Starting phenix.real_space_refine on Sun Mar 24 14:48:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxk_11523/03_2024/6zxk_11523.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxk_11523/03_2024/6zxk_11523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxk_11523/03_2024/6zxk_11523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxk_11523/03_2024/6zxk_11523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxk_11523/03_2024/6zxk_11523.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxk_11523/03_2024/6zxk_11523.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 40 5.16 5 C 26530 2.51 5 N 7357 2.21 5 O 8365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 190": "OE1" <-> "OE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 212": "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 TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 699": "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 GLU 441": "OE1" <-> "OE2" 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 GLU 188": "OE1" <-> "OE2" 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 PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 439": "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 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 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 512": "OD1" <-> "OD2" Residue "D GLU 525": "OE1" <-> "OE2" 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 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 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 512": "OD1" <-> "OD2" Residue "E PHE 531": "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 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 TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 520": "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 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 GLU 441": "OE1" <-> "OE2" Residue "G ASP 451": "OD1" <-> "OD2" 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 PHE 678": "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 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H ASP 136": "OD1" <-> "OD2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "H PHE 190": "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 415": "OD1" <-> "OD2" Residue "H TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 508": "OD1" <-> "OD2" Residue "H GLU 561": "OE1" <-> "OE2" Residue "H PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 647": "OD1" <-> "OD2" Residue "H ARG 664": "NH1" <-> "NH2" Residue "H ASP 706": "OD1" <-> "OD2" Residue "H PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 137": "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 PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 226": "OE1" <-> "OE2" Residue "I ARG 267": "NH1" <-> "NH2" Residue "I TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 415": "OD1" <-> "OD2" Residue "I GLU 497": "OE1" <-> "OE2" Residue "I TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 200": "OD1" <-> "OD2" Residue "J PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 261": "OD1" <-> "OD2" Residue "J TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 415": "OD1" <-> "OD2" Residue "J TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42292 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3984 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "B" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 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: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 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: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3970 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 505} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 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: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 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: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 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: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 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: 5401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5401 Classifications: {'peptide': 699} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 680} Chain breaks: 1 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 297 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 4, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 13, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 172 Chain: "I" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 4734 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 310} Link IDs: {'PTRANS': 18, 'TRANS': 691} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1138 Unresolved non-hydrogen angles: 1430 Unresolved non-hydrogen dihedrals: 932 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 9, 'TYR:plan': 11, 'ASN:plan1': 20, 'TRP:plan': 1, 'ASP:plan': 29, 'PHE:plan': 12, 'GLU:plan': 39, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 652 Chain: "J" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 4318 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 16, 'TRANS': 644} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1159 Unresolved non-hydrogen angles: 1439 Unresolved non-hydrogen dihedrals: 960 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 22, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 11, 'GLU:plan': 41, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 654 Time building chain proxies: 20.50, per 1000 atoms: 0.48 Number of scatterers: 42292 At special positions: 0 Unit cell: (181.9, 180.83, 176.55, 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 40 16.00 O 8365 8.00 N 7357 7.00 C 26530 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: 15.86 Conformation dependent library (CDL) restraints added in 8.5 seconds 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11038 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 80 sheets defined 35.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.19 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.525A pdb=" N HIS A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.705A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.938A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.556A pdb=" N MET A 350 " --> pdb=" O TRP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 477 through 487 Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.970A pdb=" N THR A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.561A pdb=" N LEU A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.500A pdb=" N ASP A 579 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.509A pdb=" N VAL A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 637 removed outlier: 3.505A pdb=" N LYS A 637 " --> pdb=" O ASP A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 637' Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.557A pdb=" N LEU A 663 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 664 " --> pdb=" O ASP A 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 660 through 664' Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.866A pdb=" N ASP A 683 " --> pdb=" O LYS A 680 " (cutoff:3.500A) 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: 3.726A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.768A pdb=" N VAL B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.843A 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: 4.006A 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 568 Processing helix chain 'B' and resid 576 through 581 removed outlier: 4.494A pdb=" N ASP B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.623A pdb=" N GLU B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 615 " --> pdb=" O VAL B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 637 removed outlier: 3.531A 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: 3.849A 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: 3.815A pdb=" N VAL C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 4.013A 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 removed outlier: 3.587A pdb=" N PHE C 439 " --> pdb=" O ASN C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Proline residue: C 482 - end of helix removed outlier: 3.504A pdb=" N THR C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 522 through 532 removed outlier: 3.598A pdb=" N GLY C 532 " --> pdb=" O LYS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 576 through 581 removed outlier: 4.457A pdb=" N ASP C 579 " --> pdb=" O THR C 576 " (cutoff:3.500A) removed outlier: 3.545A 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 638 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.606A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.627A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.866A 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 removed outlier: 3.674A pdb=" N PHE D 439 " --> pdb=" O ASN D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Proline residue: D 482 - end of helix Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 522 through 531 Processing helix chain 'D' and resid 555 through 568 Processing helix chain 'D' and resid 576 through 581 removed outlier: 4.246A pdb=" N ASP D 579 " --> pdb=" O THR D 576 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 615 removed outlier: 3.517A pdb=" N VAL D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 614 " --> pdb=" O SER D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 637 removed outlier: 3.516A pdb=" N LYS D 637 " --> pdb=" O ASP D 634 " (cutoff:3.500A) No H-bonds generated for '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: 3.843A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.630A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.922A 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 486 Processing helix chain 'E' and resid 512 through 517 removed outlier: 3.844A pdb=" N THR E 517 " --> pdb=" O PRO E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 removed outlier: 3.541A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 568 Processing helix chain 'E' and resid 576 through 581 removed outlier: 4.541A pdb=" N ASP E 579 " --> pdb=" O THR E 576 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 581 " --> pdb=" O LEU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 615 removed outlier: 3.535A pdb=" N VAL E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) Processing helix 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 212 removed outlier: 4.022A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.575A pdb=" N VAL F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.966A 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 513 through 518 Processing helix chain 'F' and resid 522 through 531 Processing helix chain 'F' and resid 555 through 570 removed outlier: 3.699A pdb=" N ASN F 564 " --> pdb=" O GLN F 560 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN F 565 " --> pdb=" O ASN F 561 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 569 " --> pdb=" O GLN F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 581 removed outlier: 4.447A pdb=" N ASP F 579 " --> pdb=" O THR F 576 " (cutoff:3.500A) removed outlier: 3.547A 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 212 removed outlier: 4.089A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.932A 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 removed outlier: 3.595A pdb=" N PHE G 439 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 487 Proline residue: G 482 - end of helix Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.825A pdb=" N THR G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 removed outlier: 3.663A pdb=" N GLY G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 568 Processing helix chain 'G' and resid 576 through 581 removed outlier: 4.576A pdb=" N ASP G 579 " --> pdb=" O THR G 576 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 615 removed outlier: 3.520A pdb=" N VAL G 612 " --> pdb=" O ASP G 608 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU G 614 " --> pdb=" O SER G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 638 removed outlier: 3.531A pdb=" N LYS G 637 " --> pdb=" O ASP G 634 " (cutoff:3.500A) Processing helix chain 'G' and resid 702 through 706 Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 140 through 159 removed outlier: 4.212A pdb=" N ASN H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.826A 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: 4.039A pdb=" N VAL H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.643A pdb=" N ASP H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 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: 3.995A pdb=" N LEU H 254 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 257 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 259 " --> pdb=" O SER H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 278 removed outlier: 3.696A pdb=" N GLN H 276 " --> pdb=" O GLU H 272 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) removed outlier: 3.526A 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 Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.635A pdb=" N ILE H 307 " --> pdb=" O LYS H 303 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 321 removed outlier: 3.908A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 345 Processing helix chain 'H' and resid 371 through 381 removed outlier: 4.023A pdb=" N PHE H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU H 381 " --> pdb=" O LYS H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 removed outlier: 3.847A pdb=" N GLN H 393 " --> pdb=" O ASN H 389 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP H 394 " --> pdb=" O GLN H 390 " (cutoff:3.500A) 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: 3.577A pdb=" N ALA H 452 " --> pdb=" O ALA H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 474 removed outlier: 3.791A pdb=" N GLU H 470 " --> pdb=" O GLY H 466 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN H 474 " --> pdb=" O GLU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 575 removed outlier: 3.716A pdb=" N ILE H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS H 558 " --> pdb=" O LYS H 554 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 572 " --> pdb=" O GLN H 568 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 573 " --> pdb=" O GLU H 569 " (cutoff:3.500A) Processing helix chain 'H' and resid 591 through 610 removed outlier: 3.687A pdb=" N ILE H 595 " --> pdb=" O TYR H 591 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR H 600 " --> pdb=" O VAL H 596 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU H 601 " --> pdb=" O GLU H 597 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN H 609 " --> pdb=" O GLU H 605 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE H 610 " --> pdb=" O TRP H 606 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 624 removed outlier: 3.541A pdb=" N ILE H 615 " --> pdb=" O GLN H 611 " (cutoff:3.500A) Processing helix chain 'H' and resid 635 through 639 Processing helix chain 'H' and resid 640 through 647 removed outlier: 3.766A pdb=" N THR H 644 " --> pdb=" O ALA H 640 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS H 645 " --> pdb=" O GLU H 641 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN H 646 " --> pdb=" O GLN H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 679 through 701 removed outlier: 3.856A pdb=" N GLY H 683 " --> pdb=" O ASN H 679 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP H 694 " --> pdb=" O HIS H 690 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU H 700 " --> pdb=" O ALA H 696 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP H 701 " --> pdb=" O GLY H 697 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 721 removed outlier: 4.003A pdb=" N ASP H 716 " --> pdb=" O LYS H 712 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE H 717 " --> pdb=" O LYS H 713 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU H 720 " --> pdb=" O ASP H 716 " (cutoff:3.500A) Processing helix chain 'H' and resid 728 through 731 Processing helix chain 'H' and resid 732 through 745 removed outlier: 3.582A pdb=" N LEU H 743 " --> pdb=" O GLU H 739 " (cutoff:3.500A) Processing helix chain 'H' and resid 748 through 759 removed outlier: 3.522A pdb=" N ARG H 752 " --> pdb=" O ASP H 748 " (cutoff:3.500A) Processing helix chain 'H' and resid 759 through 770 removed outlier: 3.634A pdb=" N GLN H 764 " --> pdb=" O PRO H 760 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN H 767 " --> pdb=" O PHE H 763 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 44 removed outlier: 4.245A pdb=" N LYS I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU I 38 " --> pdb=" O GLU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 65 removed outlier: 3.537A pdb=" N LYS I 56 " --> pdb=" O GLU I 52 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.970A pdb=" N LEU I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.081A pdb=" N ALA I 96 " --> pdb=" O ILE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 removed outlier: 3.706A pdb=" N ASN I 146 " --> pdb=" O GLU I 142 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 147 " --> pdb=" O LYS I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.536A pdb=" N LYS I 178 " --> pdb=" O LEU I 174 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.631A pdb=" N GLU I 196 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 209 removed outlier: 3.645A pdb=" N LEU I 206 " --> pdb=" O SER I 202 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU I 207 " --> pdb=" O VAL I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 Processing helix chain 'I' and resid 226 through 237 removed outlier: 4.303A pdb=" N ASP I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) removed outlier: 4.869A 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: 3.781A pdb=" N TYR I 278 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TRP I 281 " --> pdb=" O HIS I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 298 removed outlier: 4.013A pdb=" N LEU I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 312 removed outlier: 3.823A pdb=" N SER I 312 " --> pdb=" O ILE I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 321 removed outlier: 4.076A pdb=" N GLU I 317 " --> pdb=" O GLN I 313 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 327 removed outlier: 3.862A 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: 3.904A pdb=" N LEU I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS I 377 " --> pdb=" O LYS I 373 " (cutoff:3.500A) removed outlier: 3.573A 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 removed outlier: 3.575A pdb=" N GLN I 411 " --> pdb=" O ASP I 407 " (cutoff:3.500A) 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: 3.747A 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 572 removed outlier: 3.611A pdb=" N LYS I 558 " --> pdb=" O LYS I 554 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 562 " --> pdb=" O LYS I 558 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS I 572 " --> pdb=" O GLN I 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 591 through 608 removed outlier: 3.550A pdb=" N ILE I 595 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR I 600 " --> pdb=" O VAL I 596 " (cutoff:3.500A) removed outlier: 3.559A 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 639 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: 3.910A pdb=" N HIS I 690 " --> pdb=" O HIS I 686 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA I 691 " --> pdb=" O GLU I 687 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 721 removed outlier: 4.171A pdb=" N LYS I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS I 713 " --> pdb=" O THR I 709 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP I 716 " --> pdb=" O LYS I 712 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE I 717 " --> pdb=" O LYS I 713 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU I 720 " --> pdb=" O ASP I 716 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU I 721 " --> pdb=" O ILE I 717 " (cutoff:3.500A) Processing helix chain 'I' and resid 722 through 725 removed outlier: 3.703A 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 732 through 745 Processing helix chain 'I' and resid 748 through 759 removed outlier: 3.632A pdb=" N VAL I 755 " --> pdb=" O GLU I 751 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN I 756 " --> pdb=" O ARG I 752 " (cutoff:3.500A) Processing helix chain 'I' and resid 759 through 772 removed outlier: 4.217A pdb=" N GLN I 764 " --> pdb=" O PRO I 760 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE I 765 " --> pdb=" O LYS I 761 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS I 771 " --> pdb=" O ASN I 767 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE I 772 " --> pdb=" O ASP I 768 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 65 removed outlier: 3.540A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 77 removed outlier: 3.992A pdb=" N LEU J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 4.020A pdb=" N ALA J 96 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 158 removed outlier: 3.787A pdb=" N ASN J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 167 through 179 removed outlier: 3.632A pdb=" N LYS J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN J 179 " --> pdb=" O ASN J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 193 through 197 removed outlier: 3.577A pdb=" N GLU J 196 " --> pdb=" O GLN J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 209 removed outlier: 3.716A pdb=" N LEU J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU J 207 " --> pdb=" O VAL J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 226 removed outlier: 3.509A pdb=" N GLU J 226 " --> pdb=" O ALA J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 237 removed outlier: 4.161A pdb=" N ASP J 231 " --> pdb=" O PRO J 227 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL J 232 " --> pdb=" O GLN J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 251 Processing helix chain 'J' and resid 252 through 261 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.692A pdb=" N HIS J 277 " --> pdb=" O LYS J 273 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR J 278 " --> pdb=" O ILE J 274 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS J 280 " --> pdb=" O GLN J 276 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP J 281 " --> pdb=" O HIS J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 298 Processing helix chain 'J' and resid 313 through 320 removed outlier: 4.016A pdb=" N GLU J 317 " --> pdb=" O GLN J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 333 through 338 Processing helix chain 'J' and resid 372 through 383 removed outlier: 3.803A pdb=" N LEU J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 396 Processing helix chain 'J' and resid 406 through 421 removed outlier: 3.691A pdb=" N LYS J 410 " --> pdb=" O LEU J 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN J 411 " --> pdb=" O ASP J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 446 No H-bonds generated for 'chain 'J' and resid 444 through 446' Processing helix chain 'J' and resid 447 through 452 removed outlier: 3.680A pdb=" N ALA J 452 " --> pdb=" O ALA J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 473 removed outlier: 3.710A pdb=" N GLU J 470 " --> pdb=" O GLY J 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 551 through 572 removed outlier: 3.506A pdb=" N LYS J 558 " --> pdb=" O LYS J 554 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU J 561 " --> pdb=" O THR J 557 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS J 572 " --> pdb=" O GLN J 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 591 through 610 removed outlier: 3.661A pdb=" N ILE J 595 " --> pdb=" O TYR J 591 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR J 600 " --> pdb=" O VAL J 596 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU J 601 " --> pdb=" O GLU J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 624 Processing helix chain 'J' and resid 635 through 640 removed outlier: 4.763A pdb=" N ALA J 640 " --> pdb=" O LEU J 636 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 646 Processing helix chain 'J' and resid 648 through 652 Processing helix chain 'J' and resid 679 through 700 removed outlier: 3.959A pdb=" N HIS J 690 " --> pdb=" O HIS J 686 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 721 removed outlier: 4.271A pdb=" N LYS J 712 " --> pdb=" O VAL J 708 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS J 713 " --> pdb=" O THR J 709 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP J 716 " --> pdb=" O LYS J 712 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE J 717 " --> pdb=" O LYS J 713 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU J 721 " --> pdb=" O ILE J 717 " (cutoff:3.500A) Processing helix chain 'J' and resid 722 through 725 removed outlier: 3.698A pdb=" N LEU J 725 " --> pdb=" O GLY J 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 722 through 725' Processing helix chain 'J' and resid 728 through 731 Processing helix chain 'J' and resid 732 through 745 Processing helix chain 'J' and resid 748 through 759 removed outlier: 3.518A pdb=" N VAL J 755 " --> pdb=" O GLU J 751 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN J 756 " --> pdb=" O ARG J 752 " (cutoff:3.500A) Processing helix chain 'J' and resid 759 through 772 removed outlier: 4.108A pdb=" N GLN J 764 " --> pdb=" O PRO J 760 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE J 765 " --> pdb=" O LYS J 761 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE J 770 " --> pdb=" O ILE J 766 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS J 771 " --> pdb=" O ASN J 767 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE J 772 " --> pdb=" O ASP J 768 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 3.620A pdb=" N ASP A 195 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 202 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 3.516A pdb=" N SER A 272 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 368 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.974A 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: 5.041A pdb=" N THR A 390 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 385 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 392 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 381 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 451 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 364 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 419 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.306A 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: 8.716A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 592 " --> pdb=" O ASP A 551 " (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 removed outlier: 6.590A pdb=" N HIS A 597 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.525A pdb=" N LEU A 627 " --> pdb=" O ILE A 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.648A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ALA A 700 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU A 725 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.626A pdb=" N ASP B 195 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 4.011A 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: 5.038A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 294 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 368 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 4.088A 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: 5.038A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 294 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.726A 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: 4.178A 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 removed outlier: 3.714A pdb=" N ARG B 592 " --> pdb=" O ASP B 551 " (cutoff:3.500A) 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 removed outlier: 6.663A pdb=" N HIS B 597 " --> pdb=" O VAL B 605 " (cutoff:3.500A) 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: 3.570A pdb=" N GLY B 641 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 645 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 697 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA B 700 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU B 725 " --> pdb=" O ALA B 700 " (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: 7.196A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 368 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 3.979A 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: 7.267A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 448 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER C 329 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLU C 267 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR C 295 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP C 265 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ARG C 297 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N HIS C 263 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 7.196A 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: 4.283A 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: 8.514A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 592 " --> pdb=" O ASP C 551 " (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: 6.394A 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: 3.530A pdb=" N ASN C 697 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL C 696 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 728 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 6.132A 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: 3.576A pdb=" N ASP D 195 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D 202 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 262 through 273 removed outlier: 7.238A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 262 through 273 removed outlier: 7.238A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 293 through 297 removed outlier: 3.511A pdb=" N LEU D 448 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR D 381 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA D 392 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR D 390 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 458 through 462 removed outlier: 4.303A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.573A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AD8, first strand: chain 'D' and resid 596 through 598 Processing sheet with id=AD9, first strand: chain 'D' and resid 628 through 629 Processing sheet with id=AE1, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.917A pdb=" N VAL D 696 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 728 " --> pdb=" O VAL D 696 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 698 " --> pdb=" O ILE D 726 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 192 through 197 removed outlier: 3.673A pdb=" N PHE E 202 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 389 through 394 removed outlier: 7.075A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 384 " --> pdb=" O ARG E 449 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 294 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 389 through 394 removed outlier: 7.075A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 384 " --> pdb=" O ARG E 449 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 294 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE E 364 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 419 " --> pdb=" O ILE E 364 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 458 through 462 removed outlier: 4.204A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.575A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 592 " --> pdb=" O ASP E 551 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AE8, first strand: chain 'E' and resid 596 through 598 removed outlier: 6.548A pdb=" N HIS E 597 " --> pdb=" O VAL E 605 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 628 through 629 Processing sheet with id=AF1, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.952A pdb=" N ALA E 700 " --> pdb=" O LEU E 725 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU E 725 " --> pdb=" O ALA E 700 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 192 through 197 Processing sheet with id=AF3, first strand: chain 'F' and resid 358 through 360 removed outlier: 6.650A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 389 through 394 removed outlier: 5.012A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR F 381 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP F 451 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 384 " --> pdb=" O ARG F 449 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 449 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN F 328 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER F 294 " --> pdb=" O ALA F 333 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU F 267 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR F 295 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP F 265 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ARG F 297 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N HIS F 263 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 364 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 419 " --> pdb=" O ILE F 364 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 458 through 462 removed outlier: 4.326A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.576A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG F 592 " --> pdb=" O ASP F 551 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AF8, first strand: chain 'F' and resid 596 through 598 removed outlier: 6.854A pdb=" N HIS F 597 " --> pdb=" O VAL F 605 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 628 through 629 Processing sheet with id=AG1, first strand: chain 'F' and resid 654 through 655 removed outlier: 3.816A pdb=" N GLY F 641 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL F 696 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER F 728 " --> pdb=" O VAL F 696 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL F 698 " --> pdb=" O ILE F 726 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AG3, first strand: chain 'G' and resid 389 through 394 removed outlier: 4.946A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP G 451 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU G 448 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN G 368 " --> pdb=" O ASN G 409 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 389 through 394 removed outlier: 4.946A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP G 451 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU G 448 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 458 through 462 removed outlier: 4.495A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 501 through 506 Processing sheet with id=AG7, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AG8, first strand: chain 'G' and resid 596 through 598 Processing sheet with id=AG9, first strand: chain 'G' and resid 628 through 629 Processing sheet with id=AH1, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.293A pdb=" N VAL G 696 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER G 728 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL G 698 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 724 " --> pdb=" O ALA G 700 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AH3, first strand: chain 'H' and resid 436 through 441 removed outlier: 3.614A pdb=" N GLU H 439 " --> pdb=" O TRP H 501 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS H 548 " --> pdb=" O GLU H 528 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU H 528 " --> pdb=" O LYS H 548 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY H 526 " --> pdb=" O VAL H 550 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 436 through 441 removed outlier: 3.614A pdb=" N GLU H 439 " --> pdb=" O TRP H 501 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 485 through 486 Processing sheet with id=AH6, first strand: chain 'H' and resid 630 through 632 removed outlier: 3.547A pdb=" N LEU H 658 " --> pdb=" O LEU H 667 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.855A pdb=" N ILE I 131 " --> pdb=" O TYR I 82 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL I 128 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 103 through 105 removed outlier: 3.525A pdb=" N ILE I 104 " --> pdb=" O ALA I 112 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 436 through 442 removed outlier: 3.697A pdb=" N LEU I 437 " --> pdb=" O ILE I 503 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG I 498 " --> pdb=" O ILE I 543 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE I 545 " --> pdb=" O ARG I 498 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LYS I 500 " --> pdb=" O ILE I 545 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA I 547 " --> pdb=" O LYS I 500 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG I 502 " --> pdb=" O ALA I 547 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL I 549 " --> pdb=" O ARG I 502 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN I 504 " --> pdb=" O VAL I 549 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP I 531 " --> pdb=" O ASP I 546 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS I 548 " --> pdb=" O ILE I 529 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE I 529 " --> pdb=" O LYS I 548 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL I 550 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU I 527 " --> pdb=" O VAL I 550 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 485 through 487 removed outlier: 3.869A pdb=" N LYS I 518 " --> pdb=" O LEU I 514 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 583 through 586 removed outlier: 3.619A pdb=" N PHE I 631 " --> pdb=" O THR I 584 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 83 through 84 removed outlier: 3.527A pdb=" N VAL J 128 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 103 through 105 Processing sheet with id=AI5, first strand: chain 'J' and resid 436 through 442 removed outlier: 3.947A pdb=" N LEU J 437 " --> pdb=" O ILE J 503 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE J 503 " --> pdb=" O LEU J 437 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU J 499 " --> pdb=" O MET J 441 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG J 498 " --> pdb=" O ILE J 543 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE J 545 " --> pdb=" O ARG J 498 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LYS J 500 " --> pdb=" O ILE J 545 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA J 547 " --> pdb=" O LYS J 500 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG J 502 " --> pdb=" O ALA J 547 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 549 " --> pdb=" O ARG J 502 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN J 504 " --> pdb=" O VAL J 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP J 531 " --> pdb=" O ASP J 546 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS J 548 " --> pdb=" O ILE J 529 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE J 529 " --> pdb=" O LYS J 548 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL J 550 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU J 527 " --> pdb=" O VAL J 550 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 455 through 456 removed outlier: 6.064A pdb=" N LYS J 462 " --> pdb=" O ASP J 456 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 485 through 487 Processing sheet with id=AI8, first strand: chain 'J' and resid 583 through 585 removed outlier: 4.748A pdb=" N THR J 584 " --> pdb=" O PHE J 629 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE J 631 " --> pdb=" O THR J 584 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG J 628 " --> pdb=" O ILE J 666 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU J 668 " --> pdb=" O ARG J 628 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL J 630 " --> pdb=" O LEU J 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 1639 hydrogen bonds defined for protein. 4500 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: 22.30 Time building geometry restraints manager: 17.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8548 1.32 - 1.44: 9866 1.44 - 1.57: 24498 1.57 - 1.69: 2 1.69 - 1.81: 80 Bond restraints: 42994 Sorted by residual: bond pdb=" C PRO D 176 " pdb=" O PRO D 176 " ideal model delta sigma weight residual 1.233 1.199 0.034 9.90e-03 1.02e+04 1.17e+01 bond pdb=" CD LYS B 291 " pdb=" CE LYS B 291 " ideal model delta sigma weight residual 1.520 1.421 0.099 3.00e-02 1.11e+03 1.09e+01 bond pdb=" N VAL A 175 " pdb=" CA VAL A 175 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.06e+01 bond pdb=" N ILE J 83 " pdb=" CA ILE J 83 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" N ILE H 298 " pdb=" CA ILE H 298 " ideal model delta sigma weight residual 1.462 1.493 -0.032 1.01e-02 9.80e+03 9.87e+00 ... (remaining 42989 not shown) Histogram of bond angle deviations from ideal: 90.60 - 103.99: 578 103.99 - 117.38: 30916 117.38 - 130.77: 26995 130.77 - 144.16: 127 144.16 - 157.55: 1 Bond angle restraints: 58617 Sorted by residual: angle pdb=" C ILE H 88 " pdb=" N THR H 89 " pdb=" CA THR H 89 " ideal model delta sigma weight residual 122.20 157.55 -35.35 3.42e+00 8.55e-02 1.07e+02 angle pdb=" CB MET F 587 " pdb=" CG MET F 587 " pdb=" SD MET F 587 " ideal model delta sigma weight residual 112.70 93.31 19.39 3.00e+00 1.11e-01 4.18e+01 angle pdb=" CA PRO J 67 " pdb=" N PRO J 67 " pdb=" CD PRO J 67 " ideal model delta sigma weight residual 112.00 103.25 8.75 1.40e+00 5.10e-01 3.91e+01 angle pdb=" N PRO J 67 " pdb=" CD PRO J 67 " pdb=" CG PRO J 67 " ideal model delta sigma weight residual 103.20 94.79 8.41 1.50e+00 4.44e-01 3.14e+01 angle pdb=" CA MET A 434 " pdb=" CB MET A 434 " pdb=" CG MET A 434 " ideal model delta sigma weight residual 114.10 125.04 -10.94 2.00e+00 2.50e-01 2.99e+01 ... (remaining 58612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 24179 17.35 - 34.71: 1502 34.71 - 52.06: 231 52.06 - 69.42: 44 69.42 - 86.77: 25 Dihedral angle restraints: 25981 sinusoidal: 8998 harmonic: 16983 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 36.40 -36.40 0 5.00e+00 4.00e-02 5.30e+01 dihedral pdb=" C TYR J 579 " pdb=" N TYR J 579 " pdb=" CA TYR J 579 " pdb=" CB TYR J 579 " ideal model delta harmonic sigma weight residual -122.60 -136.09 13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" CA LYS D 197 " pdb=" C LYS D 197 " pdb=" N ASN D 198 " pdb=" CA ASN D 198 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 25978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5993 0.095 - 0.190: 829 0.190 - 0.284: 77 0.284 - 0.379: 4 0.379 - 0.474: 3 Chirality restraints: 6906 Sorted by residual: chirality pdb=" CA TYR J 579 " pdb=" N TYR J 579 " pdb=" C TYR J 579 " pdb=" CB TYR J 579 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CB VAL J 550 " pdb=" CA VAL J 550 " pdb=" CG1 VAL J 550 " pdb=" CG2 VAL J 550 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB VAL A 175 " pdb=" CA VAL A 175 " pdb=" CG1 VAL A 175 " pdb=" CG2 VAL A 175 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 6903 not shown) Planarity restraints: 7726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 384 " -0.100 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO I 385 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO I 385 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO I 385 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 66 " -0.086 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO J 67 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO J 67 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO J 67 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 486 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLU F 486 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU F 486 " -0.027 2.00e-02 2.50e+03 pdb=" N THR F 487 " -0.025 2.00e-02 2.50e+03 ... (remaining 7723 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 437 2.54 - 3.13: 37996 3.13 - 3.72: 62631 3.72 - 4.31: 85575 4.31 - 4.90: 135891 Nonbonded interactions: 322530 Sorted by model distance: nonbonded pdb=" OE1 GLU A 486 " pdb=" NZ LYS A 586 " model vdw 1.950 2.520 nonbonded pdb=" CG PRO D 176 " pdb=" OD2 ASP D 185 " model vdw 1.969 3.440 nonbonded pdb=" NH2 ARG G 592 " pdb=" OD1 ASN G 602 " model vdw 2.018 2.520 nonbonded pdb=" O ILE A 210 " pdb=" NZ LYS A 214 " model vdw 2.026 2.520 nonbonded pdb=" OD1 ASN F 561 " pdb=" NE2 GLN F 565 " model vdw 2.062 2.520 ... (remaining 322525 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 174 through 274 or (resid 287 and (name N or name CA or na \ me C or name O or name CB )) or resid 288 through 659 or (resid 660 through 665 \ and (name N or name CA or name C or name O or name CB )) or resid 666 through 66 \ 7 or (resid 668 through 671 and (name N or name CA or name C or name O or name C \ B )) or resid 672 through 680 or (resid 681 through 685 and (name N or name CA o \ r name C or name O or name CB )) or resid 686 through 734)) selection = (chain 'B' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'C' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'D' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'E' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'F' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'G' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) } ncs_group { reference = (chain 'H' and ((resid 55 through 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 name CA or name \ C or name O or name CB )) or resid 70 through 72 or (resid 73 and (name N or na \ me CA or name C or name O or name CB )) or resid 74 through 79 or (resid 80 and \ (name N or name CA or name C or name O or name CB )) or resid 81 through 86 or ( \ resid 87 through 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 94 or (resid 95 through 96 and (name N or name CA or name C or \ name O or name CB )) or resid 97 or (resid 98 through 103 and (name N or name CA \ or name C or name O or name CB )) or resid 104 or (resid 105 through 106 and (n \ ame N or name CA or name C or name O or name CB )) or resid 107 through 110 or ( \ resid 111 through 113 and (name N or name CA or name C or name O or name CB )) o \ r resid 114 through 115 or (resid 116 and (name N or name CA or name C or name O \ or name CB )) or resid 117 through 119 or (resid 120 through 121 and (name N or \ name CA or name C or name O or name CB )) or resid 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 throug \ h 126 and (name N or name CA or name C or name O or name CB )) or resid 127 thro \ ugh 161 or (resid 162 and (name N or name CA or name C or name O or name CB )) o \ r resid 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 167 or (resid 168 through 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 192 or (resid 19 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 194 or (resi \ d 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thro \ ugh 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 262 or (resid 263 through 270 and (name N or nam \ e CA or name C or name O or name CB )) or resid 271 through 272 or (resid 273 th \ rough 276 and (name N or name CA or name C or name O or name CB )) or resid 277 \ through 279 or (resid 280 and (name N or name CA or name C or name O or name CB \ )) or resid 281 through 283 or (resid 284 through 288 and (name N or name CA or \ name C or name O or name CB )) or resid 289 or (resid 290 and (name N or name CA \ or name C or name O or name CB )) or (resid 291 through 301 and (name N or name \ CA or name C or name O or name CB )) or (resid 309 through 320 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 332 through 338 and (name N o \ r name CA or name C or name O or name CB )) or (resid 369 through 384 and (name \ N or name CA or name C or name O or name CB )) or resid 385 through 387 or (resi \ d 388 through 391 and (name N or name CA or name C or name O or name CB )) or re \ sid 392 or (resid 393 through 395 and (name N or name CA or name C or name O or \ name CB )) or resid 396 through 397 or (resid 405 through 407 and (name N or nam \ e CA or name C or name O or name CB )) or resid 408 or (resid 409 through 414 an \ d (name N or name CA or name C or name O or name CB )) or resid 415 or (resid 41 \ 6 through 417 and (name N or name CA or name C or name O or name CB )) or resid \ 418 through 419 or (resid 420 through 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 or (resid 433 through 436 and (name N or name CA \ or name C or name O or name CB )) or resid 437 through 445 or (resid 446 throug \ h 450 and (name N or name CA or name C or name O or name CB )) or (resid 451 thr \ ough 453 and (name N or name CA or name C or name O or name CB )) or resid 454 t \ hrough 456 or (resid 457 through 459 and (name N or name CA or name C or name O \ or name CB )) or resid 460 through 463 or (resid 464 through 465 and (name N or \ name CA or name C or name O or name CB )) or resid 466 through 471 or (resid 472 \ through 473 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 74 or (resid 475 through 476 and (name N or name CA or name C or name O or name \ CB )) or resid 477 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 and (name N or name CA or name C or name O or name CB )) or resid 488 or (r \ esid 489 through 491 and (name N or name CA or name C or name O or name CB )) or \ resid 492 through 494 or (resid 495 through 498 and (name N or name CA or name \ C or name O or name CB )) or resid 499 through 507 or (resid 508 through 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 513 o \ r (resid 514 through 516 and (name N or name CA or name C or name O or name CB ) \ ) or resid 517 or (resid 518 through 525 and (name N or name CA or name C or nam \ e O or name CB )) or resid 526 or (resid 527 through 533 and (name N or name CA \ or name C or name O or name CB )) or resid 534 through 536 or (resid 537 and (na \ me N or name CA or name C or name O or name CB )) or resid 538 through 540 or (r \ esid 541 through 542 and (name N or name CA or name C or name O or name CB )) or \ resid 543 through 547 or (resid 548 and (name N or name CA or name C or name O \ or name CB )) or resid 549 or (resid 550 and (name N or name CA or name C or nam \ e O or name CB )) or resid 551 through 557 or (resid 558 and (name N or name CA \ or name C or name O or name CB )) or resid 559 through 560 or (resid 561 through \ 563 and (name N or name CA or name C or name O or name CB )) or resid 564 or (r \ esid 565 and (name N or name CA or name C or name O or name CB )) or resid 566 o \ r (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 through 574 and (name N or name CA or name C or nam \ e O or name CB )) or resid 575 through 577 or (resid 578 through 579 and (name N \ or name CA or name C or name O or name CB )) or resid 580 or (resid 581 through \ 582 and (name N or name CA or name C or name O or name CB )) or resid 583 throu \ gh 584 or (resid 585 and (name N or name CA or name C or name O or name CB )) or \ resid 586 through 590 or (resid 591 through 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 596 or (resid 597 and (name N or \ name CA or name C or name O or name CB )) or resid 598 through 601 or (resid 602 \ through 604 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 05 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 617 and (name N or name CA or name C or \ name O or name CB )) or resid 618 through 619 or (resid 620 through 621 and (na \ me N or name CA or name C or name O or name CB )) or resid 622 or (resid 623 thr \ ough 624 and (name N or name CA or name C or name O or name CB )) or resid 625 t \ hrough 627 or (resid 628 and (name N or name CA or name C or name O or name CB ) \ ) or resid 629 through 630 or (resid 631 through 636 and (name N or name CA or n \ ame C or name O or name CB )) or resid 637 or (resid 638 through 656 and (name N \ or name CA or name C or name O or name CB )) or resid 657 or (resid 658 through \ 669 and (name N or name CA or name C or name O or name CB )) or resid 670 or (r \ esid 671 through 673 and (name N or name CA or name C or name 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 through 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 )) or resid 697 or (resid \ 698 through 710 and (name N or name CA or name C or name O or name CB )) or res \ id 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 728 and (name N or name \ CA or name C or name O or name CB )) or resid 729 or (resid 730 through 759 and \ (name N or name CA or name C or name O or name CB )) or resid 760 or (resid 761 \ through 763 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 64 through 765 or (resid 766 through 767 and (name N or name CA or name C or nam \ e O or name CB )) or resid 768 through 769 or (resid 770 and (name N or name CA \ or name C or name O or name CB )) or resid 771 through 773)) selection = (chain 'I' and ((resid 55 through 56 and (name N or name CA or name C or name O \ or name CB )) or resid 57 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 87 or (resid 88 through 90 and (n \ ame N or name CA or name C or name O or name CB )) or resid 91 through 110 or (r \ esid 111 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 115 or (resid 116 and (name N or name CA or name C or name O \ or name CB )) or resid 117 through 119 or (resid 120 through 121 and (name N or \ name CA or name C or name O or name CB )) or resid 122 through 161 or (resid 162 \ and (name N or name CA or name C or name O or name CB )) or resid 163 through 1 \ 67 or (resid 168 through 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 through 262 or (resid 263 through 270 and (name N or name CA \ or name C or name O or name CB )) or resid 271 or (resid 272 through 276 and (na \ me N or name CA or name C or name O or name CB )) or resid 277 or (resid 278 thr \ ough 280 and (name N or name CA or name C or name O or name CB )) or resid 281 t \ hrough 282 or (resid 283 through 288 and (name N or name CA or name C or name O \ or name CB )) or (resid 289 through 301 and (name N or name CA or name C or name \ O or name CB )) or resid 309 through 320 or resid 332 through 338 or resid 369 \ through 397 or resid 405 through 412 or (resid 413 through 414 and (name N or na \ me CA or name C or name O or name CB )) or resid 415 through 422 or (resid 423 t \ hrough 427 and (name N or name CA or name C or name O or name CB )) or resid 428 \ or resid 433 through 463 or (resid 464 through 465 and (name N or name CA or na \ me C or name O or name CB )) or resid 466 through 471 or (resid 472 through 473 \ and (name N or name CA or name C or name O or name CB )) or resid 474 or (resid \ 475 through 476 and (name N or name CA or name C or name O or name CB )) or resi \ d 477 through 490 or (resid 491 and (name N or name CA or name C or name O or na \ me CB )) or resid 492 through 494 or (resid 495 through 498 and (name N or name \ CA or name C or name O or name CB )) or resid 499 or (resid 500 and (name N or n \ ame CA or name C or name O or name CB )) or resid 501 through 515 or (resid 516 \ and (name N or name CA or name C or name O or name CB )) or resid 517 or (resid \ 518 through 525 and (name N or name CA or name C or name O or name CB )) or (res \ id 526 through 533 and (name N or name CA or name C or name O or name CB )) or r \ esid 534 through 536 or (resid 537 and (name N or name CA or name C or name O or \ name CB )) or resid 538 through 539 or (resid 540 through 542 and (name N or na \ me CA or name C or name O or name CB )) or resid 543 through 547 or (resid 548 a \ nd (name N or name CA or name C or name O or name CB )) or resid 549 through 562 \ or (resid 563 and (name N or name CA or name C or name O or name CB )) or resid \ 564 through 590 or (resid 591 through 592 and (name N or name CA or name C or n \ ame O or name CB )) or resid 593 through 596 or (resid 597 and (name N or name C \ A or name C or name O or name CB )) or resid 598 through 606 or (resid 607 throu \ gh 614 and (name N or name CA or name C or name O or name CB )) or resid 615 thr \ ough 620 or (resid 621 and (name N or name CA or name C or name O or name CB )) \ or resid 622 through 753 or (resid 754 through 759 and (name N or name CA or nam \ e C or name O or name CB )) or resid 760 through 773)) selection = (chain 'J' and (resid 55 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 79 or (resid 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 87 or (resid 88 throu \ gh 90 and (name N or name CA or name C or name O or name CB )) or resid 91 throu \ gh 124 or (resid 125 through 126 and (name N or name CA or name C or name O or n \ ame CB )) or resid 127 through 192 or (resid 193 and (name N or name CA or name \ C or name O or name CB )) or resid 194 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 273 o \ r (resid 274 through 276 and (name N or name CA or name C or name O or name CB ) \ ) or resid 277 or (resid 278 through 280 and (name N or name CA or name C or nam \ e O or name CB )) or resid 281 through 282 or (resid 283 through 288 and (name N \ or name CA or name C or name O or name CB )) or (resid 289 through 338 and (nam \ e N or name CA or name C or name O or name CB )) or resid 369 through 389 or (re \ sid 390 through 391 and (name N or name CA or name C or name O or name CB )) or \ resid 392 through 393 or (resid 394 through 395 and (name N or name CA or name C \ or name O or name CB )) or resid 396 through 397 or (resid 405 through 407 and \ (name N or name CA or name C or name O or name CB )) or resid 408 through 410 or \ (resid 411 through 414 and (name N or name CA or name C or name O or name CB )) \ or resid 415 through 419 or (resid 420 through 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 or (resid 433 through 436 and (name N \ or name CA or name C or name O or name CB )) or resid 437 through 501 or (resid \ 502 and (name N or name CA or name C or name O or name CB )) or resid 503 throug \ h 518 or (resid 519 through 525 and (name N or name CA or name C or name O or na \ me CB )) or resid 526 through 549 or (resid 550 and (name N or name CA or name C \ or name O or name CB )) or resid 551 through 578 or (resid 579 and (name N or n \ ame CA or name C or name O or name CB )) or resid 580 or (resid 581 through 582 \ and (name N or name CA or name C or name O or name CB )) or resid 583 through 58 \ 4 or (resid 585 and (name N or name CA or name C or name O or name CB )) or resi \ d 586 through 663 or (resid 664 through 669 and (name N or name CA or name C or \ name O or name CB )) or resid 670 through 689 or (resid 690 through 696 and (nam \ e N or name CA or name C or name O or name CB )) or resid 697 or (resid 698 thro \ ugh 710 and (name N or name CA or name C or name O or name CB )) or resid 711 th \ rough 746 or (resid 747 through 759 and (name N or name CA or name C or name O o \ r name CB )) or resid 760 through 769 or (resid 770 and (name N or name CA or na \ me C or name O or name CB )) or resid 771 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 10.570 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 114.280 Find NCS groups from input model: 3.720 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 : 0.011 0.135 42994 Z= 0.743 Angle : 1.211 35.345 58617 Z= 0.670 Chirality : 0.065 0.474 6906 Planarity : 0.007 0.150 7726 Dihedral : 12.007 86.769 14943 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.94 % Favored : 91.65 % Rotamer: Outliers : 0.34 % Allowed : 0.93 % Favored : 98.73 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.10), residues: 5704 helix: -2.03 (0.11), residues: 1616 sheet: -1.01 (0.15), residues: 988 loop : -2.20 (0.10), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP H 570 HIS 0.020 0.003 HIS B 263 PHE 0.036 0.003 PHE A 554 TYR 0.061 0.004 TYR H 82 ARG 0.007 0.001 ARG E 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1099 time to evaluate : 4.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 SER cc_start: 0.8389 (p) cc_final: 0.8161 (p) REVERT: A 243 ILE cc_start: 0.9554 (tt) cc_final: 0.9308 (tt) REVERT: A 261 ILE cc_start: 0.9278 (mt) cc_final: 0.8859 (pt) REVERT: A 368 ASN cc_start: 0.9000 (t0) cc_final: 0.8699 (t0) REVERT: A 434 MET cc_start: 0.8163 (tpt) cc_final: 0.7729 (tmm) REVERT: A 436 TYR cc_start: 0.8974 (t80) cc_final: 0.8664 (t80) REVERT: A 439 PHE cc_start: 0.9090 (t80) cc_final: 0.8544 (t80) REVERT: A 450 LEU cc_start: 0.8792 (mt) cc_final: 0.8278 (mp) REVERT: A 453 ASP cc_start: 0.8663 (p0) cc_final: 0.8429 (p0) REVERT: A 512 ASP cc_start: 0.8467 (t70) cc_final: 0.8172 (t70) REVERT: A 551 ASP cc_start: 0.7248 (m-30) cc_final: 0.6901 (m-30) REVERT: A 595 ARG cc_start: 0.8638 (mtm110) cc_final: 0.8404 (mtm110) REVERT: A 602 ASN cc_start: 0.8929 (m-40) cc_final: 0.8410 (m110) REVERT: A 633 LYS cc_start: 0.9565 (tmtt) cc_final: 0.9209 (tppt) REVERT: A 635 ILE cc_start: 0.9489 (tp) cc_final: 0.9150 (mm) REVERT: A 643 ILE cc_start: 0.8803 (mm) cc_final: 0.8344 (mm) REVERT: B 227 SER cc_start: 0.8394 (p) cc_final: 0.8135 (p) REVERT: B 243 ILE cc_start: 0.9344 (tt) cc_final: 0.8984 (tt) REVERT: B 265 ASP cc_start: 0.7931 (t0) cc_final: 0.7399 (t0) REVERT: B 328 ASN cc_start: 0.8670 (m-40) cc_final: 0.8467 (m-40) REVERT: B 368 ASN cc_start: 0.8988 (t0) cc_final: 0.8760 (t0) REVERT: B 394 ILE cc_start: 0.8290 (mm) cc_final: 0.8013 (mm) REVERT: B 414 LYS cc_start: 0.8868 (mptt) cc_final: 0.8590 (mmtm) REVERT: B 444 LYS cc_start: 0.9179 (pttm) cc_final: 0.8910 (ptpp) REVERT: B 450 LEU cc_start: 0.9325 (mt) cc_final: 0.8969 (mt) REVERT: B 453 ASP cc_start: 0.8793 (p0) cc_final: 0.8570 (p0) REVERT: B 459 ILE cc_start: 0.9099 (mt) cc_final: 0.8795 (mt) REVERT: B 486 GLU cc_start: 0.8064 (tp30) cc_final: 0.7686 (tp30) REVERT: B 522 THR cc_start: 0.8697 (p) cc_final: 0.8409 (p) REVERT: B 563 LYS cc_start: 0.9345 (mmmt) cc_final: 0.9064 (mmtm) REVERT: B 577 VAL cc_start: 0.8916 (m) cc_final: 0.8386 (p) REVERT: B 635 ILE cc_start: 0.9031 (mm) cc_final: 0.8780 (mm) REVERT: C 434 MET cc_start: 0.8113 (ppp) cc_final: 0.7601 (ppp) REVERT: C 444 LYS cc_start: 0.9377 (tptp) cc_final: 0.9110 (tppt) REVERT: C 462 TYR cc_start: 0.8899 (t80) cc_final: 0.8671 (t80) REVERT: C 486 GLU cc_start: 0.8020 (tp30) cc_final: 0.7716 (tp30) REVERT: C 525 GLU cc_start: 0.7578 (pt0) cc_final: 0.7038 (pt0) REVERT: C 551 ASP cc_start: 0.8424 (t0) cc_final: 0.8094 (t0) REVERT: C 602 ASN cc_start: 0.8851 (m-40) cc_final: 0.8406 (m110) REVERT: C 616 HIS cc_start: 0.8428 (m90) cc_final: 0.8013 (m90) REVERT: C 637 LYS cc_start: 0.9377 (mmmm) cc_final: 0.8847 (mmtm) REVERT: C 724 ILE cc_start: 0.9275 (mm) cc_final: 0.8917 (tt) REVERT: D 185 ASP cc_start: 0.8576 (p0) cc_final: 0.8311 (p0) REVERT: D 242 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8086 (mtt90) REVERT: D 250 GLU cc_start: 0.8408 (pm20) cc_final: 0.7976 (mp0) REVERT: D 261 ILE cc_start: 0.9337 (mt) cc_final: 0.9115 (tp) REVERT: D 394 ILE cc_start: 0.9395 (mm) cc_final: 0.9153 (mp) REVERT: D 472 ASP cc_start: 0.8681 (t0) cc_final: 0.8152 (t0) REVERT: D 486 GLU cc_start: 0.8214 (tp30) cc_final: 0.7817 (tp30) REVERT: D 514 LEU cc_start: 0.8837 (tp) cc_final: 0.8524 (tt) REVERT: D 525 GLU cc_start: 0.8978 (tp30) cc_final: 0.8437 (tp30) REVERT: D 551 ASP cc_start: 0.8057 (m-30) cc_final: 0.7364 (m-30) REVERT: D 578 LEU cc_start: 0.9377 (tt) cc_final: 0.8980 (tt) REVERT: E 185 ASP cc_start: 0.9077 (p0) cc_final: 0.8702 (p0) REVERT: E 195 ASP cc_start: 0.8087 (t70) cc_final: 0.7822 (t0) REVERT: E 385 LEU cc_start: 0.8669 (mm) cc_final: 0.7656 (mm) REVERT: E 389 GLN cc_start: 0.8276 (mp10) cc_final: 0.7815 (mp10) REVERT: E 416 LEU cc_start: 0.9142 (mp) cc_final: 0.8933 (mp) REVERT: E 434 MET cc_start: 0.8737 (ppp) cc_final: 0.8387 (ppp) REVERT: E 472 ASP cc_start: 0.8745 (t0) cc_final: 0.8409 (t0) REVERT: E 485 GLN cc_start: 0.8867 (mt0) cc_final: 0.8651 (mt0) REVERT: E 541 GLN cc_start: 0.7905 (mt0) cc_final: 0.7246 (mm-40) REVERT: E 580 LYS cc_start: 0.9542 (mmmt) cc_final: 0.9298 (mmmm) REVERT: F 376 ASN cc_start: 0.8873 (m-40) cc_final: 0.8512 (t0) REVERT: F 440 LEU cc_start: 0.9338 (mt) cc_final: 0.8863 (mt) REVERT: F 444 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8687 (ptpt) REVERT: F 470 ARG cc_start: 0.7964 (tmm-80) cc_final: 0.7702 (tmm-80) REVERT: F 472 ASP cc_start: 0.8199 (t0) cc_final: 0.7679 (t0) REVERT: F 590 LEU cc_start: 0.9035 (tp) cc_final: 0.8791 (tt) REVERT: F 608 ASP cc_start: 0.7081 (t70) cc_final: 0.6832 (t70) REVERT: F 616 HIS cc_start: 0.9353 (m90) cc_final: 0.9132 (m90) REVERT: F 633 LYS cc_start: 0.9058 (pptt) cc_final: 0.8808 (pptt) REVERT: G 190 GLU cc_start: 0.8590 (tp30) cc_final: 0.8301 (tm-30) REVERT: G 222 SER cc_start: 0.8884 (t) cc_final: 0.8551 (t) REVERT: G 250 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7571 (mm-30) REVERT: G 326 ASN cc_start: 0.8126 (m-40) cc_final: 0.7775 (m110) REVERT: G 383 LEU cc_start: 0.8828 (tp) cc_final: 0.8610 (tp) REVERT: G 439 PHE cc_start: 0.9442 (t80) cc_final: 0.9080 (t80) REVERT: G 465 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8083 (mp0) REVERT: G 525 GLU cc_start: 0.7911 (pt0) cc_final: 0.7457 (pt0) REVERT: G 589 ILE cc_start: 0.8996 (mt) cc_final: 0.8730 (mm) REVERT: G 593 ASP cc_start: 0.8999 (t70) cc_final: 0.8644 (t0) REVERT: G 595 ARG cc_start: 0.9058 (ttp80) cc_final: 0.8800 (ttp-110) REVERT: G 617 ARG cc_start: 0.8936 (ttp80) cc_final: 0.8508 (ttp80) REVERT: G 703 LYS cc_start: 0.8549 (ptpp) cc_final: 0.8347 (ptpp) REVERT: H 158 ASP cc_start: 0.8009 (t70) cc_final: 0.7514 (t70) REVERT: H 187 ASP cc_start: 0.8697 (m-30) cc_final: 0.8434 (m-30) REVERT: H 226 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8355 (tp30) REVERT: H 228 GLN cc_start: 0.8932 (mm110) cc_final: 0.8533 (mm-40) REVERT: H 246 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8583 (mppt) REVERT: H 415 ASP cc_start: 0.8475 (m-30) cc_final: 0.8170 (m-30) REVERT: H 472 LYS cc_start: 0.9035 (pttm) cc_final: 0.8478 (pttm) REVERT: H 474 ASN cc_start: 0.7728 (m110) cc_final: 0.7459 (m-40) REVERT: H 499 LEU cc_start: 0.9049 (mp) cc_final: 0.8529 (mp) REVERT: H 533 GLN cc_start: 0.8412 (pm20) cc_final: 0.7965 (pm20) REVERT: H 541 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7948 (mt-10) REVERT: H 658 LEU cc_start: 0.8581 (tt) cc_final: 0.8313 (tt) REVERT: H 684 PHE cc_start: 0.8876 (t80) cc_final: 0.8667 (t80) REVERT: H 688 PHE cc_start: 0.9154 (t80) cc_final: 0.8810 (t80) REVERT: H 693 ASP cc_start: 0.8231 (t0) cc_final: 0.8022 (t0) REVERT: H 761 LYS cc_start: 0.9234 (mttt) cc_final: 0.8846 (pttp) REVERT: I 42 HIS cc_start: 0.8469 (m170) cc_final: 0.8223 (m-70) REVERT: I 61 LYS cc_start: 0.9166 (mmpt) cc_final: 0.8919 (mmtm) REVERT: I 153 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8896 (ttmm) REVERT: I 158 ASP cc_start: 0.7996 (m-30) cc_final: 0.7746 (m-30) REVERT: I 171 LEU cc_start: 0.9318 (tp) cc_final: 0.9069 (tp) REVERT: I 184 ASP cc_start: 0.8409 (p0) cc_final: 0.8064 (p0) REVERT: I 243 TYR cc_start: 0.9154 (t80) cc_final: 0.8830 (t80) REVERT: I 256 LEU cc_start: 0.8717 (mp) cc_final: 0.8498 (mp) REVERT: I 277 HIS cc_start: 0.8753 (t-90) cc_final: 0.8006 (t-170) REVERT: I 467 ILE cc_start: 0.8307 (mp) cc_final: 0.7699 (mp) REVERT: I 544 ARG cc_start: 0.8221 (tpt90) cc_final: 0.7817 (tpt-90) REVERT: I 570 TRP cc_start: 0.5651 (m100) cc_final: 0.4939 (m100) REVERT: I 597 GLU cc_start: 0.7163 (mp0) cc_final: 0.6711 (mp0) REVERT: J 153 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8711 (mtmt) REVERT: J 190 PHE cc_start: 0.9045 (m-10) cc_final: 0.8777 (m-10) REVERT: J 207 GLU cc_start: 0.8847 (tt0) cc_final: 0.8645 (mm-30) REVERT: J 221 PHE cc_start: 0.9081 (t80) cc_final: 0.8139 (t80) REVERT: J 277 HIS cc_start: 0.7320 (t-90) cc_final: 0.7080 (t-90) REVERT: J 411 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8441 (tp-100) REVERT: J 581 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7502 (pptt) REVERT: J 582 LEU cc_start: 0.9440 (tp) cc_final: 0.9103 (tp) REVERT: J 584 THR cc_start: 0.7281 (p) cc_final: 0.6577 (p) REVERT: J 586 ASN cc_start: 0.8116 (m-40) cc_final: 0.7488 (m-40) REVERT: J 590 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7662 (mmm-85) outliers start: 14 outliers final: 2 residues processed: 1106 average time/residue: 0.5434 time to fit residues: 968.9605 Evaluate side-chains 879 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 876 time to evaluate : 4.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain J residue 581 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 481 optimal weight: 6.9990 chunk 432 optimal weight: 9.9990 chunk 239 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 291 optimal weight: 0.0570 chunk 230 optimal weight: 0.6980 chunk 446 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 271 optimal weight: 6.9990 chunk 332 optimal weight: 0.9980 chunk 517 optimal weight: 0.0770 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN B 541 GLN B 602 ASN C 458 ASN ** C 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 HIS E 246 ASN E 328 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN E 616 HIS F 458 ASN F 553 ASN ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 GLN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 228 GLN ** H 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS I 262 GLN I 496 ASN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 42994 Z= 0.206 Angle : 0.716 15.954 58617 Z= 0.371 Chirality : 0.048 0.268 6906 Planarity : 0.005 0.081 7726 Dihedral : 4.906 47.809 6121 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 2.15 % Allowed : 11.80 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.32 (0.11), residues: 5704 helix: -0.41 (0.12), residues: 1653 sheet: -0.47 (0.15), residues: 1013 loop : -1.25 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 570 HIS 0.007 0.001 HIS B 263 PHE 0.029 0.002 PHE I 765 TYR 0.029 0.002 TYR I 513 ARG 0.009 0.001 ARG J 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1088 time to evaluate : 4.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.8917 (tttp) cc_final: 0.8621 (ttpt) REVERT: A 227 SER cc_start: 0.8188 (p) cc_final: 0.7929 (p) REVERT: A 235 ASP cc_start: 0.8326 (m-30) cc_final: 0.8007 (m-30) REVERT: A 434 MET cc_start: 0.8253 (tpt) cc_final: 0.7360 (tmm) REVERT: A 436 TYR cc_start: 0.8904 (t80) cc_final: 0.8436 (t80) REVERT: A 447 GLN cc_start: 0.8930 (tt0) cc_final: 0.8171 (tm-30) REVERT: A 470 ARG cc_start: 0.7547 (tpt-90) cc_final: 0.7346 (tpt-90) REVERT: A 551 ASP cc_start: 0.7398 (m-30) cc_final: 0.7053 (m-30) REVERT: A 555 ASP cc_start: 0.8117 (t0) cc_final: 0.7422 (t0) REVERT: A 563 LYS cc_start: 0.8974 (tmmt) cc_final: 0.8718 (ptmt) REVERT: A 600 ARG cc_start: 0.8267 (mmp80) cc_final: 0.7989 (mmp80) REVERT: A 602 ASN cc_start: 0.8732 (m-40) cc_final: 0.8316 (m110) REVERT: A 632 ASP cc_start: 0.9237 (p0) cc_final: 0.8842 (p0) REVERT: A 633 LYS cc_start: 0.9561 (tmtt) cc_final: 0.9316 (tppt) REVERT: A 635 ILE cc_start: 0.9446 (tp) cc_final: 0.9229 (mm) REVERT: A 703 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7769 (mmtm) REVERT: B 190 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7660 (mt-10) REVERT: B 227 SER cc_start: 0.8275 (p) cc_final: 0.8039 (p) REVERT: B 265 ASP cc_start: 0.8004 (t0) cc_final: 0.7534 (t0) REVERT: B 267 GLU cc_start: 0.7389 (mp0) cc_final: 0.7069 (mp0) REVERT: B 378 LEU cc_start: 0.9087 (tp) cc_final: 0.8691 (mm) REVERT: B 414 LYS cc_start: 0.9039 (mptt) cc_final: 0.8701 (mmtm) REVERT: B 444 LYS cc_start: 0.9069 (pttm) cc_final: 0.8805 (tppt) REVERT: B 486 GLU cc_start: 0.8056 (tp30) cc_final: 0.7805 (tp30) REVERT: B 563 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8875 (mmtm) REVERT: B 577 VAL cc_start: 0.8895 (m) cc_final: 0.8406 (p) REVERT: B 602 ASN cc_start: 0.9041 (m-40) cc_final: 0.8832 (m110) REVERT: B 633 LYS cc_start: 0.8992 (pptt) cc_final: 0.8557 (pptt) REVERT: B 635 ILE cc_start: 0.9161 (mm) cc_final: 0.8836 (mm) REVERT: B 703 LYS cc_start: 0.8347 (mmtp) cc_final: 0.8095 (mmtp) REVERT: B 722 LYS cc_start: 0.9252 (tppt) cc_final: 0.8798 (tppt) REVERT: C 389 GLN cc_start: 0.7799 (mp10) cc_final: 0.7481 (mp10) REVERT: C 434 MET cc_start: 0.8038 (ppp) cc_final: 0.7378 (ppp) REVERT: C 444 LYS cc_start: 0.9450 (tptp) cc_final: 0.9099 (tppt) REVERT: C 525 GLU cc_start: 0.7703 (pt0) cc_final: 0.7203 (pt0) REVERT: C 551 ASP cc_start: 0.8315 (t0) cc_final: 0.7863 (t0) REVERT: C 578 LEU cc_start: 0.8306 (tp) cc_final: 0.7993 (tt) REVERT: C 583 LEU cc_start: 0.9272 (mt) cc_final: 0.9061 (mp) REVERT: C 587 MET cc_start: 0.8872 (mtp) cc_final: 0.8565 (mtt) REVERT: C 637 LYS cc_start: 0.9396 (mmmm) cc_final: 0.9064 (mmmt) REVERT: D 202 PHE cc_start: 0.7785 (p90) cc_final: 0.7455 (p90) REVERT: D 250 GLU cc_start: 0.8094 (pm20) cc_final: 0.7770 (mp0) REVERT: D 261 ILE cc_start: 0.9286 (mt) cc_final: 0.9059 (tp) REVERT: D 359 ARG cc_start: 0.7450 (mtt90) cc_final: 0.7140 (mpp80) REVERT: D 407 PRO cc_start: 0.8923 (Cg_exo) cc_final: 0.8712 (Cg_endo) REVERT: D 444 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8583 (ptpt) REVERT: D 448 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8170 (mm) REVERT: D 463 ASN cc_start: 0.8288 (t0) cc_final: 0.7685 (t0) REVERT: D 472 ASP cc_start: 0.8107 (t0) cc_final: 0.7296 (t0) REVERT: D 486 GLU cc_start: 0.8297 (tp30) cc_final: 0.8092 (tp30) REVERT: D 515 GLU cc_start: 0.6738 (tp30) cc_final: 0.6426 (tp30) REVERT: D 551 ASP cc_start: 0.7871 (m-30) cc_final: 0.6988 (p0) REVERT: D 587 MET cc_start: 0.8731 (ptp) cc_final: 0.8298 (ptp) REVERT: D 602 ASN cc_start: 0.8730 (m-40) cc_final: 0.8493 (m110) REVERT: E 185 ASP cc_start: 0.9101 (p0) cc_final: 0.8841 (p0) REVERT: E 195 ASP cc_start: 0.7908 (t70) cc_final: 0.7443 (t0) REVERT: E 202 PHE cc_start: 0.8479 (p90) cc_final: 0.8060 (p90) REVERT: E 359 ARG cc_start: 0.7919 (pmt170) cc_final: 0.7684 (ptt-90) REVERT: E 385 LEU cc_start: 0.8665 (mm) cc_final: 0.8337 (mm) REVERT: E 391 LEU cc_start: 0.9146 (mm) cc_final: 0.8815 (mm) REVERT: E 434 MET cc_start: 0.8856 (ppp) cc_final: 0.8446 (ppp) REVERT: E 444 LYS cc_start: 0.9226 (tppt) cc_final: 0.8972 (tppt) REVERT: E 449 ARG cc_start: 0.9331 (mtm110) cc_final: 0.9084 (mtm110) REVERT: E 472 ASP cc_start: 0.8483 (t0) cc_final: 0.8129 (t0) REVERT: E 479 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6933 (mt-10) REVERT: E 512 ASP cc_start: 0.7437 (t0) cc_final: 0.6819 (t0) REVERT: E 515 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7807 (mm-30) REVERT: E 580 LYS cc_start: 0.9505 (mmmt) cc_final: 0.8715 (mmmt) REVERT: F 376 ASN cc_start: 0.8865 (m-40) cc_final: 0.8510 (t0) REVERT: F 389 GLN cc_start: 0.8606 (mp10) cc_final: 0.8391 (mp10) REVERT: F 438 GLN cc_start: 0.9336 (mt0) cc_final: 0.8947 (mt0) REVERT: F 440 LEU cc_start: 0.9232 (mt) cc_final: 0.8987 (mt) REVERT: F 444 LYS cc_start: 0.8980 (ptpp) cc_final: 0.8755 (ptpp) REVERT: F 449 ARG cc_start: 0.8520 (mtm110) cc_final: 0.7444 (ptt-90) REVERT: F 462 TYR cc_start: 0.8067 (t80) cc_final: 0.7621 (t80) REVERT: F 471 VAL cc_start: 0.8559 (m) cc_final: 0.8031 (t) REVERT: F 472 ASP cc_start: 0.8088 (t0) cc_final: 0.7328 (t0) REVERT: F 479 GLU cc_start: 0.8407 (mp0) cc_final: 0.8108 (mp0) REVERT: F 499 ASN cc_start: 0.8502 (m110) cc_final: 0.7793 (m-40) REVERT: F 521 MET cc_start: 0.7512 (tpt) cc_final: 0.7309 (tpt) REVERT: F 551 ASP cc_start: 0.7379 (t0) cc_final: 0.6253 (p0) REVERT: F 560 GLN cc_start: 0.9239 (tp-100) cc_final: 0.8891 (tp40) REVERT: F 601 ASN cc_start: 0.9300 (p0) cc_final: 0.8914 (p0) REVERT: F 633 LYS cc_start: 0.9066 (pptt) cc_final: 0.8396 (pptt) REVERT: G 250 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7486 (tp30) REVERT: G 326 ASN cc_start: 0.7746 (m-40) cc_final: 0.7276 (m-40) REVERT: G 403 GLN cc_start: 0.7910 (pm20) cc_final: 0.7551 (pm20) REVERT: G 439 PHE cc_start: 0.9385 (t80) cc_final: 0.8868 (t80) REVERT: G 443 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8623 (mm-30) REVERT: G 485 GLN cc_start: 0.8623 (mt0) cc_final: 0.8410 (mt0) REVERT: G 505 ILE cc_start: 0.9437 (mm) cc_final: 0.9108 (mm) REVERT: G 549 GLU cc_start: 0.8711 (mp0) cc_final: 0.8467 (mp0) REVERT: G 557 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8815 (tp-100) REVERT: G 560 GLN cc_start: 0.9279 (tp-100) cc_final: 0.8887 (mm-40) REVERT: G 593 ASP cc_start: 0.8935 (t70) cc_final: 0.8453 (t0) REVERT: G 595 ARG cc_start: 0.9025 (ttp80) cc_final: 0.8810 (ttp-110) REVERT: G 617 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8506 (ttp80) REVERT: G 703 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8337 (ptpp) REVERT: H 74 TYR cc_start: 0.7584 (t80) cc_final: 0.6861 (t80) REVERT: H 118 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6007 (p90) REVERT: H 158 ASP cc_start: 0.7969 (t70) cc_final: 0.7565 (t70) REVERT: H 184 ASP cc_start: 0.8699 (m-30) cc_final: 0.8459 (m-30) REVERT: H 187 ASP cc_start: 0.8571 (m-30) cc_final: 0.8284 (m-30) REVERT: H 201 PHE cc_start: 0.8948 (m-80) cc_final: 0.8530 (m-80) REVERT: H 215 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7845 (pt0) REVERT: H 236 TYR cc_start: 0.7787 (m-80) cc_final: 0.7371 (m-80) REVERT: H 244 MET cc_start: 0.8862 (tpp) cc_final: 0.7909 (tpp) REVERT: H 248 ASN cc_start: 0.9012 (p0) cc_final: 0.8573 (p0) REVERT: H 254 LEU cc_start: 0.9099 (tt) cc_final: 0.8451 (tp) REVERT: H 393 GLN cc_start: 0.8470 (pm20) cc_final: 0.8002 (pm20) REVERT: H 415 ASP cc_start: 0.8181 (m-30) cc_final: 0.7951 (m-30) REVERT: H 434 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7686 (tmtt) REVERT: H 541 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7449 (mt-10) REVERT: H 548 LYS cc_start: 0.7445 (mmmt) cc_final: 0.7208 (tptp) REVERT: H 589 ASN cc_start: 0.7429 (m110) cc_final: 0.6830 (m110) REVERT: H 693 ASP cc_start: 0.8558 (t0) cc_final: 0.8248 (t0) REVERT: H 718 PHE cc_start: 0.7943 (t80) cc_final: 0.7641 (t80) REVERT: H 737 PHE cc_start: 0.8783 (m-80) cc_final: 0.8178 (m-10) REVERT: H 741 PHE cc_start: 0.8567 (t80) cc_final: 0.8202 (t80) REVERT: I 61 LYS cc_start: 0.9057 (mmpt) cc_final: 0.8593 (mttm) REVERT: I 72 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: I 158 ASP cc_start: 0.8048 (m-30) cc_final: 0.7799 (m-30) REVERT: I 171 LEU cc_start: 0.8991 (tp) cc_final: 0.8746 (tp) REVERT: I 184 ASP cc_start: 0.8128 (p0) cc_final: 0.7718 (p0) REVERT: I 201 PHE cc_start: 0.8709 (m-80) cc_final: 0.8480 (m-80) REVERT: I 277 HIS cc_start: 0.8588 (t-90) cc_final: 0.8084 (t-90) REVERT: I 531 ASP cc_start: 0.7539 (t0) cc_final: 0.6933 (t0) REVERT: I 533 GLN cc_start: 0.7370 (pm20) cc_final: 0.7038 (pm20) REVERT: I 537 GLN cc_start: 0.9016 (tp40) cc_final: 0.8499 (mp10) REVERT: I 570 TRP cc_start: 0.6035 (m100) cc_final: 0.5824 (m100) REVERT: I 588 HIS cc_start: 0.8300 (m-70) cc_final: 0.8071 (m-70) REVERT: I 769 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8381 (mm-40) REVERT: J 108 TYR cc_start: 0.7498 (m-80) cc_final: 0.7087 (m-80) REVERT: J 153 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8531 (mtpt) REVERT: J 205 PHE cc_start: 0.8359 (t80) cc_final: 0.7774 (t80) REVERT: J 217 PHE cc_start: 0.8015 (t80) cc_final: 0.7613 (t80) REVERT: J 221 PHE cc_start: 0.8893 (t80) cc_final: 0.8316 (t80) REVERT: J 436 TYR cc_start: 0.5863 (m-10) cc_final: 0.5589 (m-10) REVERT: J 546 ASP cc_start: 0.7795 (m-30) cc_final: 0.7593 (m-30) REVERT: J 582 LEU cc_start: 0.9331 (tp) cc_final: 0.8979 (tp) REVERT: J 584 THR cc_start: 0.7454 (p) cc_final: 0.7088 (p) REVERT: J 586 ASN cc_start: 0.7947 (m-40) cc_final: 0.7688 (m-40) REVERT: J 629 PHE cc_start: 0.8748 (m-10) cc_final: 0.8299 (m-10) outliers start: 88 outliers final: 54 residues processed: 1123 average time/residue: 0.5424 time to fit residues: 996.0227 Evaluate side-chains 1000 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 942 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 708 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 579 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 287 optimal weight: 0.0870 chunk 160 optimal weight: 3.9990 chunk 430 optimal weight: 7.9990 chunk 352 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 518 optimal weight: 4.9990 chunk 560 optimal weight: 40.0000 chunk 461 optimal weight: 40.0000 chunk 514 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 416 optimal weight: 7.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS B 268 ASN B 363 ASN B 553 ASN ** C 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN D 499 ASN E 561 ASN ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN F 541 GLN G 553 ASN ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN ** H 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 745 HIS H 767 ASN I 228 GLN J 186 GLN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 42994 Z= 0.442 Angle : 0.721 12.896 58617 Z= 0.377 Chirality : 0.048 0.192 6906 Planarity : 0.005 0.061 7726 Dihedral : 4.891 48.462 6116 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 4.38 % Allowed : 15.30 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -1.03 (0.11), residues: 5704 helix: -0.18 (0.13), residues: 1673 sheet: -0.26 (0.15), residues: 1029 loop : -1.08 (0.11), residues: 3002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 570 HIS 0.013 0.002 HIS D 616 PHE 0.031 0.002 PHE I 471 TYR 0.025 0.002 TYR F 259 ARG 0.009 0.001 ARG G 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 919 time to evaluate : 4.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7289 (tt0) REVERT: A 218 LYS cc_start: 0.9031 (tttp) cc_final: 0.8668 (ttpt) REVERT: A 265 ASP cc_start: 0.8331 (t0) cc_final: 0.7454 (p0) REVERT: A 447 GLN cc_start: 0.8950 (tt0) cc_final: 0.8119 (tm-30) REVERT: A 470 ARG cc_start: 0.7573 (tpt-90) cc_final: 0.7347 (tpt-90) REVERT: A 549 GLU cc_start: 0.8787 (mp0) cc_final: 0.8396 (mp0) REVERT: A 551 ASP cc_start: 0.7760 (m-30) cc_final: 0.7408 (m-30) REVERT: A 602 ASN cc_start: 0.8839 (m-40) cc_final: 0.8401 (m110) REVERT: A 633 LYS cc_start: 0.9588 (tmtt) cc_final: 0.9229 (tppt) REVERT: A 703 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7947 (mmtm) REVERT: B 231 ASP cc_start: 0.8675 (p0) cc_final: 0.8412 (p0) REVERT: B 265 ASP cc_start: 0.8021 (t0) cc_final: 0.7621 (t0) REVERT: B 267 GLU cc_start: 0.7469 (mp0) cc_final: 0.7249 (mp0) REVERT: B 268 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.7967 (p0) REVERT: B 363 ASN cc_start: 0.9166 (m110) cc_final: 0.8134 (p0) REVERT: B 403 GLN cc_start: 0.8366 (mp10) cc_final: 0.8084 (mp10) REVERT: B 434 MET cc_start: 0.7719 (tmm) cc_final: 0.7491 (tmm) REVERT: B 444 LYS cc_start: 0.9056 (pttm) cc_final: 0.8802 (tppt) REVERT: B 453 ASP cc_start: 0.8802 (p0) cc_final: 0.8555 (p0) REVERT: B 486 GLU cc_start: 0.8168 (tp30) cc_final: 0.7905 (tp30) REVERT: B 629 LEU cc_start: 0.9005 (tp) cc_final: 0.8500 (mm) REVERT: B 633 LYS cc_start: 0.8970 (pptt) cc_final: 0.8459 (pptt) REVERT: B 635 ILE cc_start: 0.9171 (mm) cc_final: 0.8867 (mm) REVERT: B 636 ARG cc_start: 0.8737 (ptt-90) cc_final: 0.8189 (ptp90) REVERT: B 703 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8250 (mmtp) REVERT: B 722 LYS cc_start: 0.9353 (tppt) cc_final: 0.9058 (tppt) REVERT: C 434 MET cc_start: 0.8207 (ppp) cc_final: 0.7547 (ppp) REVERT: C 444 LYS cc_start: 0.9539 (tptp) cc_final: 0.9228 (tppt) REVERT: C 551 ASP cc_start: 0.8503 (t0) cc_final: 0.8112 (t0) REVERT: C 579 ASP cc_start: 0.8686 (t0) cc_final: 0.8471 (t0) REVERT: C 587 MET cc_start: 0.8958 (mtp) cc_final: 0.8562 (mtp) REVERT: C 616 HIS cc_start: 0.8521 (m90) cc_final: 0.8213 (m90) REVERT: C 632 ASP cc_start: 0.8919 (t0) cc_final: 0.8554 (p0) REVERT: C 637 LYS cc_start: 0.9396 (mmmm) cc_final: 0.9185 (mmmt) REVERT: D 250 GLU cc_start: 0.8210 (pm20) cc_final: 0.7921 (mp0) REVERT: D 291 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8505 (mptt) REVERT: D 335 ASP cc_start: 0.8505 (t0) cc_final: 0.8287 (t0) REVERT: D 444 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8679 (mmtt) REVERT: D 445 THR cc_start: 0.9052 (t) cc_final: 0.8709 (p) REVERT: D 472 ASP cc_start: 0.8309 (t0) cc_final: 0.7574 (t0) REVERT: D 486 GLU cc_start: 0.8396 (tp30) cc_final: 0.8141 (tp30) REVERT: D 497 ASP cc_start: 0.7976 (p0) cc_final: 0.7555 (p0) REVERT: D 499 ASN cc_start: 0.8444 (m-40) cc_final: 0.7670 (m-40) REVERT: D 514 LEU cc_start: 0.8411 (tp) cc_final: 0.8162 (tt) REVERT: D 551 ASP cc_start: 0.7948 (m-30) cc_final: 0.7091 (p0) REVERT: D 602 ASN cc_start: 0.8919 (m-40) cc_final: 0.8577 (m110) REVERT: D 703 LYS cc_start: 0.8991 (mppt) cc_final: 0.8773 (mptt) REVERT: E 185 ASP cc_start: 0.9129 (p0) cc_final: 0.8820 (p0) REVERT: E 195 ASP cc_start: 0.8098 (t70) cc_final: 0.7769 (t0) REVERT: E 202 PHE cc_start: 0.8681 (p90) cc_final: 0.8407 (p90) REVERT: E 224 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 359 ARG cc_start: 0.7978 (pmt170) cc_final: 0.7689 (ptt-90) REVERT: E 385 LEU cc_start: 0.8748 (mm) cc_final: 0.8417 (mm) REVERT: E 391 LEU cc_start: 0.9212 (mm) cc_final: 0.8864 (mm) REVERT: E 402 SER cc_start: 0.8905 (m) cc_final: 0.8586 (p) REVERT: E 434 MET cc_start: 0.8721 (ppp) cc_final: 0.8141 (ppp) REVERT: E 449 ARG cc_start: 0.9341 (mtm110) cc_final: 0.9136 (mtm110) REVERT: E 472 ASP cc_start: 0.8895 (t0) cc_final: 0.8475 (t0) REVERT: E 497 ASP cc_start: 0.7967 (p0) cc_final: 0.7651 (p0) REVERT: E 499 ASN cc_start: 0.8593 (m110) cc_final: 0.8031 (m-40) REVERT: E 512 ASP cc_start: 0.7978 (t0) cc_final: 0.7111 (t0) REVERT: E 515 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8127 (mm-30) REVERT: E 593 ASP cc_start: 0.7188 (t0) cc_final: 0.6818 (t0) REVERT: E 722 LYS cc_start: 0.8499 (tptt) cc_final: 0.8015 (tptp) REVERT: F 376 ASN cc_start: 0.8986 (m-40) cc_final: 0.8582 (t0) REVERT: F 472 ASP cc_start: 0.8196 (t0) cc_final: 0.7447 (t0) REVERT: F 479 GLU cc_start: 0.8336 (mp0) cc_final: 0.8007 (mp0) REVERT: F 497 ASP cc_start: 0.8009 (p0) cc_final: 0.7758 (p0) REVERT: F 499 ASN cc_start: 0.8761 (m110) cc_final: 0.8001 (m-40) REVERT: F 551 ASP cc_start: 0.7660 (t0) cc_final: 0.6581 (p0) REVERT: F 601 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8774 (p0) REVERT: F 636 ARG cc_start: 0.8585 (mpp80) cc_final: 0.8382 (ptp90) REVERT: G 250 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7430 (tp30) REVERT: G 439 PHE cc_start: 0.9320 (t80) cc_final: 0.9056 (t80) REVERT: G 560 GLN cc_start: 0.9264 (tp-100) cc_final: 0.8902 (mm-40) REVERT: G 593 ASP cc_start: 0.8960 (t70) cc_final: 0.8403 (t0) REVERT: G 595 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8787 (ttp-110) REVERT: G 617 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8531 (ttp80) REVERT: G 636 ARG cc_start: 0.8006 (mpp-170) cc_final: 0.7685 (ptp-170) REVERT: H 65 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8721 (mmtt) REVERT: H 118 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6373 (p90) REVERT: H 158 ASP cc_start: 0.8067 (t70) cc_final: 0.7634 (t70) REVERT: H 184 ASP cc_start: 0.8676 (m-30) cc_final: 0.8376 (p0) REVERT: H 187 ASP cc_start: 0.8547 (m-30) cc_final: 0.8235 (m-30) REVERT: H 201 PHE cc_start: 0.9068 (m-80) cc_final: 0.8599 (m-80) REVERT: H 236 TYR cc_start: 0.8072 (m-80) cc_final: 0.7826 (m-80) REVERT: H 244 MET cc_start: 0.8711 (tpp) cc_final: 0.7880 (tpp) REVERT: H 248 ASN cc_start: 0.8907 (p0) cc_final: 0.8475 (p0) REVERT: H 393 GLN cc_start: 0.8549 (pm20) cc_final: 0.8050 (pm20) REVERT: H 398 LEU cc_start: 0.8330 (mm) cc_final: 0.7047 (pp) REVERT: H 415 ASP cc_start: 0.8155 (m-30) cc_final: 0.7927 (m-30) REVERT: H 434 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7215 (ttpp) REVERT: H 441 MET cc_start: 0.8221 (tpp) cc_final: 0.7946 (tpt) REVERT: H 472 LYS cc_start: 0.9043 (tttp) cc_final: 0.8623 (tptm) REVERT: H 510 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6952 (mmm-85) REVERT: H 541 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7636 (mt-10) REVERT: H 548 LYS cc_start: 0.7478 (mmmt) cc_final: 0.7251 (tptp) REVERT: H 589 ASN cc_start: 0.7632 (m110) cc_final: 0.6962 (m110) REVERT: H 638 ASN cc_start: 0.8834 (m110) cc_final: 0.8024 (t0) REVERT: H 693 ASP cc_start: 0.8552 (t0) cc_final: 0.8171 (t0) REVERT: H 707 LEU cc_start: 0.8190 (tp) cc_final: 0.7856 (tp) REVERT: H 718 PHE cc_start: 0.7890 (t80) cc_final: 0.7599 (t80) REVERT: H 737 PHE cc_start: 0.8728 (m-80) cc_final: 0.8226 (m-10) REVERT: H 764 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8527 (pm20) REVERT: I 38 GLU cc_start: 0.7966 (mp0) cc_final: 0.7505 (mp0) REVERT: I 61 LYS cc_start: 0.9171 (mmpt) cc_final: 0.8748 (mttm) REVERT: I 82 TYR cc_start: 0.7096 (p90) cc_final: 0.6506 (p90) REVERT: I 184 ASP cc_start: 0.8372 (p0) cc_final: 0.7936 (p0) REVERT: I 277 HIS cc_start: 0.8417 (t-90) cc_final: 0.7844 (t-170) REVERT: I 475 PHE cc_start: 0.8517 (t80) cc_final: 0.8248 (t80) REVERT: I 531 ASP cc_start: 0.7634 (t0) cc_final: 0.6899 (t0) REVERT: I 533 GLN cc_start: 0.7501 (pm20) cc_final: 0.7258 (pm20) REVERT: I 537 GLN cc_start: 0.9065 (tp40) cc_final: 0.8779 (tm-30) REVERT: I 588 HIS cc_start: 0.8429 (m-70) cc_final: 0.8161 (m-70) REVERT: I 769 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8479 (mm-40) REVERT: J 74 TYR cc_start: 0.8872 (t80) cc_final: 0.8552 (t80) REVERT: J 108 TYR cc_start: 0.7626 (m-80) cc_final: 0.7186 (m-80) REVERT: J 117 HIS cc_start: 0.7306 (t-90) cc_final: 0.7058 (t-90) REVERT: J 153 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8716 (mtpt) REVERT: J 205 PHE cc_start: 0.8453 (t80) cc_final: 0.7993 (t80) REVERT: J 217 PHE cc_start: 0.8063 (t80) cc_final: 0.7778 (t80) REVERT: J 221 PHE cc_start: 0.9020 (t80) cc_final: 0.8466 (t80) REVERT: J 235 LEU cc_start: 0.8649 (tp) cc_final: 0.8327 (mt) REVERT: J 236 TYR cc_start: 0.8759 (m-80) cc_final: 0.8456 (m-80) REVERT: J 499 LEU cc_start: 0.7277 (tt) cc_final: 0.7069 (tt) REVERT: J 544 ARG cc_start: 0.6918 (tpp-160) cc_final: 0.6573 (tpt170) REVERT: J 582 LEU cc_start: 0.9275 (tp) cc_final: 0.8698 (tp) REVERT: J 586 ASN cc_start: 0.8071 (m-40) cc_final: 0.7700 (m-40) REVERT: J 590 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7223 (mmm-85) REVERT: J 629 PHE cc_start: 0.8715 (m-10) cc_final: 0.8033 (m-10) outliers start: 179 outliers final: 130 residues processed: 1016 average time/residue: 0.5245 time to fit residues: 866.1948 Evaluate side-chains 974 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 838 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 376 ASN Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 439 PHE Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 601 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain H residue 118 TYR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 510 ARG Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 584 THR Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 708 VAL Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 534 ILE Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 580 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 512 optimal weight: 8.9990 chunk 389 optimal weight: 0.0270 chunk 269 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 chunk 247 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 520 optimal weight: 8.9990 chunk 550 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 493 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN C 246 ASN ** C 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 HIS ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** G 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 GLN ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 745 HIS J 146 ASN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 42994 Z= 0.248 Angle : 0.629 11.368 58617 Z= 0.324 Chirality : 0.046 0.199 6906 Planarity : 0.004 0.052 7726 Dihedral : 4.565 29.163 6113 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 3.70 % Allowed : 17.83 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 5704 helix: -0.00 (0.13), residues: 1668 sheet: 0.05 (0.16), residues: 1025 loop : -0.95 (0.11), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 570 HIS 0.010 0.001 HIS D 616 PHE 0.030 0.001 PHE I 247 TYR 0.024 0.001 TYR D 436 ARG 0.010 0.001 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 925 time to evaluate : 6.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.9007 (tttp) cc_final: 0.8773 (ttpt) REVERT: A 235 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: A 265 ASP cc_start: 0.8326 (t0) cc_final: 0.7678 (p0) REVERT: A 434 MET cc_start: 0.7246 (tpp) cc_final: 0.6862 (tpp) REVERT: A 446 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7900 (mmtt) REVERT: A 447 GLN cc_start: 0.8895 (tt0) cc_final: 0.8058 (tm-30) REVERT: A 479 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7286 (tt0) REVERT: A 549 GLU cc_start: 0.8771 (mp0) cc_final: 0.8472 (mp0) REVERT: A 551 ASP cc_start: 0.7711 (m-30) cc_final: 0.7355 (m-30) REVERT: A 595 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8031 (ptt90) REVERT: A 602 ASN cc_start: 0.8823 (m-40) cc_final: 0.8326 (m110) REVERT: A 632 ASP cc_start: 0.9333 (p0) cc_final: 0.8755 (p0) REVERT: A 633 LYS cc_start: 0.9578 (tmtt) cc_final: 0.9263 (tppt) REVERT: A 635 ILE cc_start: 0.9464 (tp) cc_final: 0.9099 (mm) REVERT: A 703 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7968 (mmtm) REVERT: B 192 TYR cc_start: 0.9406 (p90) cc_final: 0.8923 (p90) REVERT: B 265 ASP cc_start: 0.7913 (t0) cc_final: 0.7538 (t0) REVERT: B 267 GLU cc_start: 0.7367 (mp0) cc_final: 0.7017 (mp0) REVERT: B 403 GLN cc_start: 0.8319 (mp10) cc_final: 0.8015 (mp10) REVERT: B 444 LYS cc_start: 0.9005 (pttm) cc_final: 0.8758 (tppt) REVERT: B 486 GLU cc_start: 0.8126 (tp30) cc_final: 0.7846 (tp30) REVERT: B 561 ASN cc_start: 0.8959 (t0) cc_final: 0.8718 (t0) REVERT: B 594 LYS cc_start: 0.8603 (ptmt) cc_final: 0.8393 (ptmt) REVERT: B 629 LEU cc_start: 0.9039 (tp) cc_final: 0.8531 (mm) REVERT: B 633 LYS cc_start: 0.8948 (pptt) cc_final: 0.8604 (pptt) REVERT: B 635 ILE cc_start: 0.9144 (mm) cc_final: 0.8834 (mm) REVERT: B 636 ARG cc_start: 0.8681 (ptt-90) cc_final: 0.8113 (ptp90) REVERT: B 703 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8340 (mmtp) REVERT: B 722 LYS cc_start: 0.9381 (tppt) cc_final: 0.9123 (tppt) REVERT: C 444 LYS cc_start: 0.9544 (tptp) cc_final: 0.9244 (tppt) REVERT: C 454 GLN cc_start: 0.8388 (mp10) cc_final: 0.8020 (mp10) REVERT: C 483 GLN cc_start: 0.8725 (mp10) cc_final: 0.8444 (mp10) REVERT: C 497 ASP cc_start: 0.7917 (p0) cc_final: 0.7562 (p0) REVERT: C 499 ASN cc_start: 0.8832 (m-40) cc_final: 0.8376 (m-40) REVERT: C 551 ASP cc_start: 0.8483 (t0) cc_final: 0.8076 (t0) REVERT: C 587 MET cc_start: 0.8806 (mtp) cc_final: 0.8407 (mtp) REVERT: C 616 HIS cc_start: 0.8560 (m90) cc_final: 0.8246 (m90) REVERT: C 637 LYS cc_start: 0.9368 (mmmm) cc_final: 0.9117 (mmmt) REVERT: D 250 GLU cc_start: 0.8162 (pm20) cc_final: 0.7849 (mp0) REVERT: D 291 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8493 (mmtt) REVERT: D 346 TRP cc_start: 0.8356 (m-10) cc_final: 0.8065 (m-10) REVERT: D 444 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8691 (mmtt) REVERT: D 472 ASP cc_start: 0.8132 (t0) cc_final: 0.7314 (t0) REVERT: D 497 ASP cc_start: 0.8081 (p0) cc_final: 0.7492 (p0) REVERT: D 499 ASN cc_start: 0.8431 (m110) cc_final: 0.7524 (m-40) REVERT: D 551 ASP cc_start: 0.7915 (m-30) cc_final: 0.6980 (p0) REVERT: D 569 LEU cc_start: 0.9001 (mm) cc_final: 0.8628 (mm) REVERT: D 602 ASN cc_start: 0.8896 (m-40) cc_final: 0.8561 (m110) REVERT: D 614 GLU cc_start: 0.9058 (pp20) cc_final: 0.8511 (pp20) REVERT: D 633 LYS cc_start: 0.8815 (tptt) cc_final: 0.8540 (tppt) REVERT: D 703 LYS cc_start: 0.9008 (mppt) cc_final: 0.8756 (mptt) REVERT: E 185 ASP cc_start: 0.8977 (p0) cc_final: 0.8733 (p0) REVERT: E 195 ASP cc_start: 0.8022 (t70) cc_final: 0.7750 (t0) REVERT: E 200 ARG cc_start: 0.8086 (mtm180) cc_final: 0.7875 (mpp80) REVERT: E 202 PHE cc_start: 0.8768 (p90) cc_final: 0.8518 (p90) REVERT: E 359 ARG cc_start: 0.7925 (pmt170) cc_final: 0.7530 (ptt-90) REVERT: E 385 LEU cc_start: 0.8796 (mm) cc_final: 0.8517 (mm) REVERT: E 391 LEU cc_start: 0.9237 (mm) cc_final: 0.8884 (mm) REVERT: E 434 MET cc_start: 0.8596 (ppp) cc_final: 0.8139 (ppp) REVERT: E 444 LYS cc_start: 0.9234 (tppt) cc_final: 0.8989 (tppt) REVERT: E 449 ARG cc_start: 0.9307 (mtm110) cc_final: 0.9100 (mtm110) REVERT: E 472 ASP cc_start: 0.8706 (t0) cc_final: 0.8344 (t0) REVERT: E 512 ASP cc_start: 0.7822 (t0) cc_final: 0.6887 (t0) REVERT: E 515 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8124 (mm-30) REVERT: E 593 ASP cc_start: 0.7093 (t0) cc_final: 0.6629 (t0) REVERT: F 376 ASN cc_start: 0.8914 (m-40) cc_final: 0.8490 (t0) REVERT: F 449 ARG cc_start: 0.8582 (mtm110) cc_final: 0.7400 (ptp90) REVERT: F 472 ASP cc_start: 0.8092 (t0) cc_final: 0.7140 (t0) REVERT: F 479 GLU cc_start: 0.8397 (mp0) cc_final: 0.8055 (mp0) REVERT: F 497 ASP cc_start: 0.8052 (p0) cc_final: 0.7650 (p0) REVERT: F 499 ASN cc_start: 0.8723 (m110) cc_final: 0.7846 (m-40) REVERT: F 551 ASP cc_start: 0.7621 (t0) cc_final: 0.6470 (p0) REVERT: G 190 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7950 (tm-30) REVERT: G 250 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7432 (tp30) REVERT: G 329 SER cc_start: 0.9120 (p) cc_final: 0.8777 (t) REVERT: G 439 PHE cc_start: 0.9342 (t80) cc_final: 0.9075 (t80) REVERT: G 444 LYS cc_start: 0.9210 (ptpp) cc_final: 0.8926 (pttm) REVERT: G 529 ILE cc_start: 0.9347 (tp) cc_final: 0.8936 (tp) REVERT: G 560 GLN cc_start: 0.9258 (tp-100) cc_final: 0.8860 (mm-40) REVERT: G 565 GLN cc_start: 0.9091 (mt0) cc_final: 0.8681 (tt0) REVERT: G 593 ASP cc_start: 0.8985 (t70) cc_final: 0.8389 (t0) REVERT: G 595 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8814 (ttp-110) REVERT: G 617 ARG cc_start: 0.9015 (ttp80) cc_final: 0.8533 (ttp80) REVERT: G 636 ARG cc_start: 0.8060 (mpp-170) cc_final: 0.7647 (ptp-170) REVERT: G 703 LYS cc_start: 0.8726 (ptpp) cc_final: 0.8421 (ptpp) REVERT: H 65 LYS cc_start: 0.9135 (mmmt) cc_final: 0.8815 (mmmt) REVERT: H 74 TYR cc_start: 0.7853 (t80) cc_final: 0.6890 (t80) REVERT: H 118 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6539 (p90) REVERT: H 158 ASP cc_start: 0.8047 (t70) cc_final: 0.7671 (t70) REVERT: H 170 PHE cc_start: 0.8745 (t80) cc_final: 0.8437 (t80) REVERT: H 184 ASP cc_start: 0.8604 (m-30) cc_final: 0.8306 (p0) REVERT: H 187 ASP cc_start: 0.8484 (m-30) cc_final: 0.8251 (m-30) REVERT: H 201 PHE cc_start: 0.9071 (m-80) cc_final: 0.8696 (m-80) REVERT: H 215 GLU cc_start: 0.8156 (pt0) cc_final: 0.7918 (pp20) REVERT: H 244 MET cc_start: 0.8646 (tpp) cc_final: 0.7873 (tpp) REVERT: H 248 ASN cc_start: 0.8648 (p0) cc_final: 0.8402 (p0) REVERT: H 296 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7976 (mm) REVERT: H 384 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7727 (mm-40) REVERT: H 393 GLN cc_start: 0.8557 (pm20) cc_final: 0.8279 (pm20) REVERT: H 398 LEU cc_start: 0.8390 (mm) cc_final: 0.7182 (pp) REVERT: H 434 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7575 (ttpp) REVERT: H 436 TYR cc_start: 0.6677 (m-10) cc_final: 0.6279 (m-10) REVERT: H 510 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6643 (mmm-85) REVERT: H 541 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7680 (mt-10) REVERT: H 548 LYS cc_start: 0.7525 (mmmt) cc_final: 0.7279 (tptp) REVERT: H 589 ASN cc_start: 0.7676 (m110) cc_final: 0.7009 (m110) REVERT: H 638 ASN cc_start: 0.8827 (m110) cc_final: 0.8031 (t0) REVERT: H 680 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8843 (p0) REVERT: H 718 PHE cc_start: 0.7743 (t80) cc_final: 0.7505 (t80) REVERT: H 737 PHE cc_start: 0.8749 (m-80) cc_final: 0.8081 (m-10) REVERT: H 764 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: I 38 GLU cc_start: 0.8027 (mp0) cc_final: 0.7611 (mp0) REVERT: I 61 LYS cc_start: 0.9185 (mmpt) cc_final: 0.8760 (mtmm) REVERT: I 72 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8283 (mm-30) REVERT: I 184 ASP cc_start: 0.8284 (p0) cc_final: 0.7721 (p0) REVERT: I 243 TYR cc_start: 0.9274 (t80) cc_final: 0.8960 (t80) REVERT: I 277 HIS cc_start: 0.8357 (t-90) cc_final: 0.7806 (t-170) REVERT: I 537 GLN cc_start: 0.9096 (tp40) cc_final: 0.8578 (mp10) REVERT: I 542 TYR cc_start: 0.8501 (m-80) cc_final: 0.7521 (m-80) REVERT: I 588 HIS cc_start: 0.8487 (m-70) cc_final: 0.8203 (m-70) REVERT: I 769 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8543 (mm-40) REVERT: J 108 TYR cc_start: 0.7643 (m-80) cc_final: 0.7245 (m-80) REVERT: J 117 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6851 (t-90) REVERT: J 153 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8724 (mtmm) REVERT: J 205 PHE cc_start: 0.8505 (t80) cc_final: 0.8084 (t80) REVERT: J 217 PHE cc_start: 0.7995 (t80) cc_final: 0.7341 (t80) REVERT: J 221 PHE cc_start: 0.9040 (t80) cc_final: 0.8501 (t80) REVERT: J 235 LEU cc_start: 0.8710 (tp) cc_final: 0.8334 (mt) REVERT: J 236 TYR cc_start: 0.8658 (m-80) cc_final: 0.8405 (m-80) REVERT: J 582 LEU cc_start: 0.9275 (tp) cc_final: 0.8684 (tp) REVERT: J 586 ASN cc_start: 0.8064 (m-40) cc_final: 0.7768 (m-40) REVERT: J 590 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7181 (mmm-85) REVERT: J 629 PHE cc_start: 0.8769 (m-10) cc_final: 0.8069 (m-10) outliers start: 151 outliers final: 99 residues processed: 1003 average time/residue: 0.5286 time to fit residues: 862.9261 Evaluate side-chains 970 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 862 time to evaluate : 4.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 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 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 484 ILE 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 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 510 ARG Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 680 ASP Chi-restraints excluded: chain H residue 708 VAL Chi-restraints excluded: chain H residue 764 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 115 HIS Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 579 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 458 optimal weight: 20.0000 chunk 312 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 410 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 470 optimal weight: 10.0000 chunk 380 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 281 optimal weight: 0.9990 chunk 494 optimal weight: 50.0000 chunk 139 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 438 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** C 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 ASN ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 GLN ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 604 ASN H 620 ASN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 GLN J 277 HIS J 690 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 42994 Z= 0.341 Angle : 0.654 10.135 58617 Z= 0.337 Chirality : 0.046 0.209 6906 Planarity : 0.004 0.054 7726 Dihedral : 4.560 29.665 6113 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 4.70 % Allowed : 18.95 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.11), residues: 5704 helix: 0.07 (0.13), residues: 1680 sheet: 0.17 (0.16), residues: 1031 loop : -0.90 (0.11), residues: 2993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 281 HIS 0.007 0.001 HIS D 616 PHE 0.019 0.002 PHE J 468 TYR 0.027 0.002 TYR J 243 ARG 0.009 0.001 ARG J 544 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 882 time to evaluate : 5.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.9025 (tttp) cc_final: 0.8757 (ttpt) REVERT: A 235 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: A 265 ASP cc_start: 0.8319 (t0) cc_final: 0.7547 (p0) REVERT: A 434 MET cc_start: 0.7432 (tpp) cc_final: 0.7176 (tpp) REVERT: A 446 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7839 (mmtt) REVERT: A 447 GLN cc_start: 0.8883 (tt0) cc_final: 0.8009 (tm-30) REVERT: A 479 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7626 (tt0) REVERT: A 549 GLU cc_start: 0.8765 (mp0) cc_final: 0.8472 (mp0) REVERT: A 551 ASP cc_start: 0.7834 (m-30) cc_final: 0.7522 (m-30) REVERT: A 602 ASN cc_start: 0.8851 (m-40) cc_final: 0.8355 (m110) REVERT: A 632 ASP cc_start: 0.9313 (p0) cc_final: 0.8862 (p0) REVERT: A 633 LYS cc_start: 0.9563 (tmtt) cc_final: 0.9265 (tppt) REVERT: A 635 ILE cc_start: 0.9466 (tp) cc_final: 0.9022 (mm) REVERT: A 636 ARG cc_start: 0.8385 (ptt-90) cc_final: 0.7740 (ptt-90) REVERT: A 703 LYS cc_start: 0.8327 (mmtm) cc_final: 0.8037 (mmtm) REVERT: B 265 ASP cc_start: 0.8021 (t0) cc_final: 0.7538 (t0) REVERT: B 363 ASN cc_start: 0.9138 (m-40) cc_final: 0.8181 (p0) REVERT: B 403 GLN cc_start: 0.8399 (mp10) cc_final: 0.8071 (mp10) REVERT: B 444 LYS cc_start: 0.8996 (pttm) cc_final: 0.8768 (tppt) REVERT: B 462 TYR cc_start: 0.8336 (t80) cc_final: 0.8114 (t80) REVERT: B 486 GLU cc_start: 0.8070 (tp30) cc_final: 0.7727 (tm-30) REVERT: B 563 LYS cc_start: 0.9281 (mmmm) cc_final: 0.8853 (mtmm) REVERT: B 635 ILE cc_start: 0.9154 (mm) cc_final: 0.8850 (mm) REVERT: B 636 ARG cc_start: 0.8715 (ptt-90) cc_final: 0.8241 (ptp90) REVERT: B 703 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8394 (mmtp) REVERT: B 722 LYS cc_start: 0.9399 (tppt) cc_final: 0.9191 (tppt) REVERT: C 444 LYS cc_start: 0.9562 (tptp) cc_final: 0.9263 (tppt) REVERT: C 454 GLN cc_start: 0.8408 (mp10) cc_final: 0.8045 (mp10) REVERT: C 483 GLN cc_start: 0.8839 (mp10) cc_final: 0.8507 (mp10) REVERT: C 551 ASP cc_start: 0.8542 (t0) cc_final: 0.8161 (t0) REVERT: C 587 MET cc_start: 0.8843 (mtp) cc_final: 0.8417 (mtp) REVERT: C 632 ASP cc_start: 0.8929 (t0) cc_final: 0.8583 (p0) REVERT: D 250 GLU cc_start: 0.8196 (pm20) cc_final: 0.7943 (mp0) REVERT: D 291 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8586 (mmtt) REVERT: D 334 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6086 (mp) REVERT: D 346 TRP cc_start: 0.8395 (m-10) cc_final: 0.8124 (m-10) REVERT: D 444 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8716 (mmtt) REVERT: D 445 THR cc_start: 0.9068 (t) cc_final: 0.8732 (p) REVERT: D 472 ASP cc_start: 0.8191 (t0) cc_final: 0.7366 (t0) REVERT: D 497 ASP cc_start: 0.8095 (p0) cc_final: 0.7513 (p0) REVERT: D 499 ASN cc_start: 0.8482 (m110) cc_final: 0.7495 (m-40) REVERT: D 551 ASP cc_start: 0.7891 (m-30) cc_final: 0.6983 (p0) REVERT: D 569 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8536 (mm) REVERT: D 614 GLU cc_start: 0.9040 (pp20) cc_final: 0.8523 (pp20) REVERT: D 633 LYS cc_start: 0.8769 (tptt) cc_final: 0.8460 (tppt) REVERT: D 703 LYS cc_start: 0.9032 (mppt) cc_final: 0.8765 (mptt) REVERT: E 195 ASP cc_start: 0.8121 (t70) cc_final: 0.7840 (t0) REVERT: E 359 ARG cc_start: 0.7891 (pmt170) cc_final: 0.7613 (mtm180) REVERT: E 385 LEU cc_start: 0.8807 (mm) cc_final: 0.8524 (mm) REVERT: E 391 LEU cc_start: 0.9242 (mm) cc_final: 0.8894 (mm) REVERT: E 402 SER cc_start: 0.8899 (m) cc_final: 0.8600 (p) REVERT: E 434 MET cc_start: 0.8668 (ppp) cc_final: 0.8152 (ppp) REVERT: E 472 ASP cc_start: 0.8735 (t0) cc_final: 0.8530 (t0) REVERT: E 499 ASN cc_start: 0.8688 (m110) cc_final: 0.8196 (m-40) REVERT: E 512 ASP cc_start: 0.7944 (t0) cc_final: 0.6952 (t0) REVERT: E 515 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8094 (mm-30) REVERT: F 376 ASN cc_start: 0.8906 (m-40) cc_final: 0.8526 (t0) REVERT: F 449 ARG cc_start: 0.8629 (mtm110) cc_final: 0.7511 (ptp90) REVERT: F 479 GLU cc_start: 0.8415 (mp0) cc_final: 0.8184 (mp0) REVERT: F 551 ASP cc_start: 0.7684 (t0) cc_final: 0.6497 (p0) REVERT: F 563 LYS cc_start: 0.9384 (pptt) cc_final: 0.9173 (ptpp) REVERT: F 636 ARG cc_start: 0.8386 (ptp90) cc_final: 0.7765 (mtt90) REVERT: G 250 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7447 (tp30) REVERT: G 329 SER cc_start: 0.9117 (p) cc_final: 0.8767 (t) REVERT: G 439 PHE cc_start: 0.9308 (t80) cc_final: 0.9079 (t80) REVERT: G 444 LYS cc_start: 0.9211 (ptpp) cc_final: 0.8976 (pttm) REVERT: G 529 ILE cc_start: 0.9365 (tp) cc_final: 0.8963 (tp) REVERT: G 560 GLN cc_start: 0.9282 (tp-100) cc_final: 0.8695 (mm-40) REVERT: G 593 ASP cc_start: 0.8969 (t70) cc_final: 0.8284 (t0) REVERT: G 595 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8811 (ttp-110) REVERT: G 617 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8580 (ttp80) REVERT: G 703 LYS cc_start: 0.8792 (ptpp) cc_final: 0.8469 (ptpp) REVERT: H 65 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8883 (mmmt) REVERT: H 118 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6529 (p90) REVERT: H 158 ASP cc_start: 0.7994 (t70) cc_final: 0.7638 (t70) REVERT: H 170 PHE cc_start: 0.8822 (t80) cc_final: 0.8495 (t80) REVERT: H 187 ASP cc_start: 0.8463 (m-30) cc_final: 0.8001 (m-30) REVERT: H 201 PHE cc_start: 0.9038 (m-80) cc_final: 0.8672 (m-80) REVERT: H 215 GLU cc_start: 0.8178 (pt0) cc_final: 0.7900 (pp20) REVERT: H 244 MET cc_start: 0.8519 (tpp) cc_final: 0.7521 (tpp) REVERT: H 384 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7739 (mm-40) REVERT: H 393 GLN cc_start: 0.8549 (pm20) cc_final: 0.8256 (pm20) REVERT: H 398 LEU cc_start: 0.8393 (mm) cc_final: 0.7198 (pp) REVERT: H 434 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.6994 (ttpp) REVERT: H 510 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6178 (mmm-85) REVERT: H 541 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7740 (mt-10) REVERT: H 548 LYS cc_start: 0.7525 (mmmt) cc_final: 0.7301 (tptp) REVERT: H 589 ASN cc_start: 0.7785 (m110) cc_final: 0.7131 (m110) REVERT: H 617 LYS cc_start: 0.9194 (ttpt) cc_final: 0.8992 (mtmt) REVERT: H 638 ASN cc_start: 0.8973 (m110) cc_final: 0.8261 (t0) REVERT: H 658 LEU cc_start: 0.7901 (tt) cc_final: 0.7485 (mt) REVERT: H 680 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8855 (p0) REVERT: H 718 PHE cc_start: 0.7740 (t80) cc_final: 0.7507 (t80) REVERT: H 737 PHE cc_start: 0.8755 (m-80) cc_final: 0.8290 (m-10) REVERT: I 38 GLU cc_start: 0.8084 (mp0) cc_final: 0.7722 (mp0) REVERT: I 61 LYS cc_start: 0.9227 (mmpt) cc_final: 0.8766 (mtmm) REVERT: I 72 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8289 (mm-30) REVERT: I 82 TYR cc_start: 0.6974 (p90) cc_final: 0.6599 (p90) REVERT: I 153 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8644 (tmtt) REVERT: I 184 ASP cc_start: 0.8357 (p0) cc_final: 0.7849 (p0) REVERT: I 277 HIS cc_start: 0.8275 (t-90) cc_final: 0.7702 (t-170) REVERT: I 531 ASP cc_start: 0.7664 (t0) cc_final: 0.7045 (t0) REVERT: I 588 HIS cc_start: 0.8529 (m-70) cc_final: 0.8227 (m-70) REVERT: J 108 TYR cc_start: 0.7609 (m-80) cc_final: 0.7322 (m-80) REVERT: J 117 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6930 (t-90) REVERT: J 153 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8808 (mtpt) REVERT: J 170 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: J 190 PHE cc_start: 0.8829 (m-10) cc_final: 0.8589 (m-80) REVERT: J 217 PHE cc_start: 0.7914 (t80) cc_final: 0.7291 (t80) REVERT: J 221 PHE cc_start: 0.9046 (t80) cc_final: 0.8502 (t80) REVERT: J 235 LEU cc_start: 0.8758 (tp) cc_final: 0.8398 (mt) REVERT: J 236 TYR cc_start: 0.8710 (m-80) cc_final: 0.8423 (m-80) REVERT: J 502 ARG cc_start: 0.7074 (ptp-110) cc_final: 0.6801 (ttm110) REVERT: J 546 ASP cc_start: 0.7535 (m-30) cc_final: 0.6385 (p0) REVERT: J 579 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6807 (m-10) REVERT: J 582 LEU cc_start: 0.9293 (tp) cc_final: 0.8665 (tp) REVERT: J 586 ASN cc_start: 0.8087 (m-40) cc_final: 0.7754 (m-40) REVERT: J 590 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7209 (mmm-85) REVERT: J 629 PHE cc_start: 0.8782 (m-10) cc_final: 0.8035 (m-80) outliers start: 192 outliers final: 146 residues processed: 995 average time/residue: 0.5392 time to fit residues: 873.7175 Evaluate side-chains 1000 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 843 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 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 227 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 555 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 638 ILE Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 484 ILE 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 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 510 ARG Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain H residue 584 THR Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 634 ILE Chi-restraints excluded: chain H residue 680 ASP Chi-restraints excluded: chain H residue 708 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 170 PHE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 501 TRP Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 626 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 185 optimal weight: 0.7980 chunk 496 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 323 optimal weight: 5.9990 chunk 136 optimal weight: 0.3980 chunk 551 optimal weight: 0.5980 chunk 457 optimal weight: 8.9990 chunk 255 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 182 optimal weight: 0.6980 chunk 289 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 GLN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 ASN G 246 ASN G 326 ASN ** G 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 GLN H 594 ASN H 604 ASN ** H 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42994 Z= 0.175 Angle : 0.624 12.086 58617 Z= 0.316 Chirality : 0.045 0.229 6906 Planarity : 0.004 0.045 7726 Dihedral : 4.319 27.146 6113 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 3.50 % Allowed : 20.69 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5704 helix: 0.19 (0.13), residues: 1678 sheet: 0.31 (0.16), residues: 1036 loop : -0.77 (0.11), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 281 HIS 0.008 0.001 HIS H 424 PHE 0.060 0.001 PHE H 765 TYR 0.022 0.001 TYR D 436 ARG 0.020 0.001 ARG H 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 931 time to evaluate : 4.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7535 (ttp-110) cc_final: 0.6729 (ptm160) REVERT: A 218 LYS cc_start: 0.8998 (tttp) cc_final: 0.8728 (ttpt) REVERT: A 265 ASP cc_start: 0.8294 (t0) cc_final: 0.7708 (p0) REVERT: A 434 MET cc_start: 0.7559 (tpp) cc_final: 0.7273 (tpp) REVERT: A 447 GLN cc_start: 0.8806 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 549 GLU cc_start: 0.8714 (mp0) cc_final: 0.8453 (mp0) REVERT: A 551 ASP cc_start: 0.7763 (m-30) cc_final: 0.7416 (m-30) REVERT: A 602 ASN cc_start: 0.8812 (m-40) cc_final: 0.8300 (m110) REVERT: A 632 ASP cc_start: 0.9312 (p0) cc_final: 0.8869 (p0) REVERT: A 633 LYS cc_start: 0.9567 (tmtt) cc_final: 0.9248 (tppt) REVERT: A 635 ILE cc_start: 0.9469 (tp) cc_final: 0.8993 (mm) REVERT: A 636 ARG cc_start: 0.8378 (ptt-90) cc_final: 0.7715 (ptt-90) REVERT: A 703 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8053 (mmtm) REVERT: B 265 ASP cc_start: 0.8097 (t0) cc_final: 0.7740 (t0) REVERT: B 267 GLU cc_start: 0.7677 (mp0) cc_final: 0.7314 (mp0) REVERT: B 363 ASN cc_start: 0.9069 (m-40) cc_final: 0.8136 (p0) REVERT: B 366 TYR cc_start: 0.9104 (m-80) cc_final: 0.8484 (m-80) REVERT: B 403 GLN cc_start: 0.8317 (mp10) cc_final: 0.7945 (mp10) REVERT: B 434 MET cc_start: 0.7911 (tmm) cc_final: 0.7673 (tmm) REVERT: B 486 GLU cc_start: 0.8069 (tp30) cc_final: 0.7785 (tp30) REVERT: B 563 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8815 (mtmm) REVERT: B 635 ILE cc_start: 0.9214 (mm) cc_final: 0.8927 (mm) REVERT: B 636 ARG cc_start: 0.8713 (ptt-90) cc_final: 0.8271 (ptp90) REVERT: B 703 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8359 (mmtp) REVERT: B 722 LYS cc_start: 0.9413 (tppt) cc_final: 0.9199 (tppt) REVERT: C 444 LYS cc_start: 0.9551 (tptp) cc_final: 0.9259 (tppt) REVERT: C 454 GLN cc_start: 0.8216 (mp10) cc_final: 0.7935 (mp10) REVERT: C 483 GLN cc_start: 0.8768 (mp10) cc_final: 0.8470 (mp10) REVERT: C 499 ASN cc_start: 0.8868 (m-40) cc_final: 0.8532 (m-40) REVERT: C 551 ASP cc_start: 0.8387 (t0) cc_final: 0.7985 (t0) REVERT: C 586 LYS cc_start: 0.9246 (mmmm) cc_final: 0.8974 (mmmt) REVERT: C 587 MET cc_start: 0.8739 (mtp) cc_final: 0.8380 (mtp) REVERT: C 632 ASP cc_start: 0.8967 (t0) cc_final: 0.8625 (p0) REVERT: D 250 GLU cc_start: 0.8171 (pm20) cc_final: 0.7930 (mp0) REVERT: D 263 HIS cc_start: 0.8377 (p90) cc_final: 0.8027 (p-80) REVERT: D 291 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8566 (mmtt) REVERT: D 346 TRP cc_start: 0.8282 (m-10) cc_final: 0.7987 (m-10) REVERT: D 363 ASN cc_start: 0.8741 (m-40) cc_final: 0.8184 (t0) REVERT: D 434 MET cc_start: 0.8360 (tpp) cc_final: 0.7772 (tpp) REVERT: D 444 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8700 (mmtt) REVERT: D 445 THR cc_start: 0.9070 (t) cc_final: 0.8732 (p) REVERT: D 472 ASP cc_start: 0.7796 (t0) cc_final: 0.7037 (t0) REVERT: D 551 ASP cc_start: 0.7821 (m-30) cc_final: 0.7087 (p0) REVERT: D 569 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8541 (mm) REVERT: D 602 ASN cc_start: 0.8801 (m-40) cc_final: 0.8561 (m110) REVERT: D 614 GLU cc_start: 0.8996 (pp20) cc_final: 0.8379 (pp20) REVERT: D 703 LYS cc_start: 0.9019 (mppt) cc_final: 0.8476 (mmtp) REVERT: E 195 ASP cc_start: 0.7980 (t70) cc_final: 0.7712 (t0) REVERT: E 359 ARG cc_start: 0.7885 (pmt170) cc_final: 0.7620 (mtm180) REVERT: E 385 LEU cc_start: 0.8841 (mm) cc_final: 0.8578 (mm) REVERT: E 391 LEU cc_start: 0.9203 (mm) cc_final: 0.8885 (mm) REVERT: E 434 MET cc_start: 0.8673 (ppp) cc_final: 0.8130 (ppp) REVERT: E 444 LYS cc_start: 0.9243 (tppt) cc_final: 0.9001 (tppt) REVERT: E 449 ARG cc_start: 0.9273 (mtm110) cc_final: 0.8983 (mtm110) REVERT: E 472 ASP cc_start: 0.8678 (t0) cc_final: 0.8212 (t0) REVERT: E 499 ASN cc_start: 0.8685 (m110) cc_final: 0.8208 (m-40) REVERT: E 512 ASP cc_start: 0.7799 (t0) cc_final: 0.7442 (t0) REVERT: F 224 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7101 (tm-30) REVERT: F 376 ASN cc_start: 0.8853 (m-40) cc_final: 0.8418 (t0) REVERT: F 444 LYS cc_start: 0.8959 (ptpp) cc_final: 0.8662 (pttm) REVERT: F 479 GLU cc_start: 0.8450 (mp0) cc_final: 0.8118 (mp0) REVERT: F 499 ASN cc_start: 0.8929 (m-40) cc_final: 0.8292 (m-40) REVERT: F 551 ASP cc_start: 0.7636 (t0) cc_final: 0.6449 (p0) REVERT: F 563 LYS cc_start: 0.9392 (pptt) cc_final: 0.9167 (ptpp) REVERT: F 590 LEU cc_start: 0.8743 (tp) cc_final: 0.8505 (tp) REVERT: F 703 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8928 (mmtt) REVERT: G 190 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7947 (tm-30) REVERT: G 250 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7388 (tp30) REVERT: G 329 SER cc_start: 0.9073 (p) cc_final: 0.8734 (t) REVERT: G 439 PHE cc_start: 0.9344 (t80) cc_final: 0.9081 (t80) REVERT: G 444 LYS cc_start: 0.9193 (ptpp) cc_final: 0.8956 (pttm) REVERT: G 529 ILE cc_start: 0.9342 (tp) cc_final: 0.8998 (tp) REVERT: G 560 GLN cc_start: 0.9267 (tp-100) cc_final: 0.8709 (mm-40) REVERT: G 565 GLN cc_start: 0.9038 (mt0) cc_final: 0.8750 (tt0) REVERT: G 593 ASP cc_start: 0.8878 (t70) cc_final: 0.8403 (t0) REVERT: G 617 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8650 (ttp80) REVERT: H 65 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8897 (mmmt) REVERT: H 74 TYR cc_start: 0.7756 (t80) cc_final: 0.6793 (t80) REVERT: H 158 ASP cc_start: 0.7977 (t70) cc_final: 0.7656 (t70) REVERT: H 170 PHE cc_start: 0.8698 (t80) cc_final: 0.8420 (t80) REVERT: H 187 ASP cc_start: 0.8233 (m-30) cc_final: 0.7998 (m-30) REVERT: H 201 PHE cc_start: 0.9016 (m-80) cc_final: 0.8703 (m-80) REVERT: H 215 GLU cc_start: 0.8166 (pt0) cc_final: 0.7849 (pp20) REVERT: H 244 MET cc_start: 0.8495 (tpp) cc_final: 0.7467 (tpp) REVERT: H 281 TRP cc_start: 0.8042 (t-100) cc_final: 0.7719 (t-100) REVERT: H 384 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7786 (mm-40) REVERT: H 393 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8238 (pm20) REVERT: H 398 LEU cc_start: 0.8362 (mm) cc_final: 0.7155 (pp) REVERT: H 434 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8145 (tmmt) REVERT: H 472 LYS cc_start: 0.9078 (tttp) cc_final: 0.8790 (tppt) REVERT: H 510 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6171 (mmm-85) REVERT: H 541 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7674 (mt-10) REVERT: H 548 LYS cc_start: 0.7565 (mmmt) cc_final: 0.7346 (tptp) REVERT: H 589 ASN cc_start: 0.7674 (m110) cc_final: 0.7021 (m110) REVERT: H 617 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8915 (mtmt) REVERT: H 638 ASN cc_start: 0.8921 (m110) cc_final: 0.8287 (t0) REVERT: H 658 LEU cc_start: 0.7813 (tt) cc_final: 0.7378 (mt) REVERT: H 680 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8736 (p0) REVERT: H 718 PHE cc_start: 0.7757 (t80) cc_final: 0.7329 (t80) REVERT: H 736 PHE cc_start: 0.8047 (t80) cc_final: 0.7504 (t80) REVERT: H 737 PHE cc_start: 0.8867 (m-80) cc_final: 0.8168 (m-10) REVERT: H 742 ARG cc_start: 0.8830 (mtm110) cc_final: 0.8419 (ptp-110) REVERT: I 37 LYS cc_start: 0.8516 (pttm) cc_final: 0.8097 (ptpp) REVERT: I 38 GLU cc_start: 0.8056 (mp0) cc_final: 0.7659 (mp0) REVERT: I 61 LYS cc_start: 0.9202 (mmpt) cc_final: 0.8716 (mttp) REVERT: I 72 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: I 82 TYR cc_start: 0.6790 (p90) cc_final: 0.6430 (p90) REVERT: I 150 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8796 (mm-30) REVERT: I 153 LYS cc_start: 0.9074 (ttmm) cc_final: 0.8623 (tmtt) REVERT: I 184 ASP cc_start: 0.8181 (p0) cc_final: 0.7594 (p0) REVERT: I 246 LYS cc_start: 0.9234 (tptp) cc_final: 0.8989 (mmtm) REVERT: I 277 HIS cc_start: 0.8250 (t-90) cc_final: 0.7742 (t-170) REVERT: I 472 LYS cc_start: 0.9170 (ptpp) cc_final: 0.8937 (ptmt) REVERT: I 588 HIS cc_start: 0.8542 (m-70) cc_final: 0.8254 (m-70) REVERT: I 769 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8550 (mm-40) REVERT: J 108 TYR cc_start: 0.7619 (m-80) cc_final: 0.7308 (m-80) REVERT: J 110 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8385 (mmtm) REVERT: J 117 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6778 (t-90) REVERT: J 153 LYS cc_start: 0.9105 (ttmm) cc_final: 0.8847 (mtpt) REVERT: J 190 PHE cc_start: 0.8850 (m-10) cc_final: 0.8576 (m-80) REVERT: J 221 PHE cc_start: 0.9019 (t80) cc_final: 0.8562 (t80) REVERT: J 544 ARG cc_start: 0.6376 (tpp-160) cc_final: 0.5749 (tpt170) REVERT: J 545 ILE cc_start: 0.7601 (mp) cc_final: 0.7231 (tt) REVERT: J 546 ASP cc_start: 0.7405 (m-30) cc_final: 0.6100 (p0) REVERT: J 579 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6369 (m-10) REVERT: J 582 LEU cc_start: 0.9275 (tp) cc_final: 0.8707 (tp) REVERT: J 586 ASN cc_start: 0.8140 (m-40) cc_final: 0.7793 (m-40) REVERT: J 629 PHE cc_start: 0.8750 (m-10) cc_final: 0.8049 (m-80) outliers start: 143 outliers final: 100 residues processed: 1005 average time/residue: 0.5544 time to fit residues: 915.1414 Evaluate side-chains 985 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 877 time to evaluate : 5.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 510 ARG Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 680 ASP Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 501 TRP Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 626 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 531 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 402 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 464 optimal weight: 50.0000 chunk 307 optimal weight: 3.9990 chunk 549 optimal weight: 2.9990 chunk 343 optimal weight: 0.7980 chunk 334 optimal weight: 0.0370 chunk 253 optimal weight: 8.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- 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** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN C 388 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN D 499 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN G 326 ASN ** G 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 GLN ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 HIS J 690 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 42994 Z= 0.334 Angle : 0.660 12.093 58617 Z= 0.338 Chirality : 0.046 0.257 6906 Planarity : 0.004 0.051 7726 Dihedral : 4.443 28.049 6113 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 4.19 % Allowed : 21.52 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.11), residues: 5704 helix: 0.11 (0.13), residues: 1722 sheet: 0.34 (0.16), residues: 1012 loop : -0.88 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 570 HIS 0.007 0.001 HIS D 616 PHE 0.018 0.002 PHE J 217 TYR 0.035 0.002 TYR H 621 ARG 0.006 0.001 ARG G 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 889 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7548 (ttp-110) cc_final: 0.7293 (ttp-110) REVERT: A 235 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: A 265 ASP cc_start: 0.8336 (t0) cc_final: 0.7527 (p0) REVERT: A 434 MET cc_start: 0.7653 (tpp) cc_final: 0.7410 (tpp) REVERT: A 446 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7886 (mmtt) REVERT: A 447 GLN cc_start: 0.8848 (tt0) cc_final: 0.7980 (tm-30) REVERT: A 549 GLU cc_start: 0.8735 (mp0) cc_final: 0.8440 (mp0) REVERT: A 602 ASN cc_start: 0.8855 (m-40) cc_final: 0.8345 (m110) REVERT: A 632 ASP cc_start: 0.9305 (p0) cc_final: 0.8833 (p0) REVERT: A 633 LYS cc_start: 0.9564 (tmtt) cc_final: 0.9176 (tptt) REVERT: A 635 ILE cc_start: 0.9469 (tp) cc_final: 0.9097 (mm) REVERT: A 703 LYS cc_start: 0.8458 (mmtm) cc_final: 0.8157 (mmtm) REVERT: B 265 ASP cc_start: 0.8077 (t0) cc_final: 0.7767 (t0) REVERT: B 267 GLU cc_start: 0.7785 (mp0) cc_final: 0.7409 (mp0) REVERT: B 363 ASN cc_start: 0.9117 (m-40) cc_final: 0.8170 (p0) REVERT: B 403 GLN cc_start: 0.8468 (mp10) cc_final: 0.8106 (mp10) REVERT: B 481 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8230 (mt) REVERT: B 486 GLU cc_start: 0.8023 (tp30) cc_final: 0.7797 (tm-30) REVERT: B 563 LYS cc_start: 0.9289 (mmmm) cc_final: 0.8808 (mmtm) REVERT: B 580 LYS cc_start: 0.9335 (mmmm) cc_final: 0.9045 (mmmt) REVERT: B 635 ILE cc_start: 0.9217 (mm) cc_final: 0.8938 (mm) REVERT: B 703 LYS cc_start: 0.8703 (mmtp) cc_final: 0.8359 (mmtp) REVERT: C 388 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8896 (m-40) REVERT: C 444 LYS cc_start: 0.9569 (tptp) cc_final: 0.9283 (tppt) REVERT: C 454 GLN cc_start: 0.8231 (mp10) cc_final: 0.7972 (mp10) REVERT: C 483 GLN cc_start: 0.8869 (mp10) cc_final: 0.8564 (mp10) REVERT: C 486 GLU cc_start: 0.8568 (tp30) cc_final: 0.8271 (tp30) REVERT: C 499 ASN cc_start: 0.8860 (m-40) cc_final: 0.8408 (m-40) REVERT: C 551 ASP cc_start: 0.8493 (t0) cc_final: 0.8132 (t0) REVERT: C 582 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8334 (mmtt) REVERT: C 586 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8933 (mmmt) REVERT: C 587 MET cc_start: 0.8813 (mtp) cc_final: 0.8413 (mtp) REVERT: C 637 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8603 (ttpt) REVERT: D 250 GLU cc_start: 0.8221 (pm20) cc_final: 0.7998 (mp0) REVERT: D 291 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8561 (mmtt) REVERT: D 346 TRP cc_start: 0.8334 (m-10) cc_final: 0.8078 (m-10) REVERT: D 434 MET cc_start: 0.8359 (tpp) cc_final: 0.7752 (tpp) REVERT: D 444 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8830 (tppt) REVERT: D 472 ASP cc_start: 0.8023 (t0) cc_final: 0.7235 (t0) REVERT: D 497 ASP cc_start: 0.8424 (p0) cc_final: 0.7775 (p0) REVERT: D 499 ASN cc_start: 0.8542 (m-40) cc_final: 0.8038 (m-40) REVERT: D 551 ASP cc_start: 0.7844 (m-30) cc_final: 0.7002 (p0) REVERT: D 569 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8507 (mm) REVERT: D 614 GLU cc_start: 0.9027 (pp20) cc_final: 0.8503 (pp20) REVERT: D 703 LYS cc_start: 0.9010 (mppt) cc_final: 0.8498 (mmtp) REVERT: E 195 ASP cc_start: 0.8093 (t70) cc_final: 0.7788 (t0) REVERT: E 197 LYS cc_start: 0.8762 (tptt) cc_final: 0.8547 (tmtt) REVERT: E 238 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8559 (mttt) REVERT: E 359 ARG cc_start: 0.7852 (pmt170) cc_final: 0.7290 (ptt-90) REVERT: E 385 LEU cc_start: 0.8859 (mm) cc_final: 0.8591 (mm) REVERT: E 387 LYS cc_start: 0.9218 (ptmm) cc_final: 0.8824 (pptt) REVERT: E 391 LEU cc_start: 0.9192 (mm) cc_final: 0.8869 (mm) REVERT: E 434 MET cc_start: 0.8764 (ppp) cc_final: 0.8123 (ppp) REVERT: E 444 LYS cc_start: 0.9238 (tppt) cc_final: 0.8982 (tppt) REVERT: E 449 ARG cc_start: 0.9292 (mtm110) cc_final: 0.8965 (mtm110) REVERT: E 472 ASP cc_start: 0.8854 (t0) cc_final: 0.8339 (t0) REVERT: E 497 ASP cc_start: 0.7964 (p0) cc_final: 0.7571 (p0) REVERT: E 499 ASN cc_start: 0.8690 (m110) cc_final: 0.8240 (m-40) REVERT: E 512 ASP cc_start: 0.8023 (t0) cc_final: 0.7644 (t0) REVERT: E 514 LEU cc_start: 0.9531 (tt) cc_final: 0.9289 (tt) REVERT: F 224 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7353 (tm-30) REVERT: F 376 ASN cc_start: 0.8901 (m-40) cc_final: 0.8433 (t0) REVERT: F 444 LYS cc_start: 0.8985 (ptpp) cc_final: 0.8734 (pttm) REVERT: F 449 ARG cc_start: 0.8599 (mtm110) cc_final: 0.7457 (ptp90) REVERT: F 479 GLU cc_start: 0.8425 (mp0) cc_final: 0.8188 (mp0) REVERT: F 499 ASN cc_start: 0.8825 (m-40) cc_final: 0.8148 (m-40) REVERT: F 551 ASP cc_start: 0.7728 (t0) cc_final: 0.6507 (p0) REVERT: F 563 LYS cc_start: 0.9343 (pptt) cc_final: 0.9112 (ptpp) REVERT: F 587 MET cc_start: 0.8891 (ptp) cc_final: 0.8367 (ptp) REVERT: F 633 LYS cc_start: 0.9058 (pptt) cc_final: 0.8530 (pptt) REVERT: F 637 LYS cc_start: 0.8973 (mptt) cc_final: 0.8454 (mmtt) REVERT: G 190 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7895 (tm-30) REVERT: G 250 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7421 (tp30) REVERT: G 329 SER cc_start: 0.9070 (p) cc_final: 0.8725 (t) REVERT: G 439 PHE cc_start: 0.9305 (t80) cc_final: 0.9058 (t80) REVERT: G 444 LYS cc_start: 0.9198 (ptpp) cc_final: 0.8982 (pttm) REVERT: G 470 ARG cc_start: 0.7628 (tpp-160) cc_final: 0.7328 (tpp-160) REVERT: G 529 ILE cc_start: 0.9342 (tp) cc_final: 0.8990 (tp) REVERT: G 560 GLN cc_start: 0.9290 (tp-100) cc_final: 0.8744 (mm-40) REVERT: G 565 GLN cc_start: 0.9043 (mt0) cc_final: 0.8516 (tt0) REVERT: G 569 LEU cc_start: 0.9168 (mt) cc_final: 0.8846 (mt) REVERT: G 617 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8649 (ttp80) REVERT: G 703 LYS cc_start: 0.8718 (ptpp) cc_final: 0.8432 (mptt) REVERT: H 65 LYS cc_start: 0.9187 (mmmt) cc_final: 0.8912 (mmmt) REVERT: H 74 TYR cc_start: 0.7974 (t80) cc_final: 0.6909 (t80) REVERT: H 158 ASP cc_start: 0.7981 (t70) cc_final: 0.7653 (t70) REVERT: H 170 PHE cc_start: 0.8841 (t80) cc_final: 0.8590 (t80) REVERT: H 201 PHE cc_start: 0.8905 (m-80) cc_final: 0.8634 (m-80) REVERT: H 215 GLU cc_start: 0.8132 (pt0) cc_final: 0.7839 (pp20) REVERT: H 244 MET cc_start: 0.8544 (tpp) cc_final: 0.7550 (tpp) REVERT: H 259 LEU cc_start: 0.8959 (mp) cc_final: 0.8758 (mt) REVERT: H 281 TRP cc_start: 0.8134 (t-100) cc_final: 0.7875 (t-100) REVERT: H 393 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: H 398 LEU cc_start: 0.8376 (mm) cc_final: 0.7205 (pp) REVERT: H 434 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8142 (tmmt) REVERT: H 472 LYS cc_start: 0.9087 (tttp) cc_final: 0.8870 (tppt) REVERT: H 510 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6186 (mmm-85) REVERT: H 541 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7617 (mt-10) REVERT: H 548 LYS cc_start: 0.7548 (mmmt) cc_final: 0.7332 (tptp) REVERT: H 589 ASN cc_start: 0.7839 (m110) cc_final: 0.7327 (m110) REVERT: H 638 ASN cc_start: 0.8964 (m110) cc_final: 0.8347 (t0) REVERT: H 680 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8784 (p0) REVERT: H 718 PHE cc_start: 0.7883 (t80) cc_final: 0.7411 (t80) REVERT: H 736 PHE cc_start: 0.8081 (t80) cc_final: 0.7524 (t80) REVERT: H 737 PHE cc_start: 0.8884 (m-80) cc_final: 0.8285 (m-10) REVERT: H 742 ARG cc_start: 0.8850 (mtm110) cc_final: 0.8424 (ptp-110) REVERT: I 38 GLU cc_start: 0.8115 (mp0) cc_final: 0.7776 (mp0) REVERT: I 61 LYS cc_start: 0.9229 (mmpt) cc_final: 0.8779 (mttp) REVERT: I 72 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: I 82 TYR cc_start: 0.6903 (p90) cc_final: 0.6571 (p90) REVERT: I 153 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8638 (tmtt) REVERT: I 184 ASP cc_start: 0.8380 (p0) cc_final: 0.7846 (p0) REVERT: I 245 ASP cc_start: 0.8329 (t0) cc_final: 0.7955 (t0) REVERT: I 246 LYS cc_start: 0.9252 (tptp) cc_final: 0.8956 (mmtm) REVERT: I 277 HIS cc_start: 0.8259 (t-90) cc_final: 0.7775 (t-170) REVERT: I 531 ASP cc_start: 0.7707 (t0) cc_final: 0.7294 (t0) REVERT: I 545 ILE cc_start: 0.8605 (mp) cc_final: 0.8206 (tp) REVERT: I 588 HIS cc_start: 0.8587 (m-70) cc_final: 0.8321 (m-70) REVERT: I 769 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8543 (mm-40) REVERT: J 108 TYR cc_start: 0.7645 (m-80) cc_final: 0.7355 (m-80) REVERT: J 153 LYS cc_start: 0.9128 (ttmm) cc_final: 0.8867 (mtpt) REVERT: J 190 PHE cc_start: 0.8910 (m-10) cc_final: 0.8616 (m-80) REVERT: J 221 PHE cc_start: 0.9033 (t80) cc_final: 0.8539 (t80) REVERT: J 546 ASP cc_start: 0.7379 (m-30) cc_final: 0.6177 (p0) REVERT: J 579 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6760 (m-10) REVERT: J 582 LEU cc_start: 0.9256 (tp) cc_final: 0.8568 (tp) REVERT: J 586 ASN cc_start: 0.8189 (m-40) cc_final: 0.7833 (m-40) REVERT: J 590 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7141 (mmm-85) REVERT: J 629 PHE cc_start: 0.8791 (m-10) cc_final: 0.8083 (m-80) outliers start: 171 outliers final: 136 residues processed: 982 average time/residue: 0.5537 time to fit residues: 890.8255 Evaluate side-chains 1004 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 857 time to evaluate : 4.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 555 ASP Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 434 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 510 ARG Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 584 THR Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 634 ILE Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 680 ASP Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 223 TYR Chi-restraints excluded: chain J residue 501 TRP Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 626 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 339 optimal weight: 0.6980 chunk 219 optimal weight: 7.9990 chunk 328 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 chunk 349 optimal weight: 0.9990 chunk 374 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 431 optimal weight: 20.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 601 ASN ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 ASN ** G 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 GLN I 469 ASN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42994 Z= 0.186 Angle : 0.639 13.026 58617 Z= 0.322 Chirality : 0.046 0.311 6906 Planarity : 0.004 0.046 7726 Dihedral : 4.264 27.557 6113 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 3.70 % Allowed : 22.67 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.11), residues: 5704 helix: 0.32 (0.13), residues: 1671 sheet: 0.43 (0.16), residues: 1026 loop : -0.75 (0.11), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 570 HIS 0.007 0.001 HIS D 616 PHE 0.028 0.001 PHE I 471 TYR 0.024 0.001 TYR B 462 ARG 0.009 0.001 ARG J 502 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 914 time to evaluate : 4.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.7230 (ttp-110) REVERT: A 265 ASP cc_start: 0.8320 (t0) cc_final: 0.7720 (p0) REVERT: A 434 MET cc_start: 0.7678 (tpp) cc_final: 0.7421 (tpp) REVERT: A 446 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7713 (mmpt) REVERT: A 447 GLN cc_start: 0.8818 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 549 GLU cc_start: 0.8697 (mp0) cc_final: 0.8425 (mp0) REVERT: A 600 ARG cc_start: 0.8351 (mmp80) cc_final: 0.7993 (mmp80) REVERT: A 602 ASN cc_start: 0.8824 (m-40) cc_final: 0.8326 (m110) REVERT: A 632 ASP cc_start: 0.9304 (p0) cc_final: 0.8669 (p0) REVERT: A 633 LYS cc_start: 0.9557 (tmtt) cc_final: 0.9264 (tptt) REVERT: A 635 ILE cc_start: 0.9473 (tp) cc_final: 0.9030 (mm) REVERT: A 703 LYS cc_start: 0.8458 (mmtm) cc_final: 0.8151 (mmtm) REVERT: B 265 ASP cc_start: 0.8130 (t0) cc_final: 0.7778 (t0) REVERT: B 267 GLU cc_start: 0.7648 (mp0) cc_final: 0.7358 (mp0) REVERT: B 363 ASN cc_start: 0.9041 (m-40) cc_final: 0.8176 (p0) REVERT: B 366 TYR cc_start: 0.9028 (m-80) cc_final: 0.8741 (m-80) REVERT: B 403 GLN cc_start: 0.8488 (mp10) cc_final: 0.8022 (mp10) REVERT: B 486 GLU cc_start: 0.8072 (tp30) cc_final: 0.7834 (tm-30) REVERT: B 560 GLN cc_start: 0.8147 (tp40) cc_final: 0.7771 (tm-30) REVERT: B 563 LYS cc_start: 0.9238 (mmmm) cc_final: 0.8902 (ptpp) REVERT: B 635 ILE cc_start: 0.9196 (mm) cc_final: 0.8923 (mm) REVERT: B 636 ARG cc_start: 0.8635 (ptt-90) cc_final: 0.8350 (ptp90) REVERT: B 703 LYS cc_start: 0.8652 (mmtp) cc_final: 0.8288 (mmtp) REVERT: C 389 GLN cc_start: 0.8144 (mp10) cc_final: 0.7481 (mp10) REVERT: C 444 LYS cc_start: 0.9561 (tptp) cc_final: 0.9262 (tppt) REVERT: C 454 GLN cc_start: 0.8182 (mp10) cc_final: 0.7937 (mp10) REVERT: C 483 GLN cc_start: 0.8786 (mp10) cc_final: 0.8534 (mp10) REVERT: C 499 ASN cc_start: 0.8902 (m-40) cc_final: 0.8539 (m-40) REVERT: C 551 ASP cc_start: 0.8387 (t0) cc_final: 0.8037 (t0) REVERT: C 582 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8302 (mmtt) REVERT: C 586 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8991 (mmmt) REVERT: C 587 MET cc_start: 0.8782 (mtp) cc_final: 0.8407 (mtp) REVERT: C 637 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8572 (ttpt) REVERT: D 250 GLU cc_start: 0.8185 (pm20) cc_final: 0.7946 (mp0) REVERT: D 263 HIS cc_start: 0.8399 (p90) cc_final: 0.8065 (p-80) REVERT: D 346 TRP cc_start: 0.8247 (m-10) cc_final: 0.7980 (m-10) REVERT: D 363 ASN cc_start: 0.8748 (m-40) cc_final: 0.7978 (t0) REVERT: D 434 MET cc_start: 0.8308 (tpp) cc_final: 0.7749 (tpp) REVERT: D 444 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8786 (tppt) REVERT: D 472 ASP cc_start: 0.7664 (t0) cc_final: 0.6924 (t0) REVERT: D 497 ASP cc_start: 0.8253 (p0) cc_final: 0.7544 (p0) REVERT: D 499 ASN cc_start: 0.8526 (m-40) cc_final: 0.7732 (p0) REVERT: D 551 ASP cc_start: 0.7798 (m-30) cc_final: 0.7041 (p0) REVERT: D 569 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8516 (mm) REVERT: D 614 GLU cc_start: 0.9000 (pp20) cc_final: 0.8480 (pp20) REVERT: D 703 LYS cc_start: 0.9024 (mppt) cc_final: 0.8459 (mmtp) REVERT: E 178 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7449 (ptp-170) REVERT: E 195 ASP cc_start: 0.7970 (t70) cc_final: 0.7665 (t0) REVERT: E 197 LYS cc_start: 0.8690 (tptt) cc_final: 0.8477 (tmtt) REVERT: E 238 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8469 (mttt) REVERT: E 359 ARG cc_start: 0.7929 (pmt170) cc_final: 0.7324 (mtm110) REVERT: E 385 LEU cc_start: 0.8865 (mm) cc_final: 0.8624 (mm) REVERT: E 387 LYS cc_start: 0.9272 (ptmm) cc_final: 0.8866 (pptt) REVERT: E 391 LEU cc_start: 0.9166 (mm) cc_final: 0.8870 (mm) REVERT: E 434 MET cc_start: 0.8721 (ppp) cc_final: 0.8130 (ppp) REVERT: E 449 ARG cc_start: 0.9258 (mtm110) cc_final: 0.8940 (mtm110) REVERT: E 452 THR cc_start: 0.9323 (m) cc_final: 0.9016 (p) REVERT: E 472 ASP cc_start: 0.8710 (t0) cc_final: 0.8368 (t0) REVERT: F 224 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7247 (tm-30) REVERT: F 376 ASN cc_start: 0.8857 (m-40) cc_final: 0.8422 (t0) REVERT: F 444 LYS cc_start: 0.8970 (ptpp) cc_final: 0.8667 (pttm) REVERT: F 449 ARG cc_start: 0.8594 (mtm110) cc_final: 0.7442 (ptp90) REVERT: F 479 GLU cc_start: 0.8463 (mp0) cc_final: 0.8127 (mp0) REVERT: F 499 ASN cc_start: 0.8819 (m-40) cc_final: 0.8172 (m-40) REVERT: F 525 GLU cc_start: 0.8113 (pt0) cc_final: 0.7828 (pp20) REVERT: F 551 ASP cc_start: 0.7634 (t0) cc_final: 0.6549 (p0) REVERT: F 563 LYS cc_start: 0.9425 (pptt) cc_final: 0.9042 (ptpp) REVERT: F 590 LEU cc_start: 0.8761 (tp) cc_final: 0.8516 (tp) REVERT: F 636 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7814 (mtt90) REVERT: F 703 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8957 (mmtp) REVERT: G 190 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8024 (tm-30) REVERT: G 250 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7394 (tp30) REVERT: G 329 SER cc_start: 0.9066 (p) cc_final: 0.8740 (t) REVERT: G 439 PHE cc_start: 0.9331 (t80) cc_final: 0.9075 (t80) REVERT: G 444 LYS cc_start: 0.9191 (ptpp) cc_final: 0.8914 (pttm) REVERT: G 446 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8270 (mmtt) REVERT: G 470 ARG cc_start: 0.7539 (tpp-160) cc_final: 0.7119 (tpp-160) REVERT: G 529 ILE cc_start: 0.9330 (tp) cc_final: 0.9014 (tp) REVERT: G 560 GLN cc_start: 0.9262 (tp-100) cc_final: 0.8721 (mm-40) REVERT: G 565 GLN cc_start: 0.9067 (mt0) cc_final: 0.8472 (tt0) REVERT: G 569 LEU cc_start: 0.9131 (mt) cc_final: 0.8784 (mt) REVERT: G 617 ARG cc_start: 0.9061 (ttp80) cc_final: 0.8631 (ttp80) REVERT: H 65 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8914 (mmmt) REVERT: H 74 TYR cc_start: 0.7700 (t80) cc_final: 0.6738 (t80) REVERT: H 118 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6278 (p90) REVERT: H 158 ASP cc_start: 0.7924 (t70) cc_final: 0.7614 (t70) REVERT: H 170 PHE cc_start: 0.8716 (t80) cc_final: 0.8461 (t80) REVERT: H 201 PHE cc_start: 0.8867 (m-80) cc_final: 0.8572 (m-80) REVERT: H 215 GLU cc_start: 0.8153 (pt0) cc_final: 0.7875 (pp20) REVERT: H 244 MET cc_start: 0.8499 (tpp) cc_final: 0.7478 (tpp) REVERT: H 268 TYR cc_start: 0.8122 (m-80) cc_final: 0.7863 (m-80) REVERT: H 281 TRP cc_start: 0.8036 (t-100) cc_final: 0.7793 (t-100) REVERT: H 384 GLN cc_start: 0.8087 (pp30) cc_final: 0.7676 (mm-40) REVERT: H 393 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8222 (pm20) REVERT: H 398 LEU cc_start: 0.8311 (mm) cc_final: 0.7109 (pp) REVERT: H 472 LYS cc_start: 0.9064 (tttp) cc_final: 0.8814 (tppt) REVERT: H 510 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6092 (mmm-85) REVERT: H 541 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7625 (mt-10) REVERT: H 548 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7377 (tptp) REVERT: H 589 ASN cc_start: 0.7651 (m110) cc_final: 0.7135 (m110) REVERT: H 638 ASN cc_start: 0.8907 (m110) cc_final: 0.8345 (t0) REVERT: H 658 LEU cc_start: 0.7872 (tt) cc_final: 0.7440 (mt) REVERT: H 680 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8689 (p0) REVERT: H 718 PHE cc_start: 0.7711 (t80) cc_final: 0.7262 (t80) REVERT: H 736 PHE cc_start: 0.8058 (t80) cc_final: 0.7535 (t80) REVERT: H 737 PHE cc_start: 0.8892 (m-80) cc_final: 0.8236 (m-10) REVERT: H 742 ARG cc_start: 0.8847 (mtm110) cc_final: 0.8447 (ptp-110) REVERT: I 37 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8209 (ptpp) REVERT: I 38 GLU cc_start: 0.8124 (mp0) cc_final: 0.7738 (mp0) REVERT: I 61 LYS cc_start: 0.9218 (mmpt) cc_final: 0.8715 (mtmm) REVERT: I 72 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8246 (mm-30) REVERT: I 184 ASP cc_start: 0.8182 (p0) cc_final: 0.7593 (p0) REVERT: I 245 ASP cc_start: 0.8283 (t0) cc_final: 0.8008 (t0) REVERT: I 246 LYS cc_start: 0.9250 (tptp) cc_final: 0.8972 (mmtm) REVERT: I 277 HIS cc_start: 0.8267 (t-90) cc_final: 0.7786 (t-170) REVERT: I 531 ASP cc_start: 0.7697 (t0) cc_final: 0.7400 (t0) REVERT: I 542 TYR cc_start: 0.8460 (m-80) cc_final: 0.8197 (m-80) REVERT: I 588 HIS cc_start: 0.8676 (m-70) cc_final: 0.8424 (m-70) REVERT: I 769 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8516 (mm-40) REVERT: J 74 TYR cc_start: 0.8841 (t80) cc_final: 0.8565 (t80) REVERT: J 108 TYR cc_start: 0.7619 (m-80) cc_final: 0.7412 (m-80) REVERT: J 153 LYS cc_start: 0.9192 (ttmm) cc_final: 0.8938 (mtmt) REVERT: J 190 PHE cc_start: 0.8943 (m-10) cc_final: 0.8678 (m-80) REVERT: J 221 PHE cc_start: 0.9076 (t80) cc_final: 0.8604 (t80) REVERT: J 235 LEU cc_start: 0.9041 (tp) cc_final: 0.8582 (mt) REVERT: J 579 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6388 (m-10) REVERT: J 582 LEU cc_start: 0.9233 (tp) cc_final: 0.8527 (tp) REVERT: J 586 ASN cc_start: 0.8141 (m-40) cc_final: 0.7789 (m-40) REVERT: J 590 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7136 (mmm-85) REVERT: J 629 PHE cc_start: 0.8789 (m-10) cc_final: 0.8068 (m-80) outliers start: 151 outliers final: 125 residues processed: 995 average time/residue: 0.5301 time to fit residues: 857.2069 Evaluate side-chains 1020 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 885 time to evaluate : 6.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 636 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 450 LEU Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 508 VAL Chi-restraints excluded: chain G residue 590 LEU 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 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 510 ARG Chi-restraints excluded: chain H residue 583 ILE Chi-restraints excluded: chain H residue 584 THR Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 680 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 223 TYR Chi-restraints excluded: chain J residue 501 TRP Chi-restraints excluded: chain J residue 534 ILE Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 626 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 499 optimal weight: 50.0000 chunk 526 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 chunk 511 optimal weight: 30.0000 chunk 308 optimal weight: 0.7980 chunk 223 optimal weight: 8.9990 chunk 402 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 462 optimal weight: 50.0000 chunk 484 optimal weight: 10.0000 chunk 510 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN D 565 GLN D 570 ASN D 602 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 ASN ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 GLN ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 620 ASN I 563 GLN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.182 42994 Z= 0.649 Angle : 0.816 11.897 58617 Z= 0.425 Chirality : 0.050 0.325 6906 Planarity : 0.005 0.063 7726 Dihedral : 4.886 31.926 6113 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.08 % Favored : 92.86 % Rotamer: Outliers : 4.90 % Allowed : 21.79 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.76 (0.11), residues: 5704 helix: -0.01 (0.13), residues: 1726 sheet: 0.23 (0.16), residues: 1022 loop : -1.05 (0.11), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 206 HIS 0.009 0.002 HIS C 253 PHE 0.024 0.002 PHE C 202 TYR 0.027 0.002 TYR F 259 ARG 0.010 0.001 ARG J 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 831 time to evaluate : 5.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: A 265 ASP cc_start: 0.8312 (t0) cc_final: 0.7468 (p0) REVERT: A 434 MET cc_start: 0.7647 (tpp) cc_final: 0.7434 (tpp) REVERT: A 446 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7769 (mmpt) REVERT: A 447 GLN cc_start: 0.8906 (tt0) cc_final: 0.7988 (tm-30) REVERT: A 512 ASP cc_start: 0.8434 (t70) cc_final: 0.8168 (t70) REVERT: A 515 GLU cc_start: 0.9413 (OUTLIER) cc_final: 0.8898 (mm-30) REVERT: A 549 GLU cc_start: 0.8773 (mp0) cc_final: 0.8454 (mp0) REVERT: A 590 LEU cc_start: 0.9154 (tt) cc_final: 0.8724 (tt) REVERT: A 602 ASN cc_start: 0.8999 (m-40) cc_final: 0.8529 (m110) REVERT: A 632 ASP cc_start: 0.9237 (p0) cc_final: 0.8759 (p0) REVERT: A 633 LYS cc_start: 0.9592 (tmtt) cc_final: 0.9242 (tptt) REVERT: A 635 ILE cc_start: 0.9479 (tp) cc_final: 0.8982 (mm) REVERT: A 636 ARG cc_start: 0.8519 (ptt180) cc_final: 0.8170 (ptt-90) REVERT: A 703 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8283 (mmtp) REVERT: B 265 ASP cc_start: 0.8192 (t0) cc_final: 0.7722 (t0) REVERT: B 267 GLU cc_start: 0.7868 (mp0) cc_final: 0.7511 (mp0) REVERT: B 363 ASN cc_start: 0.9182 (m-40) cc_final: 0.8263 (p0) REVERT: B 444 LYS cc_start: 0.9034 (pttm) cc_final: 0.8790 (tppt) REVERT: B 486 GLU cc_start: 0.8025 (tp30) cc_final: 0.7787 (tm-30) REVERT: B 546 ASP cc_start: 0.8588 (t70) cc_final: 0.8133 (t70) REVERT: B 560 GLN cc_start: 0.8260 (tp40) cc_final: 0.7854 (tm-30) REVERT: B 635 ILE cc_start: 0.9266 (mm) cc_final: 0.9013 (mm) REVERT: B 636 ARG cc_start: 0.8609 (ptt-90) cc_final: 0.8300 (ptp90) REVERT: B 638 ILE cc_start: 0.9436 (pt) cc_final: 0.8701 (tp) REVERT: B 703 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8283 (mmtp) REVERT: C 188 GLU cc_start: 0.7832 (mt-10) cc_final: 0.5841 (mt-10) REVERT: C 202 PHE cc_start: 0.9125 (p90) cc_final: 0.8554 (p90) REVERT: C 444 LYS cc_start: 0.9600 (tptp) cc_final: 0.9320 (tppt) REVERT: C 454 GLN cc_start: 0.8206 (mp10) cc_final: 0.7946 (mp10) REVERT: C 462 TYR cc_start: 0.8985 (t80) cc_final: 0.8764 (t80) REVERT: C 497 ASP cc_start: 0.8391 (p0) cc_final: 0.8019 (p0) REVERT: C 499 ASN cc_start: 0.8924 (m-40) cc_final: 0.8587 (m-40) REVERT: C 551 ASP cc_start: 0.8617 (t0) cc_final: 0.8303 (t0) REVERT: C 587 MET cc_start: 0.8903 (mtp) cc_final: 0.8474 (mtp) REVERT: D 250 GLU cc_start: 0.8316 (pm20) cc_final: 0.8070 (mp0) REVERT: D 291 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8818 (mmtt) REVERT: D 444 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8929 (tppt) REVERT: D 472 ASP cc_start: 0.8256 (t0) cc_final: 0.7438 (t0) REVERT: D 551 ASP cc_start: 0.7889 (m-30) cc_final: 0.7099 (p0) REVERT: D 565 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: D 569 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8583 (mm) REVERT: D 614 GLU cc_start: 0.9114 (pp20) cc_final: 0.8641 (pp20) REVERT: D 633 LYS cc_start: 0.9097 (tppt) cc_final: 0.8646 (tppt) REVERT: E 195 ASP cc_start: 0.8227 (t70) cc_final: 0.7082 (p0) REVERT: E 197 LYS cc_start: 0.8736 (tptt) cc_final: 0.8488 (tptt) REVERT: E 359 ARG cc_start: 0.7805 (pmt170) cc_final: 0.7154 (mtm110) REVERT: E 385 LEU cc_start: 0.8845 (mm) cc_final: 0.8569 (mm) REVERT: E 387 LYS cc_start: 0.9298 (ptmm) cc_final: 0.8886 (pptt) REVERT: E 391 LEU cc_start: 0.9262 (mm) cc_final: 0.8870 (mm) REVERT: E 402 SER cc_start: 0.8985 (m) cc_final: 0.8641 (p) REVERT: E 434 MET cc_start: 0.8691 (ppp) cc_final: 0.8097 (ppp) REVERT: E 472 ASP cc_start: 0.8920 (t0) cc_final: 0.8395 (t0) REVERT: E 497 ASP cc_start: 0.8106 (p0) cc_final: 0.7833 (p0) REVERT: E 499 ASN cc_start: 0.8747 (m110) cc_final: 0.8359 (m-40) REVERT: E 616 HIS cc_start: 0.8991 (m-70) cc_final: 0.8762 (m-70) REVERT: F 224 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7644 (tm-30) REVERT: F 444 LYS cc_start: 0.9043 (ptpp) cc_final: 0.8814 (pttm) REVERT: F 499 ASN cc_start: 0.8860 (m-40) cc_final: 0.8307 (m-40) REVERT: F 551 ASP cc_start: 0.7796 (t0) cc_final: 0.6587 (p0) REVERT: F 637 LYS cc_start: 0.9007 (mptt) cc_final: 0.8431 (mmtt) REVERT: F 703 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8903 (mmtt) REVERT: G 197 LYS cc_start: 0.8774 (tptp) cc_final: 0.8176 (tppp) REVERT: G 250 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7507 (tp30) REVERT: G 329 SER cc_start: 0.9074 (p) cc_final: 0.8731 (t) REVERT: G 444 LYS cc_start: 0.9218 (ptpp) cc_final: 0.8900 (pttm) REVERT: G 470 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.7366 (tpp-160) REVERT: G 569 LEU cc_start: 0.9185 (mt) cc_final: 0.8850 (mt) REVERT: G 593 ASP cc_start: 0.8846 (t70) cc_final: 0.8280 (t0) REVERT: G 617 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8593 (ttp80) REVERT: G 703 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8446 (mptt) REVERT: H 65 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8950 (mmmt) REVERT: H 72 GLU cc_start: 0.8562 (mp0) cc_final: 0.8150 (mm-30) REVERT: H 118 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.6714 (p90) REVERT: H 158 ASP cc_start: 0.8020 (t70) cc_final: 0.7648 (t70) REVERT: H 201 PHE cc_start: 0.8896 (m-80) cc_final: 0.8560 (m-80) REVERT: H 215 GLU cc_start: 0.8187 (pt0) cc_final: 0.7934 (pp20) REVERT: H 244 MET cc_start: 0.8560 (tpp) cc_final: 0.7582 (tpp) REVERT: H 268 TYR cc_start: 0.8149 (m-80) cc_final: 0.7873 (m-80) REVERT: H 281 TRP cc_start: 0.8092 (t-100) cc_final: 0.7734 (t-100) REVERT: H 384 GLN cc_start: 0.8117 (pp30) cc_final: 0.7241 (mp10) REVERT: H 393 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: H 398 LEU cc_start: 0.8312 (mm) cc_final: 0.7188 (pp) REVERT: H 472 LYS cc_start: 0.9114 (tttp) cc_final: 0.8913 (tppt) REVERT: H 510 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.6089 (mmm-85) REVERT: H 541 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7707 (mt-10) REVERT: H 548 LYS cc_start: 0.7579 (mmmt) cc_final: 0.7350 (tptp) REVERT: H 556 ASP cc_start: 0.8958 (m-30) cc_final: 0.8609 (p0) REVERT: H 589 ASN cc_start: 0.8097 (m110) cc_final: 0.7543 (m110) REVERT: H 621 TYR cc_start: 0.8418 (t80) cc_final: 0.8138 (t80) REVERT: H 638 ASN cc_start: 0.8983 (m110) cc_final: 0.8418 (t0) REVERT: H 649 ILE cc_start: 0.9364 (pt) cc_final: 0.9131 (tt) REVERT: H 718 PHE cc_start: 0.7742 (t80) cc_final: 0.7521 (t80) REVERT: H 737 PHE cc_start: 0.8933 (m-80) cc_final: 0.8341 (m-10) REVERT: I 38 GLU cc_start: 0.8155 (mp0) cc_final: 0.7780 (mp0) REVERT: I 61 LYS cc_start: 0.9321 (mmpt) cc_final: 0.8875 (mttp) REVERT: I 72 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: I 82 TYR cc_start: 0.7137 (p90) cc_final: 0.5776 (p90) REVERT: I 153 LYS cc_start: 0.9119 (ttmm) cc_final: 0.8665 (tmtt) REVERT: I 167 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6381 (t80) REVERT: I 182 ASP cc_start: 0.8015 (t0) cc_final: 0.7798 (t0) REVERT: I 184 ASP cc_start: 0.8430 (p0) cc_final: 0.8105 (p0) REVERT: I 245 ASP cc_start: 0.8403 (t0) cc_final: 0.8025 (t0) REVERT: I 246 LYS cc_start: 0.9262 (tptp) cc_final: 0.8959 (mmtm) REVERT: I 277 HIS cc_start: 0.8294 (t-90) cc_final: 0.7793 (t-170) REVERT: I 531 ASP cc_start: 0.7781 (t0) cc_final: 0.7516 (t0) REVERT: I 542 TYR cc_start: 0.8350 (m-80) cc_final: 0.8030 (m-80) REVERT: I 544 ARG cc_start: 0.6304 (tpp-160) cc_final: 0.6050 (tpt170) REVERT: I 588 HIS cc_start: 0.8686 (m-70) cc_final: 0.8467 (m-70) REVERT: J 74 TYR cc_start: 0.8782 (t80) cc_final: 0.8430 (t80) REVERT: J 153 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8937 (mtpt) REVERT: J 190 PHE cc_start: 0.8977 (m-10) cc_final: 0.8663 (m-80) REVERT: J 217 PHE cc_start: 0.7642 (t80) cc_final: 0.6005 (t80) REVERT: J 579 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6802 (m-10) REVERT: J 582 LEU cc_start: 0.9198 (tp) cc_final: 0.8457 (tp) REVERT: J 586 ASN cc_start: 0.8186 (m-40) cc_final: 0.7840 (m-40) REVERT: J 590 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7101 (mmm-85) REVERT: J 629 PHE cc_start: 0.8799 (m-10) cc_final: 0.8055 (m-80) outliers start: 200 outliers final: 153 residues processed: 940 average time/residue: 0.5393 time to fit residues: 824.9906 Evaluate side-chains 967 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 804 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 565 GLN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 376 ASN Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 555 ASP Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 678 PHE Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 508 VAL Chi-restraints excluded: chain G residue 555 ASP Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 639 LEU 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 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 510 ARG Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain H residue 584 THR Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 634 ILE Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 167 TYR Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 534 ILE Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 115 HIS Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 223 TYR Chi-restraints excluded: chain J residue 534 ILE Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 626 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 336 optimal weight: 0.8980 chunk 541 optimal weight: 30.0000 chunk 330 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 376 optimal weight: 3.9990 chunk 567 optimal weight: 50.0000 chunk 522 optimal weight: 0.8980 chunk 452 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 chunk 349 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN D 602 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN F 602 ASN G 326 ASN ** G 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 620 ASN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 42994 Z= 0.204 Angle : 0.693 13.624 58617 Z= 0.351 Chirality : 0.047 0.339 6906 Planarity : 0.004 0.047 7726 Dihedral : 4.483 28.422 6113 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 3.35 % Allowed : 23.78 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.11), residues: 5704 helix: 0.28 (0.13), residues: 1675 sheet: 0.32 (0.17), residues: 1012 loop : -0.82 (0.11), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 570 HIS 0.006 0.001 HIS H 645 PHE 0.020 0.001 PHE J 221 TYR 0.022 0.001 TYR C 375 ARG 0.012 0.001 ARG D 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 883 time to evaluate : 4.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: A 265 ASP cc_start: 0.8378 (t0) cc_final: 0.7510 (p0) REVERT: A 434 MET cc_start: 0.7802 (tpp) cc_final: 0.7571 (tpp) REVERT: A 446 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7832 (mmpt) REVERT: A 447 GLN cc_start: 0.8859 (tt0) cc_final: 0.7994 (tm-30) REVERT: A 549 GLU cc_start: 0.8766 (mp0) cc_final: 0.8472 (mp0) REVERT: A 600 ARG cc_start: 0.8338 (mmp80) cc_final: 0.7961 (mmp80) REVERT: A 602 ASN cc_start: 0.8881 (m-40) cc_final: 0.8370 (m110) REVERT: A 632 ASP cc_start: 0.9259 (p0) cc_final: 0.8626 (p0) REVERT: A 633 LYS cc_start: 0.9592 (tmtt) cc_final: 0.9266 (tppt) REVERT: A 635 ILE cc_start: 0.9469 (tp) cc_final: 0.9007 (mm) REVERT: A 703 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8203 (mmtm) REVERT: B 265 ASP cc_start: 0.8126 (t0) cc_final: 0.7505 (t0) REVERT: B 267 GLU cc_start: 0.7750 (mp0) cc_final: 0.7411 (mp0) REVERT: B 363 ASN cc_start: 0.9069 (m-40) cc_final: 0.8194 (p0) REVERT: B 366 TYR cc_start: 0.9097 (m-80) cc_final: 0.8856 (m-80) REVERT: B 403 GLN cc_start: 0.8509 (mp10) cc_final: 0.8271 (mp10) REVERT: B 485 GLN cc_start: 0.8803 (mt0) cc_final: 0.8456 (mt0) REVERT: B 486 GLU cc_start: 0.7977 (tp30) cc_final: 0.7725 (tm-30) REVERT: B 515 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8384 (mm-30) REVERT: B 560 GLN cc_start: 0.8166 (tp40) cc_final: 0.7815 (tm-30) REVERT: B 635 ILE cc_start: 0.9249 (mm) cc_final: 0.9025 (mm) REVERT: B 636 ARG cc_start: 0.8583 (ptt-90) cc_final: 0.8238 (ptp90) REVERT: B 703 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8257 (mmtp) REVERT: C 202 PHE cc_start: 0.9049 (p90) cc_final: 0.8541 (p90) REVERT: C 444 LYS cc_start: 0.9570 (tptp) cc_final: 0.9272 (tppt) REVERT: C 454 GLN cc_start: 0.8155 (mp10) cc_final: 0.7903 (mp10) REVERT: C 462 TYR cc_start: 0.8973 (t80) cc_final: 0.8744 (t80) REVERT: C 499 ASN cc_start: 0.8912 (m-40) cc_final: 0.8565 (m-40) REVERT: C 551 ASP cc_start: 0.8452 (t0) cc_final: 0.8055 (t0) REVERT: C 582 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8439 (mmtt) REVERT: C 586 LYS cc_start: 0.9241 (mmmm) cc_final: 0.9005 (mmmt) REVERT: C 587 MET cc_start: 0.8779 (mtp) cc_final: 0.8408 (mtp) REVERT: D 185 ASP cc_start: 0.8670 (p0) cc_final: 0.8463 (p0) REVERT: D 250 GLU cc_start: 0.8152 (pm20) cc_final: 0.7932 (mp0) REVERT: D 434 MET cc_start: 0.8182 (tpp) cc_final: 0.7566 (tpp) REVERT: D 444 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8854 (tppt) REVERT: D 472 ASP cc_start: 0.7845 (t0) cc_final: 0.7059 (t0) REVERT: D 497 ASP cc_start: 0.8327 (p0) cc_final: 0.7820 (p0) REVERT: D 499 ASN cc_start: 0.8541 (m-40) cc_final: 0.7994 (m-40) REVERT: D 551 ASP cc_start: 0.7834 (m-30) cc_final: 0.7156 (p0) REVERT: D 569 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8590 (mm) REVERT: D 602 ASN cc_start: 0.8658 (m-40) cc_final: 0.8413 (m-40) REVERT: D 614 GLU cc_start: 0.9084 (pp20) cc_final: 0.8574 (pp20) REVERT: D 703 LYS cc_start: 0.9022 (mppt) cc_final: 0.8470 (mmtp) REVERT: E 178 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7531 (ptp-170) REVERT: E 195 ASP cc_start: 0.8110 (t70) cc_final: 0.6980 (p0) REVERT: E 197 LYS cc_start: 0.8678 (tptt) cc_final: 0.7780 (tptt) REVERT: E 200 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.7734 (mtm-85) REVERT: E 359 ARG cc_start: 0.7927 (pmt170) cc_final: 0.7242 (mtm110) REVERT: E 385 LEU cc_start: 0.8860 (mm) cc_final: 0.8653 (mm) REVERT: E 387 LYS cc_start: 0.9300 (ptmm) cc_final: 0.8909 (pptt) REVERT: E 391 LEU cc_start: 0.9147 (mm) cc_final: 0.8843 (mm) REVERT: E 434 MET cc_start: 0.8773 (ppp) cc_final: 0.8401 (ppp) REVERT: E 449 ARG cc_start: 0.9269 (mtm110) cc_final: 0.9025 (mtm110) REVERT: E 452 THR cc_start: 0.9287 (m) cc_final: 0.9045 (p) REVERT: E 497 ASP cc_start: 0.8042 (p0) cc_final: 0.7748 (p0) REVERT: E 499 ASN cc_start: 0.8694 (m110) cc_final: 0.8287 (m-40) REVERT: E 529 ILE cc_start: 0.9398 (tp) cc_final: 0.9198 (tp) REVERT: E 616 HIS cc_start: 0.8897 (m-70) cc_final: 0.8650 (m-70) REVERT: F 224 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7416 (tm-30) REVERT: F 332 VAL cc_start: 0.9139 (p) cc_final: 0.8910 (p) REVERT: F 444 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8715 (pttm) REVERT: F 449 ARG cc_start: 0.8646 (mtm110) cc_final: 0.7582 (ptp90) REVERT: F 479 GLU cc_start: 0.8508 (mp0) cc_final: 0.8201 (mp0) REVERT: F 499 ASN cc_start: 0.8847 (m-40) cc_final: 0.8320 (m-40) REVERT: F 525 GLU cc_start: 0.8056 (pt0) cc_final: 0.7748 (pp20) REVERT: F 551 ASP cc_start: 0.7626 (t0) cc_final: 0.6512 (p0) REVERT: F 563 LYS cc_start: 0.9406 (pptt) cc_final: 0.9070 (ptpp) REVERT: F 587 MET cc_start: 0.8744 (ptp) cc_final: 0.8370 (ptp) REVERT: F 590 LEU cc_start: 0.8870 (tp) cc_final: 0.8633 (tp) REVERT: F 636 ARG cc_start: 0.8348 (ptp90) cc_final: 0.7802 (mtt90) REVERT: F 637 LYS cc_start: 0.8986 (mptt) cc_final: 0.8716 (mmtm) REVERT: G 190 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7964 (tm-30) REVERT: G 250 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7404 (tp30) REVERT: G 329 SER cc_start: 0.9019 (p) cc_final: 0.8679 (t) REVERT: G 444 LYS cc_start: 0.9211 (ptpp) cc_final: 0.8956 (pttm) REVERT: G 470 ARG cc_start: 0.7607 (tpp-160) cc_final: 0.7322 (tpp-160) REVERT: G 529 ILE cc_start: 0.9327 (tp) cc_final: 0.9037 (tp) REVERT: G 565 GLN cc_start: 0.9035 (mt0) cc_final: 0.8439 (tt0) REVERT: G 569 LEU cc_start: 0.9129 (mt) cc_final: 0.8804 (mt) REVERT: G 617 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8625 (ttp80) REVERT: H 65 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8899 (mmmt) REVERT: H 74 TYR cc_start: 0.7889 (t80) cc_final: 0.6812 (t80) REVERT: H 118 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.6407 (p90) REVERT: H 158 ASP cc_start: 0.8001 (t70) cc_final: 0.7726 (t70) REVERT: H 187 ASP cc_start: 0.8221 (m-30) cc_final: 0.7990 (m-30) REVERT: H 201 PHE cc_start: 0.8890 (m-80) cc_final: 0.8547 (m-80) REVERT: H 215 GLU cc_start: 0.8115 (pt0) cc_final: 0.7852 (pp20) REVERT: H 244 MET cc_start: 0.8569 (tpp) cc_final: 0.7529 (tpp) REVERT: H 268 TYR cc_start: 0.8151 (m-80) cc_final: 0.7874 (m-80) REVERT: H 281 TRP cc_start: 0.7980 (t-100) cc_final: 0.7732 (t-100) REVERT: H 384 GLN cc_start: 0.8097 (pp30) cc_final: 0.7394 (mp10) REVERT: H 393 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: H 398 LEU cc_start: 0.8350 (mm) cc_final: 0.7162 (pp) REVERT: H 472 LYS cc_start: 0.9061 (tttp) cc_final: 0.8811 (tppt) REVERT: H 510 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.5989 (mmm-85) REVERT: H 541 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7599 (mt-10) REVERT: H 548 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7346 (tptp) REVERT: H 556 ASP cc_start: 0.8913 (m-30) cc_final: 0.8561 (p0) REVERT: H 589 ASN cc_start: 0.7948 (m110) cc_final: 0.7400 (m110) REVERT: H 638 ASN cc_start: 0.8901 (m110) cc_final: 0.8391 (t0) REVERT: H 658 LEU cc_start: 0.7906 (tt) cc_final: 0.7480 (mt) REVERT: H 680 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8707 (p0) REVERT: H 718 PHE cc_start: 0.7772 (t80) cc_final: 0.7296 (t80) REVERT: H 736 PHE cc_start: 0.8122 (t80) cc_final: 0.7532 (t80) REVERT: H 737 PHE cc_start: 0.8933 (m-80) cc_final: 0.8221 (m-10) REVERT: I 38 GLU cc_start: 0.8170 (mp0) cc_final: 0.7803 (mp0) REVERT: I 61 LYS cc_start: 0.9272 (mmpt) cc_final: 0.8774 (mttp) REVERT: I 72 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: I 82 TYR cc_start: 0.6721 (p90) cc_final: 0.6433 (p90) REVERT: I 150 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8913 (mm-30) REVERT: I 153 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8609 (tmtt) REVERT: I 182 ASP cc_start: 0.8022 (t0) cc_final: 0.7795 (t0) REVERT: I 184 ASP cc_start: 0.8227 (p0) cc_final: 0.7671 (p0) REVERT: I 212 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7562 (mp0) REVERT: I 245 ASP cc_start: 0.8397 (t0) cc_final: 0.7971 (t0) REVERT: I 246 LYS cc_start: 0.9245 (tptp) cc_final: 0.8923 (mmtm) REVERT: I 277 HIS cc_start: 0.8297 (t-90) cc_final: 0.7801 (t-170) REVERT: I 531 ASP cc_start: 0.7682 (t0) cc_final: 0.7375 (t0) REVERT: I 542 TYR cc_start: 0.8454 (m-80) cc_final: 0.8160 (m-80) REVERT: I 588 HIS cc_start: 0.8744 (m-70) cc_final: 0.8539 (m-70) REVERT: I 769 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8510 (mm-40) REVERT: J 74 TYR cc_start: 0.8799 (t80) cc_final: 0.8447 (t80) REVERT: J 153 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8942 (mtmm) REVERT: J 190 PHE cc_start: 0.8958 (m-10) cc_final: 0.8658 (m-80) REVERT: J 217 PHE cc_start: 0.6945 (t80) cc_final: 0.6089 (t80) REVERT: J 221 PHE cc_start: 0.8361 (m-80) cc_final: 0.7264 (m-80) REVERT: J 235 LEU cc_start: 0.9058 (tp) cc_final: 0.8642 (mt) REVERT: J 579 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: J 582 LEU cc_start: 0.9227 (tp) cc_final: 0.8580 (tp) REVERT: J 586 ASN cc_start: 0.8158 (m-40) cc_final: 0.7812 (m-40) REVERT: J 590 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.7019 (mmm-85) REVERT: J 629 PHE cc_start: 0.8811 (m-10) cc_final: 0.8178 (m-80) outliers start: 137 outliers final: 114 residues processed: 959 average time/residue: 0.5309 time to fit residues: 835.5224 Evaluate side-chains 991 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 869 time to evaluate : 5.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 508 VAL Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 590 LEU 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 138 VAL Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 393 GLN Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 485 ILE Chi-restraints excluded: chain H residue 510 ARG Chi-restraints excluded: chain H residue 584 THR Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 653 VAL Chi-restraints excluded: chain H residue 680 ASP Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 586 ASN Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 534 ILE Chi-restraints excluded: chain J residue 543 ILE Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 626 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 359 optimal weight: 20.0000 chunk 481 optimal weight: 3.9990 chunk 138 optimal weight: 0.0870 chunk 416 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 452 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 465 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 ASN ** G 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.186944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109602 restraints weight = 72939.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113809 restraints weight = 36554.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116453 restraints weight = 24458.899| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 42994 Z= 0.215 Angle : 0.676 13.350 58617 Z= 0.341 Chirality : 0.047 0.322 6906 Planarity : 0.004 0.086 7726 Dihedral : 4.358 27.764 6113 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 3.28 % Allowed : 24.05 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 5704 helix: 0.36 (0.13), residues: 1675 sheet: 0.40 (0.17), residues: 1049 loop : -0.72 (0.12), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 570 HIS 0.004 0.001 HIS H 645 PHE 0.022 0.001 PHE H 247 TYR 0.048 0.001 TYR H 621 ARG 0.013 0.001 ARG J 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13175.98 seconds wall clock time: 234 minutes 44.12 seconds (14084.12 seconds total)