final: 0.8245 (m110) REVERT: F 633 LYS cc_start: 0.9024 (tppt) cc_final: 0.8179 (tppt) REVERT: F 634 ASP cc_start: 0.9293 (p0) cc_final: 0.8508 (p0) REVERT: F 636 ARG cc_start: 0.8148 (ptp90) cc_final: 0.7696 (ptp90) REVERT: F 637 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8235 (mttp) REVERT: G 235 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: G 389 GLN cc_start: 0.8499 (mp10) cc_final: 0.8108 (mp10) REVERT: G 441 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8899 (mt-10) REVERT: G 470 ARG cc_start: 0.7514 (tpp80) cc_final: 0.7217 (tpp-160) REVERT: G 472 ASP cc_start: 0.7773 (t70) cc_final: 0.7087 (t0) REVERT: G 582 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8649 (mmmm) REVERT: G 593 ASP cc_start: 0.8035 (t0) cc_final: 0.7640 (t0) REVERT: G 600 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7458 (tmm-80) REVERT: G 703 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7834 (mptt) REVERT: G 705 ASN cc_start: 0.8924 (m-40) cc_final: 0.8416 (p0) REVERT: H 61 LYS cc_start: 0.8855 (mptt) cc_final: 0.8616 (mmtm) REVERT: H 118 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6580 (p90) REVERT: H 189 LEU cc_start: 0.8785 (mp) cc_final: 0.8276 (mp) REVERT: H 215 GLU cc_start: 0.7978 (pt0) cc_final: 0.7705 (pp20) REVERT: H 246 LYS cc_start: 0.8351 (tptt) cc_final: 0.8024 (tmmt) REVERT: H 248 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7625 (p0) REVERT: H 250 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: H 260 LYS cc_start: 0.9351 (mtmm) cc_final: 0.8928 (mtmt) REVERT: H 268 TYR cc_start: 0.9109 (t80) cc_final: 0.8840 (t80) REVERT: H 273 LYS cc_start: 0.8847 (tttt) cc_final: 0.8466 (ptpp) REVERT: H 438 TYR cc_start: 0.8538 (m-80) cc_final: 0.8134 (m-80) REVERT: H 548 LYS cc_start: 0.7552 (tppt) cc_final: 0.7241 (tptp) REVERT: H 632 THR cc_start: 0.8736 (p) cc_final: 0.8463 (t) REVERT: H 764 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: H 772 PHE cc_start: 0.8096 (m-80) cc_final: 0.7618 (m-80) REVERT: I 61 LYS cc_start: 0.8962 (tppt) cc_final: 0.8712 (tppt) REVERT: I 102 LYS cc_start: 0.6573 (mttt) cc_final: 0.6324 (mttm) REVERT: I 162 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8330 (mmtp) REVERT: I 246 LYS cc_start: 0.8886 (tppt) cc_final: 0.8681 (tppt) REVERT: I 468 PHE cc_start: 0.8613 (t80) cc_final: 0.8179 (t80) REVERT: I 472 LYS cc_start: 0.8741 (ptpp) cc_final: 0.8162 (ptmt) REVERT: I 537 GLN cc_start: 0.7243 (tm-30) cc_final: 0.6794 (tm-30) REVERT: I 542 TYR cc_start: 0.7920 (m-80) cc_final: 0.7205 (m-80) outliers start: 134 outliers final: 103 residues processed: 854 average time/residue: 0.5147 time to fit residues: 703.5186 Evaluate side-chains 855 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 742 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 555 ASP Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 248 ASN Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 563 GLN Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 584 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 442 optimal weight: 4.9990 chunk 466 optimal weight: 30.0000 chunk 425 optimal weight: 6.9990 chunk 453 optimal weight: 0.9980 chunk 273 optimal weight: 0.6980 chunk 197 optimal weight: 8.9990 chunk 356 optimal weight: 40.0000 chunk 139 optimal weight: 0.8980 chunk 409 optimal weight: 0.0980 chunk 428 optimal weight: 5.9990 chunk 451 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 GLN G 584 ASN H 248 ASN H 250 GLN ** H 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN I 424 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38885 Z= 0.227 Angle : 0.651 13.832 52922 Z= 0.334 Chirality : 0.046 0.285 6190 Planarity : 0.004 0.045 6947 Dihedral : 4.212 32.250 5425 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.59 % Allowed : 20.16 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 5043 helix: 0.41 (0.15), residues: 1330 sheet: 0.64 (0.15), residues: 1126 loop : -0.78 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 570 HIS 0.011 0.001 HIS H 745 PHE 0.036 0.001 PHE H 337 TYR 0.032 0.001 TYR F 542 ARG 0.008 0.001 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 759 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7808 (ptp-170) cc_final: 0.7208 (ptm160) REVERT: A 180 ASN cc_start: 0.8731 (t0) cc_final: 0.8520 (t0) REVERT: A 224 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 385 LEU cc_start: 0.7906 (tt) cc_final: 0.7283 (tt) REVERT: A 389 GLN cc_start: 0.7657 (mp10) cc_final: 0.7009 (mp10) REVERT: A 434 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6672 (ppp) REVERT: A 446 LYS cc_start: 0.8636 (mmpt) cc_final: 0.8414 (mmtt) REVERT: A 453 ASP cc_start: 0.8724 (p0) cc_final: 0.8266 (p0) REVERT: A 486 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 555 ASP cc_start: 0.7069 (t70) cc_final: 0.6704 (t70) REVERT: A 599 ASP cc_start: 0.7953 (t0) cc_final: 0.7647 (t70) REVERT: A 636 ARG cc_start: 0.8419 (ptp90) cc_final: 0.8078 (ptp90) REVERT: A 637 LYS cc_start: 0.9159 (ttmt) cc_final: 0.8882 (ttpt) REVERT: A 703 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8454 (mmtp) REVERT: B 190 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7101 (mt-10) REVERT: B 224 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 335 ASP cc_start: 0.8136 (t0) cc_final: 0.7890 (p0) REVERT: B 353 ASN cc_start: 0.8219 (t0) cc_final: 0.7944 (t0) REVERT: B 403 GLN cc_start: 0.7981 (mp10) cc_final: 0.7650 (mp10) REVERT: B 434 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8355 (ppp) REVERT: B 446 LYS cc_start: 0.7990 (mmpt) cc_final: 0.7569 (mmtt) REVERT: B 479 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6861 (mm-30) REVERT: B 541 GLN cc_start: 0.8694 (pt0) cc_final: 0.8337 (pt0) REVERT: B 546 ASP cc_start: 0.8111 (t70) cc_final: 0.7804 (t0) REVERT: B 551 ASP cc_start: 0.7580 (m-30) cc_final: 0.7233 (p0) REVERT: B 595 ARG cc_start: 0.8568 (ptt-90) cc_final: 0.8166 (ptt90) REVERT: B 603 ILE cc_start: 0.9399 (tp) cc_final: 0.9120 (mp) REVERT: B 613 LYS cc_start: 0.9177 (mttt) cc_final: 0.8797 (mmtt) REVERT: B 703 LYS cc_start: 0.8280 (mmtm) cc_final: 0.7831 (mmtm) REVERT: C 291 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8558 (mtpt) REVERT: C 326 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8428 (p0) REVERT: C 387 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8402 (tptt) REVERT: C 434 MET cc_start: 0.8236 (ppp) cc_final: 0.7896 (ppp) REVERT: C 446 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7895 (mmtt) REVERT: C 497 ASP cc_start: 0.8107 (p0) cc_final: 0.7549 (p0) REVERT: C 499 ASN cc_start: 0.8577 (m-40) cc_final: 0.8052 (m-40) REVERT: C 593 ASP cc_start: 0.8073 (t0) cc_final: 0.7615 (t0) REVERT: C 599 ASP cc_start: 0.8867 (t70) cc_final: 0.8634 (t70) REVERT: D 389 GLN cc_start: 0.7743 (mp10) cc_final: 0.7287 (mp10) REVERT: D 434 MET cc_start: 0.8148 (ppp) cc_final: 0.7405 (ppp) REVERT: D 446 LYS cc_start: 0.7441 (mmmt) cc_final: 0.7101 (mmmt) REVERT: D 472 ASP cc_start: 0.7723 (t0) cc_final: 0.7303 (t0) REVERT: D 496 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8857 (tppt) REVERT: D 515 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7173 (mm-30) REVERT: D 643 ILE cc_start: 0.8488 (mm) cc_final: 0.8264 (pt) REVERT: D 703 LYS cc_start: 0.8553 (mptt) cc_final: 0.8268 (mptt) REVERT: D 727 PHE cc_start: 0.8502 (t80) cc_final: 0.7898 (t80) REVERT: E 291 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8080 (mmtp) REVERT: E 434 MET cc_start: 0.7865 (tmm) cc_final: 0.7608 (tmm) REVERT: E 446 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8378 (mmtt) REVERT: E 447 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7606 (tp40) REVERT: E 472 ASP cc_start: 0.8066 (t0) cc_final: 0.7621 (t0) REVERT: E 587 MET cc_start: 0.7709 (mtt) cc_final: 0.7404 (mtt) REVERT: E 600 ARG cc_start: 0.7838 (tpt90) cc_final: 0.6837 (tpm170) REVERT: E 633 LYS cc_start: 0.8979 (pptt) cc_final: 0.8164 (tptp) REVERT: E 639 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8212 (mp) REVERT: F 197 LYS cc_start: 0.8675 (tptp) cc_final: 0.8318 (tptp) REVERT: F 291 LYS cc_start: 0.8135 (mmmm) cc_final: 0.7671 (mmmm) REVERT: F 361 ASN cc_start: 0.8792 (t0) cc_final: 0.7736 (p0) REVERT: F 387 LYS cc_start: 0.9344 (mmmt) cc_final: 0.9016 (ptmm) REVERT: F 389 GLN cc_start: 0.7913 (mp10) cc_final: 0.7598 (mp10) REVERT: F 421 LEU cc_start: 0.9064 (tt) cc_final: 0.8786 (tt) REVERT: F 434 MET cc_start: 0.7682 (ppp) cc_final: 0.6985 (ppp) REVERT: F 446 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7680 (mmpt) REVERT: F 447 GLN cc_start: 0.7380 (mm-40) cc_final: 0.6726 (mp10) REVERT: F 449 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.8281 (mtm-85) REVERT: F 479 GLU cc_start: 0.8390 (mp0) cc_final: 0.8056 (mp0) REVERT: F 557 GLN cc_start: 0.6882 (mp10) cc_final: 0.6534 (mp10) REVERT: F 565 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8172 (mt0) REVERT: F 602 ASN cc_start: 0.8555 (m110) cc_final: 0.8262 (m110) REVERT: F 633 LYS cc_start: 0.9020 (tppt) cc_final: 0.8061 (tppt) REVERT: F 634 ASP cc_start: 0.9291 (p0) cc_final: 0.8665 (p0) REVERT: F 636 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7692 (ptp90) REVERT: F 637 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8265 (mttp) REVERT: G 235 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: G 389 GLN cc_start: 0.8506 (mp10) cc_final: 0.8109 (mp10) REVERT: G 441 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8884 (mt-10) REVERT: G 470 ARG cc_start: 0.7459 (tpp80) cc_final: 0.7198 (tpp-160) REVERT: G 472 ASP cc_start: 0.7902 (t70) cc_final: 0.7231 (t0) REVERT: G 582 LYS cc_start: 0.9023 (mmtm) cc_final: 0.8660 (mmmm) REVERT: G 587 MET cc_start: 0.8152 (ptp) cc_final: 0.7764 (ptp) REVERT: G 593 ASP cc_start: 0.8040 (t0) cc_final: 0.7639 (t0) REVERT: G 600 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7384 (tmm-80) REVERT: G 703 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7864 (mptt) REVERT: G 705 ASN cc_start: 0.8933 (m-40) cc_final: 0.8430 (p0) REVERT: H 61 LYS cc_start: 0.8832 (mptt) cc_final: 0.8591 (mmtm) REVERT: H 118 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.6554 (p90) REVERT: H 158 ASP cc_start: 0.7601 (t70) cc_final: 0.7140 (t70) REVERT: H 189 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8288 (mp) REVERT: H 215 GLU cc_start: 0.7986 (pt0) cc_final: 0.7763 (pp20) REVERT: H 248 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7371 (p0) REVERT: H 250 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: H 260 LYS cc_start: 0.9320 (mtmm) cc_final: 0.8892 (mtmt) REVERT: H 268 TYR cc_start: 0.9110 (t80) cc_final: 0.8831 (t80) REVERT: H 273 LYS cc_start: 0.8865 (tttt) cc_final: 0.8511 (ptmt) REVERT: H 438 TYR cc_start: 0.8503 (m-80) cc_final: 0.8145 (m-80) REVERT: H 548 LYS cc_start: 0.7534 (tppt) cc_final: 0.7239 (tptp) REVERT: H 632 THR cc_start: 0.8747 (p) cc_final: 0.8485 (t) REVERT: H 742 ARG cc_start: 0.8961 (tmm-80) cc_final: 0.8508 (ttp80) REVERT: H 764 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: H 772 PHE cc_start: 0.8078 (m-80) cc_final: 0.7308 (m-80) REVERT: I 61 LYS cc_start: 0.8913 (tppt) cc_final: 0.8686 (tppt) REVERT: I 162 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8255 (mmtp) REVERT: I 263 ARG cc_start: 0.8756 (mmm160) cc_final: 0.8278 (mmm160) REVERT: I 277 HIS cc_start: 0.7799 (t70) cc_final: 0.7570 (t70) REVERT: I 468 PHE cc_start: 0.8635 (t80) cc_final: 0.8186 (t80) REVERT: I 472 LYS cc_start: 0.8780 (ptpp) cc_final: 0.8252 (ptmt) REVERT: I 537 GLN cc_start: 0.7191 (tm-30) cc_final: 0.6702 (tm-30) REVERT: I 542 TYR cc_start: 0.7921 (m-80) cc_final: 0.7177 (m-80) outliers start: 139 outliers final: 115 residues processed: 838 average time/residue: 0.5301 time to fit residues: 708.6070 Evaluate side-chains 863 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 737 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 556 GLN Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 555 ASP Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 537 ASN Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 248 ASN Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 563 GLN Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 424 HIS Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 297 optimal weight: 0.0980 chunk 479 optimal weight: 9.9990 chunk 292 optimal weight: 0.6980 chunk 227 optimal weight: 0.1980 chunk 333 optimal weight: 0.6980 chunk 503 optimal weight: 30.0000 chunk 463 optimal weight: 50.0000 chunk 400 optimal weight: 5.9990 chunk 41 optimal weight: 0.0060 chunk 309 optimal weight: 9.9990 chunk 245 optimal weight: 0.6980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 584 ASN ** H 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 604 ASN I 424 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38885 Z= 0.170 Angle : 0.665 14.685 52922 Z= 0.337 Chirality : 0.046 0.331 6190 Planarity : 0.004 0.042 6947 Dihedral : 4.119 32.387 5425 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.61 % Allowed : 21.37 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.12), residues: 5043 helix: 0.58 (0.16), residues: 1295 sheet: 0.77 (0.16), residues: 1128 loop : -0.62 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 570 HIS 0.015 0.001 HIS I 424 PHE 0.034 0.001 PHE H 337 TYR 0.029 0.001 TYR F 542 ARG 0.011 0.001 ARG B 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 804 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7783 (ptp-170) cc_final: 0.7186 (ptm160) REVERT: A 180 ASN cc_start: 0.8715 (t0) cc_final: 0.8505 (t0) REVERT: A 224 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7971 (mm-30) REVERT: A 389 GLN cc_start: 0.7634 (mp10) cc_final: 0.7049 (mp10) REVERT: A 434 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6651 (ppp) REVERT: A 446 LYS cc_start: 0.8633 (mmpt) cc_final: 0.8396 (mmtt) REVERT: A 453 ASP cc_start: 0.8710 (p0) cc_final: 0.8207 (p0) REVERT: A 485 GLN cc_start: 0.8865 (mt0) cc_final: 0.8640 (mt0) REVERT: A 486 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 555 ASP cc_start: 0.6957 (t70) cc_final: 0.6256 (t70) REVERT: A 557 GLN cc_start: 0.8264 (mp10) cc_final: 0.7995 (mp10) REVERT: A 599 ASP cc_start: 0.7885 (t0) cc_final: 0.7540 (t70) REVERT: A 636 ARG cc_start: 0.8368 (ptp90) cc_final: 0.8109 (ptp90) REVERT: A 637 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8866 (ttpt) REVERT: A 703 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8480 (mmtp) REVERT: B 190 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7126 (mt-10) REVERT: B 224 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 335 ASP cc_start: 0.8111 (t0) cc_final: 0.6600 (t0) REVERT: B 434 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8356 (ppp) REVERT: B 446 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7692 (mmtt) REVERT: B 479 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6844 (mm-30) REVERT: B 546 ASP cc_start: 0.8089 (t70) cc_final: 0.7779 (t0) REVERT: B 551 ASP cc_start: 0.7575 (m-30) cc_final: 0.7255 (p0) REVERT: B 563 LYS cc_start: 0.8147 (pttm) cc_final: 0.7932 (pttm) REVERT: B 595 ARG cc_start: 0.8525 (ptt-90) cc_final: 0.8119 (ptt90) REVERT: B 603 ILE cc_start: 0.9362 (tp) cc_final: 0.9081 (mp) REVERT: B 613 LYS cc_start: 0.9146 (mttt) cc_final: 0.8834 (mmtt) REVERT: B 636 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.8067 (ptp90) REVERT: B 703 LYS cc_start: 0.8323 (mmtm) cc_final: 0.7853 (mmtm) REVERT: C 235 ASP cc_start: 0.7257 (m-30) cc_final: 0.6440 (m-30) REVERT: C 291 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8520 (mtpt) REVERT: C 326 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8481 (p0) REVERT: C 387 LYS cc_start: 0.9059 (mmmm) cc_final: 0.8407 (tptt) REVERT: C 434 MET cc_start: 0.8264 (ppp) cc_final: 0.7949 (ppp) REVERT: C 446 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7913 (mmtt) REVERT: C 450 LEU cc_start: 0.9144 (mt) cc_final: 0.8904 (mp) REVERT: C 497 ASP cc_start: 0.8091 (p0) cc_final: 0.7637 (p0) REVERT: C 499 ASN cc_start: 0.8575 (m-40) cc_final: 0.8064 (m-40) REVERT: C 593 ASP cc_start: 0.7963 (t0) cc_final: 0.7502 (t0) REVERT: D 202 PHE cc_start: 0.8955 (p90) cc_final: 0.8720 (p90) REVERT: D 212 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8099 (tm-30) REVERT: D 389 GLN cc_start: 0.7678 (mp10) cc_final: 0.7298 (mp10) REVERT: D 434 MET cc_start: 0.8159 (ppp) cc_final: 0.7397 (ppp) REVERT: D 441 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8389 (mm-30) REVERT: D 446 LYS cc_start: 0.7357 (mmmt) cc_final: 0.7048 (mmmt) REVERT: D 465 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7759 (mp0) REVERT: D 472 ASP cc_start: 0.7719 (t0) cc_final: 0.7277 (t0) REVERT: D 496 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8881 (tppt) REVERT: D 497 ASP cc_start: 0.7486 (p0) cc_final: 0.6827 (p0) REVERT: D 499 ASN cc_start: 0.8691 (m-40) cc_final: 0.7992 (m-40) REVERT: D 515 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7173 (mm-30) REVERT: D 633 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8045 (mmmt) REVERT: D 643 ILE cc_start: 0.8486 (mm) cc_final: 0.8272 (pt) REVERT: D 703 LYS cc_start: 0.8651 (mptt) cc_final: 0.8392 (mptt) REVERT: D 727 PHE cc_start: 0.8489 (t80) cc_final: 0.7879 (t80) REVERT: E 291 LYS cc_start: 0.8730 (mmmm) cc_final: 0.7958 (mmtp) REVERT: E 434 MET cc_start: 0.7973 (tmm) cc_final: 0.7687 (tmm) REVERT: E 446 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8345 (mmtt) REVERT: E 447 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7616 (tp40) REVERT: E 472 ASP cc_start: 0.7998 (t0) cc_final: 0.7515 (t0) REVERT: E 587 MET cc_start: 0.7480 (mtt) cc_final: 0.6839 (mtt) REVERT: E 600 ARG cc_start: 0.7812 (tpt90) cc_final: 0.6810 (tpm170) REVERT: E 633 LYS cc_start: 0.9004 (pptt) cc_final: 0.8226 (tptp) REVERT: F 197 LYS cc_start: 0.8692 (tptp) cc_final: 0.8333 (tptp) REVERT: F 291 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7557 (mmmm) REVERT: F 361 ASN cc_start: 0.8793 (t0) cc_final: 0.7739 (p0) REVERT: F 387 LYS cc_start: 0.9368 (mmmt) cc_final: 0.9065 (ptmm) REVERT: F 389 GLN cc_start: 0.7892 (mp10) cc_final: 0.7579 (mp10) REVERT: F 421 LEU cc_start: 0.9091 (tt) cc_final: 0.8824 (tt) REVERT: F 434 MET cc_start: 0.7677 (ppp) cc_final: 0.6959 (ppp) REVERT: F 446 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7664 (mmtt) REVERT: F 447 GLN cc_start: 0.7339 (mm-40) cc_final: 0.6683 (mp10) REVERT: F 449 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8350 (mtm-85) REVERT: F 479 GLU cc_start: 0.8398 (mp0) cc_final: 0.8113 (mp0) REVERT: F 565 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8190 (mt0) REVERT: F 633 LYS cc_start: 0.9012 (tppt) cc_final: 0.8085 (tppt) REVERT: F 634 ASP cc_start: 0.9278 (p0) cc_final: 0.8627 (p0) REVERT: F 637 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8245 (mttp) REVERT: G 235 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: G 389 GLN cc_start: 0.8491 (mp10) cc_final: 0.8099 (mp10) REVERT: G 434 MET cc_start: 0.7972 (pmm) cc_final: 0.7706 (pmm) REVERT: G 441 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8862 (mt-10) REVERT: G 470 ARG cc_start: 0.7375 (tpp80) cc_final: 0.7084 (tpp-160) REVERT: G 472 ASP cc_start: 0.7730 (t70) cc_final: 0.7151 (t0) REVERT: G 582 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8656 (mmmm) REVERT: G 587 MET cc_start: 0.8095 (ptp) cc_final: 0.7731 (ptp) REVERT: G 593 ASP cc_start: 0.7936 (t0) cc_final: 0.7538 (t0) REVERT: G 703 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7939 (mttp) REVERT: G 705 ASN cc_start: 0.8931 (m-40) cc_final: 0.8421 (p0) REVERT: H 61 LYS cc_start: 0.8832 (mptt) cc_final: 0.8608 (mmtm) REVERT: H 74 TYR cc_start: 0.7358 (t80) cc_final: 0.6301 (t80) REVERT: H 118 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6467 (p90) REVERT: H 158 ASP cc_start: 0.7558 (t70) cc_final: 0.7120 (t70) REVERT: H 215 GLU cc_start: 0.7963 (pt0) cc_final: 0.7695 (pp20) REVERT: H 248 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7484 (p0) REVERT: H 260 LYS cc_start: 0.9305 (mtmm) cc_final: 0.8883 (mtmt) REVERT: H 268 TYR cc_start: 0.9097 (t80) cc_final: 0.8815 (t80) REVERT: H 273 LYS cc_start: 0.8850 (tttt) cc_final: 0.8494 (ptmt) REVERT: H 438 TYR cc_start: 0.8434 (m-80) cc_final: 0.7952 (m-80) REVERT: H 548 LYS cc_start: 0.7513 (tppt) cc_final: 0.7223 (tptp) REVERT: H 656 LYS cc_start: 0.7536 (mmmt) cc_final: 0.7285 (mmmm) REVERT: H 742 ARG cc_start: 0.8952 (tmm-80) cc_final: 0.8603 (ttp80) REVERT: H 764 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: H 772 PHE cc_start: 0.8032 (m-80) cc_final: 0.7296 (m-80) REVERT: I 61 LYS cc_start: 0.8886 (tppt) cc_final: 0.8640 (tppt) REVERT: I 72 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7985 (mm-30) REVERT: I 162 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8266 (mmtp) REVERT: I 263 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8304 (mmm160) REVERT: I 277 HIS cc_start: 0.7814 (t70) cc_final: 0.7611 (t70) REVERT: I 468 PHE cc_start: 0.8642 (t80) cc_final: 0.8185 (t80) REVERT: I 472 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8250 (ptmt) REVERT: I 537 GLN cc_start: 0.7186 (tm-30) cc_final: 0.6568 (tm-30) REVERT: I 542 TYR cc_start: 0.8030 (m-80) cc_final: 0.7265 (m-80) outliers start: 101 outliers final: 82 residues processed: 863 average time/residue: 0.5167 time to fit residues: 714.7319 Evaluate side-chains 858 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 768 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 555 ASP Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 703 LYS Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 248 ASN Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 563 GLN Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 693 ASP Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain H residue 762 THR Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 420 ASP Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 534 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 318 optimal weight: 0.0040 chunk 426 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 369 optimal weight: 4.9990 chunk 59 optimal weight: 0.0040 chunk 111 optimal weight: 0.7980 chunk 401 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 412 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN C 376 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN H 117 HIS H 567 ASN I 411 GLN I 424 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.190085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107934 restraints weight = 58489.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113491 restraints weight = 29814.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116817 restraints weight = 18609.993| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 38885 Z= 0.310 Angle : 0.694 17.549 52922 Z= 0.354 Chirality : 0.047 0.327 6190 Planarity : 0.004 0.045 6947 Dihedral : 4.288 32.776 5425 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.87 % Allowed : 21.37 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 5043 helix: 0.38 (0.15), residues: 1348 sheet: 0.69 (0.16), residues: 1118 loop : -0.76 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 570 HIS 0.011 0.001 HIS H 745 PHE 0.029 0.002 PHE H 337 TYR 0.030 0.001 TYR F 542 ARG 0.009 0.001 ARG I 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11218.86 seconds wall clock time: 202 minutes 22.01 seconds (12142.01 seconds total)